Dear Jiansong:
 
FSL4.0 can't do parallel processing by simply entering the command "tbss_2_reg" at another terminal even though you got dual processors or networking two computers. You must use SGE to set up parallel processing.  I know FSL website said you can, but my experience is that it only applies to FSL3.0. 
 
 
Yi-Shin
 


 
On 1/26/08, Jiansong Xu <[log in to unmask]> wrote:
Dear Friends:

I'm trying to use parallel processing with tbss_2_reg.

I have 18 subjects and use a Mac with dural processors.  I got
following message after type in command in the second terminal:
wc: .commands: open: No such file or directory
13165

Any one can give me suggestions?


Best

Jiansong Xu, M.D., Ph.D.
Associate Research Scientist
Dept. of Psychiatry
Yale School of Medicine

Connecticut Mental Health Center, Room S-100
34 Park St.
New Haven, CT 06519




--
Sheu, Yi-Shin ------=_Part_2785_29673651.1201366043419-- ========================================================================= Date: Sat, 26 Jan 2008 09:01:56 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Himachandra Chebrolu <[log in to unmask]> Subject: Re: tbss_2_reg -T: parallel processing In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1869600688-1201366916=:55729" Content-Transfer-Encoding: 8bit --0-1869600688-1201366916=:55729 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I also had the same experience with FSL 4.0. The second time tbss_2_reg is run to parallelise it deletes the .commands file. So the error. I ran my analysis for now without parallelising. Cheers, HC Yi-Shin Sheu <[log in to unmask]> wrote: Dear Jiansong: FSL4.0 can't do parallel processing by simply entering the command "tbss_2_reg" at another terminal even though you got dual processors or networking two computers. You must use SGE to set up parallel processing. I know FSL website said you can, but my experience is that it only applies to FSL3.0. Yi-Shin On 1/26/08, Jiansong Xu <[log in to unmask]> wrote: Dear Friends: I'm trying to use parallel processing with tbss_2_reg. I have 18 subjects and use a Mac with dural processors. I got following message after type in command in the second terminal: wc: .commands: open: No such file or directory 13165 Any one can give me suggestions? Best Jiansong Xu, M.D., Ph.D. Associate Research Scientist Dept. of Psychiatry Yale School of Medicine Connecticut Mental Health Center, Room S-100 34 Park St. New Haven, CT 06519 -- Sheu, Yi-Shin --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-1869600688-1201366916=:55729 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
I also had the same experience with FSL 4.0. The second time tbss_2_reg is run to parallelise it deletes the .commands file. So the error. I ran my analysis for now without parallelising.
 
Cheers,
HC

Yi-Shin Sheu <[log in to unmask]> wrote:
Dear Jiansong:
 
FSL4.0 can't do parallel processing by simply entering the command "tbss_2_reg" at another terminal even though you got dual processors or networking two computers. You must use SGE to set up parallel processing.  I know FSL website said you can, but my experience is that it only applies to FSL3.0. 
 
 
Yi-Shin
 


 
On 1/26/08, Jiansong Xu <[log in to unmask]> wrote:
Dear Friends:

I'm trying to use parallel processing with tbss_2_reg.

I have 18 subjects and use a Mac with dural processors.  I got
following message after type in command in the second terminal:
wc: .commands: open: No such file or directory
13165

Any one can give me suggestions?


Best

Jiansong Xu, M.D., Ph.D.
Associate Research Scientist
Dept. of Psychiatry
Yale School of Medicine

Connecticut Mental Health Center, Room S-100
34 Park St.
New Haven, CT 06519




--
Sheu, Yi-Shin


Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-1869600688-1201366916=:55729-- ========================================================================= Date: Sat, 26 Jan 2008 12:02:41 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Cherif Sahyoun <[log in to unmask]> Subject: Re: tbss_2_reg aborts and won't pick up. In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_2082_3089961.1201366961987" ------=_Part_2082_3089961.1201366961987 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp files? it would be a shame to restart from scratch... On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> wrote: > I had the same problem. After much pain, I found that the .commands file > will be deleted if you already have files from the tbss_2_reg which was run > earlier. So I deleted all the old files in the FAi directory and then reran > the tbss_2_reg and everything seems to work fine. Hope this helps. > > Cheers, > Hima > > > *Cherif Sahyoun <[log in to unmask]>* wrote: > > Hi, > > I have run tbss_2_reg -n > when it appeared to be done I went ahead with tbss_3_postreg -S and got a > series of errors (not finding certain header files). So I went back to > look > into the directory and indeed it seems tbss_2 exited prematurely. > I tried to re-run it to pick up where it left off, but now got: > wc: .commands: No such file or directory > 28980 > > Any thoughts? > > Thanks, > cherif > > > ------------------------------ > Looking for last minute shopping deals? Find them fast with Yahoo! Search. > -- ------------------------------------------------------------------------------------------ Cherif P. Sahyoun HST-MEMP Developmental Neuroimaging of Cognitive Functions C: 617 688 8048 H: 617 424 6956 [log in to unmask] "Live as if this were your last day. Learn as if you'll live forever" Ghandi ------------------------------------------------------------------------------------------- ------=_Part_2082_3089961.1201366961987 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp files? it would be a shame to restart from scratch...

On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> wrote:
I had the same problem. After much pain, I found that the .commands file will be deleted if you already have files from the tbss_2_reg which was run earlier. So I deleted all the old files in the FAi directory and then reran the tbss_2_reg and everything seems to work fine. Hope this helps.
 
Cheers,
Hima


Cherif Sahyoun <[log in to unmask]> wrote:
Hi,

I have run tbss_2_reg -n
when it appeared to be done I went ahead with tbss_3_postreg -S and got a
series of errors (not finding certain header files). So I went back to look
into the directory and indeed it seems tbss_2 exited prematurely.
I tried to re-run it to pick up where it left off, but now got:
wc: .commands: No such file or directory
28980

Any thoughts?

Thanks,
cherif


Looking for last minute shopping deals? Find them fast with Yahoo! Search.



--
------------------------------------------------------------------------------------------
Cherif P. Sahyoun                                               HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
[log in to unmask]

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
------------------------------------------------------------------------------------------- ------=_Part_2082_3089961.1201366961987-- ========================================================================= Date: Sat, 26 Jan 2008 09:28:27 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Himachandra Chebrolu <[log in to unmask]> Subject: Re: tbss_2_reg aborts and won't pick up. In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-305436451-1201368507=:49796" Content-Transfer-Encoding: 8bit --0-305436451-1201368507=:49796 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I think I deleted all the .msf files also. I think you will be better off deleting all the files in the FAi folder other than the scaled FA images from the tbss_1_preproc step. I am not sure if there is a more efficient way, but that was what I did. Cheers, Hima Cherif Sahyoun <[log in to unmask]> wrote: Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp files? it would be a shame to restart from scratch... On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> wrote: I had the same problem. After much pain, I found that the .commands file will be deleted if you already have files from the tbss_2_reg which was run earlier. So I deleted all the old files in the FAi directory and then reran the tbss_2_reg and everything seems to work fine. Hope this helps. Cheers, Hima Cherif Sahyoun <[log in to unmask]> wrote: Hi, I have run tbss_2_reg -n when it appeared to be done I went ahead with tbss_3_postreg -S and got a series of errors (not finding certain header files). So I went back to look into the directory and indeed it seems tbss_2 exited prematurely. I tried to re-run it to pick up where it left off, but now got: wc: .commands: No such file or directory 28980 Any thoughts? Thanks, cherif --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. -- ------------------------------------------------------------------------------------------ Cherif P. Sahyoun HST-MEMP Developmental Neuroimaging of Cognitive Functions C: 617 688 8048 H: 617 424 6956 [log in to unmask] "Live as if this were your last day. Learn as if you'll live forever" Ghandi ------------------------------------------------------------------------------------------- --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search. --0-305436451-1201368507=:49796 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
I think I deleted all the .msf files also. I think you will be better off deleting all the files in the FAi folder other than the scaled FA images from the tbss_1_preproc step. I am not sure if there is a more efficient way, but that was what I did.
 
Cheers,
Hima

Cherif Sahyoun <[log in to unmask]> wrote:
Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp files? it would be a shame to restart from scratch...

On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> wrote:
I had the same problem. After much pain, I found that the .commands file will be deleted if you already have files from the tbss_2_reg which was run earlier. So I deleted all the old files in the FAi directory and then reran the tbss_2_reg and everything seems to work fine. Hope this helps.
 
Cheers,
Hima


Cherif Sahyoun <[log in to unmask]> wrote:
Hi,

I have run tbss_2_reg -n
when it appeared to be done I went ahead with tbss_3_postreg -S and got a
series of errors (not finding certain header files). So I went back to look
into the directory and indeed it seems tbss_2 exited prematurely.
I tried to re-run it to pick up where it left off, but now got:
wc: .commands: No such file or directory
28980

Any thoughts?

Thanks,
cherif


Looking for last minute shopping deals? Find them fast with Yahoo! Search.



--
------------------------------------------------------------------------------------------
Cherif P. Sahyoun                                               HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
[log in to unmask]

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
-------------------------------------------------------------------------------------------


Looking for last minute shopping deals? Find them fast with Yahoo! Search. --0-305436451-1201368507=:49796-- ========================================================================= Date: Sat, 26 Jan 2008 12:31:58 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Cherif Sahyoun <[log in to unmask]> Subject: Re: tbss_2_reg aborts and won't pick up. In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_2162_313373.1201368718501" ------=_Part_2162_313373.1201368718501 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks Hima! I'll wait a little and see if Steve and the gang have another option, otherwise I'll just do that. Thx! c On Jan 26, 2008 12:28 PM, Himachandra Chebrolu <[log in to unmask]> wrote: > I think I deleted all the .msf files also. I think you will be better off > deleting all the files in the FAi folder other than the scaled FA images > from the tbss_1_preproc step. I am not sure if there is a more efficient > way, but that was what I did. > > Cheers, > Hima > > *Cherif Sahyoun <[log in to unmask]>* wrote: > > Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp > files? it would be a shame to restart from scratch... > > On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> > wrote: > > > I had the same problem. After much pain, I found that the .commands file > > will be deleted if you already have files from the tbss_2_reg which was run > > earlier. So I deleted all the old files in the FAi directory and then reran > > the tbss_2_reg and everything seems to work fine. Hope this helps. > > > > Cheers, > > Hima > > > > > > *Cherif Sahyoun <[log in to unmask]>* wrote: > > > > Hi, > > > > I have run tbss_2_reg -n > > when it appeared to be done I went ahead with tbss_3_postreg -S and got > > a > > series of errors (not finding certain header files). So I went back to > > look > > into the directory and indeed it seems tbss_2 exited prematurely. > > I tried to re-run it to pick up where it left off, but now got: > > wc: .commands: No such file or directory > > 28980 > > > > Any thoughts? > > > > Thanks, > > cherif > > > > > > ------------------------------ > > Looking for last minute shopping deals? Find them fast with Yahoo! > > Search. > > > > > > -- > > ------------------------------------------------------------------------------------------ > Cherif P. Sahyoun HST-MEMP > > Developmental Neuroimaging of Cognitive Functions > > C: 617 688 8048 > H: 617 424 6956 > [log in to unmask] > > "Live as if this were your last day. Learn as if you'll live forever" > Ghandi > ------------------------------------------------------------------------------------------- > > > > ------------------------------ > Looking for last minute shopping deals? Find them fast with Yahoo! Search. > -- ------------------------------------------------------------------------------------------ Cherif P. Sahyoun HST-MEMP Developmental Neuroimaging of Cognitive Functions C: 617 688 8048 H: 617 424 6956 [log in to unmask] "Live as if this were your last day. Learn as if you'll live forever" Ghandi ------------------------------------------------------------------------------------------- ------=_Part_2162_313373.1201368718501 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks Hima!

I'll wait a little and see if Steve and the gang have another option, otherwise I'll just do that.

Thx!
c

On Jan 26, 2008 12:28 PM, Himachandra Chebrolu <[log in to unmask]> wrote:
I think I deleted all the .msf files also. I think you will be better off deleting all the files in the FAi folder other than the scaled FA images from the tbss_1_preproc step. I am not sure if there is a more efficient way, but that was what I did.
 
Cheers,
Hima

Cherif Sahyoun <[log in to unmask]> wrote:
Thanks Hima. Do you mean ALL the files, or just the tbss2_reg_e### temp files? it would be a shame to restart from scratch...

On Jan 26, 2008 11:54 AM, Himachandra Chebrolu <[log in to unmask]> wrote:
I had the same problem. After much pain, I found that the .commands file will be deleted if you already have files from the tbss_2_reg which was run earlier. So I deleted all the old files in the FAi directory and then reran the tbss_2_reg and everything seems to work fine. Hope this helps.
 
Cheers,
Hima


Cherif Sahyoun <[log in to unmask]> wrote:
Hi,

I have run tbss_2_reg -n
when it appeared to be done I went ahead with tbss_3_postreg -S and got a
series of errors (not finding certain header files). So I went back to look
into the directory and indeed it seems tbss_2 exited prematurely.
I tried to re-run it to pick up where it left off, but now got:
wc: .commands: No such file or directory
28980

Any thoughts?

Thanks,
cherif


Looking for last minute shopping deals? Find them fast with Yahoo! Search.



--
------------------------------------------------------------------------------------------
Cherif P. Sahyoun                                               HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
[log in to unmask]

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
-------------------------------------------------------------------------------------------


Looking for last minute shopping deals? Find them fast with Yahoo! Search.



--
------------------------------------------------------------------------------------------
Cherif P. Sahyoun                                               HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
[log in to unmask]

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
------------------------------------------------------------------------------------------- ------=_Part_2162_313373.1201368718501-- ========================================================================= Date: Sat, 26 Jan 2008 12:49:39 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Jiansong Xu <[log in to unmask]> Subject: Re: tbss_2_reg -T: parallel processing In-Reply-To: <[log in to unmask]> Content-Type: multipart/alternative; boundary=Apple-Mail-2--275719316 Mime-Version: 1.0 (Apple Message framework v915) --Apple-Mail-2--275719316 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Thanks a lot. Best Jiansong Xu, M.D., Ph.D. Associate Research Scientist Dept. of Psychiatry Yale School of Medicine Connecticut Mental Health Center, Room S-100 34 Park St. New Haven, CT 06519 On Jan 26, 2008, at 11:47 AM, Yi-Shin Sheu wrote: > Dear Jiansong: > > FSL4.0 can't do parallel processing by simply entering the command > "tbss_2_reg" at another terminal even though you got dual processors > or networking two computers. You must use SGE to set up parallel > processing. I know FSL website said you can, but my experience is > that it only applies to FSL3.0. > > > Yi-Shin > > > > > On 1/26/08, Jiansong Xu <[log in to unmask]> wrote: > Dear Friends: > > I'm trying to use parallel processing with tbss_2_reg. > > I have 18 subjects and use a Mac with dural processors. I got > following message after type in command in the second terminal: > wc: .commands: open: No such file or directory > 13165 > > Any one can give me suggestions? > > > Best > > Jiansong Xu, M.D., Ph.D. > Associate Research Scientist > Dept. of Psychiatry > Yale School of Medicine > > Connecticut Mental Health Center, Room S-100 > 34 Park St. > New Haven, CT 06519 > > > > > -- > Sheu, Yi-Shin --Apple-Mail-2--275719316 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Thanks a lot.


Best

Jiansong Xu, M.D., = Ph.D.
Associate Research Scientist
Dept. of = Psychiatry
Yale School of Medicine

Connecticut Mental Health = Center, Room S-100
34 Park St. 
New Haven, CT = 06519







On Jan 26, = 2008, at 11:47 AM, Yi-Shin Sheu wrote:

Dear = Jiansong:
 
FSL4.0 can't do parallel = processing by simply entering the command "tbss_2_reg" at another = terminal even though you got dual processors or networking two = computers. You must use SGE to set up parallel processing.  I know = FSL website said you can, but my experience is that it only applies to = FSL3.0. 
 
 
=
Yi-Shin
 


 
=
On 1/26/08, Jiansong Xu <[log in to unmask]> = wrote:
Dear = Friends:

I'm trying to use parallel processing with = tbss_2_reg.

I have 18 subjects and use a Mac with dural = processors.  I got
following message after type in command = in the second terminal:
wc: .commands: open: No such file or = directory
13165

Any one can give me = suggestions?


Best

Jiansong Xu, M.D., = Ph.D.
Associate Research Scientist
Dept. of Psychiatry
Yale = School of Medicine

Connecticut Mental Health Center, Room = S-100
34 Park St.
New Haven, CT = 06519




--
Sheu, = Yi-Shin

= --Apple-Mail-2--275719316-- ========================================================================= Date: Sat, 26 Jan 2008 15:55:20 -0600 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Jacek Jonca-Jasinski <[log in to unmask]> Subject: converting lossless jpeg dicom MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_4871_27296684.1201384520214" ------=_Part_4871_27296684.1201384520214 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I was wondering if anybody had any luck with converting 1.2.840.10008.1.2.4.70 transfer syntax (lossless JPEG) DICOMs using any of available command line tools? 1.5T GE LX Excite 11 data we are getting on MOs is saved in this form. Most of the tools I am aware of (mri_convert, mriconvert, dcm2nii) do not support compressed transfer syntax and the only conversion method that worked for us is a commercial PACS. It takes it about 36 hours to import, decode, re-encode, and export a single MO with 3 subjects (SPGR, EPI, and DTI). I am hoping to either decrease this time or at least parallelize it. Any suggestions will be greatly appreciated. Regards, Jacek Jonca-Jasinski --- Jacek Jonca-Jasinski Neuro-Imaging, Cognition, and Engineering Labs (NICE) Texas Tech University ------=_Part_4871_27296684.1201384520214 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
I was wondering if anybody had any luck with converting 1.2.840.10008.1.2.4.70 transfer syntax (lossless JPEG) DICOMs using any of available command line tools?

1.5T GE LX Excite 11 data we are getting on MOs is saved in this form. Most of the tools I am aware of (mri_convert, mriconvert, dcm2nii) do not support compressed transfer syntax and the only conversion method that worked for us is a commercial PACS. It takes it about 36 hours to import, decode, re-encode, and export a single MO with 3 subjects (SPGR, EPI, and DTI). I am hoping to either decrease this time or at least parallelize it.

Any suggestions will be greatly appreciated.

Regards,

Jacek Jonca-Jasinski

---
Jacek Jonca-Jasinski
Neuro-Imaging, Cognition, and Engineering Labs (NICE)
Texas Tech University

------=_Part_4871_27296684.1201384520214-- ========================================================================= Date: Sun, 27 Jan 2008 00:18:11 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Anastasia Ford <[log in to unmask]> Subject: Philips Scaling Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain Hello, We are trying to do tractography analysis on the Philips 3T Achieva syste= m. We have been able to=20 fit the tensors, generate the FA maps, as well as map out some tracts. We= are having difficulties=20 with the scaling imposed by the DICOM out from Philips. Do you have any s= uggestions on how to=20 rescale the data for FSLview? Also, we were wondering if there is a way = to threshold the view of=20 tracts based on the probability threshold. Finally, we are working on imp= lementing the target=20 classification tractography using a specified list of targets and applyin= g the proj_thresh of the=20 output volumes, but the images do not contain any data. Could the scaling= issue be a problem for=20 this analysis? Thanks, Anastasia ========================================================================= Date: Sun, 27 Jan 2008 00:11:47 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Li Jiang <[log in to unmask]> Subject: Re: about flirt In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, For example, with the methods I mentioned above, for one subject,the intensity of the subjects data is 52.4554, but that of the subjects data in MNI-space is only 36.1254. For another subject, the intensity is 46.7794 and 43.8556, which is similar. I don't know how to explain the different.I know that interpolation will affect a little. Compare trilinear and nearest neighbour, which is better? Thank you! Li 2008/1/26, Mark Jenkinson <[log in to unmask]>: > Hi, > > Those commands are fine for flirt. > But how are you judging that the intensity is decreased? > > Could it be due to including slightly different voxels on the > edge of your ROI mask? When you transform a binary > mask you need to rethreshold it afterwards to decide > whether to be inclusive of small partial volume overlap > (of the mask and the new voxels) or exclusive. > This could be the source of changes in average intensity > over the ROI. In addition, trilinear interpolation will do > some smoothing of the image a little - which affects sharp > peaks particularly. > > All the best, > Mark > > > On 25 Jan 2008, at 17:24, Li Jiang wrote: > > > Hi, > > > > That's what I have done. > > > > * get the transformation matrix file (*.mat) that transforms > > subject-space CBF > > volume to MNI-space > > * get ROI volume in subject-space > > * transform ROI volume into MNI-space using the same *.mat file > > * use flirt: > > > > flirt -in -ref -out -applyxfm > > -init > > > > Thanks. > > > > Li > > > > 2008/1/25, Steve Smith <[log in to unmask]>: > >> Hi, > >> > >> I'm still not sure you have a problem. How are you judging that the > >> intensity is decreased? > >> > >> Cheers. > >> > >> > >> On 22 Jan 2008, at 06:28, Li Jiang wrote: > >> > >>> Hi, > >>> > >>> Thank you very much. I still have a question. The original subject > >>> image is epi sequence.After I transform this image to highres T1 > >>> image > >>> and then to MNI-space, the intensity of the transformed sub2mni > >>> image > >>> decreased compare to the original epi image. When transform, I use > >>> trilinear interpolation and cost function is correlation ratio. > >>> How > >>> can I improve this problem? Which interpolation method and cost > >>> function should I apply? > >>> > >>> Li > >>> > >>> 2008/1/21, Steve Smith <[log in to unmask]>: > >>>> Hi, > >>>> > >>>> avscale gives you a whole set of different pieces of information > >>>> about > >>>> the spatial affine transform, including the average scaling (size) > >>>> change. It does not tell you anything about intensities. On > >>>> average, > >>>> in general, intensities don't change upon resampling, though of > >>>> course > >>>> any given voxel will change! > >>>> > >>>> Cheers. > >>>> > >>>> > >>>> On 19 Jan 2008, at 15:12, Li Jiang wrote: > >>>> > >>>>> Dear Steve Smith, > >>>>> > >>>>> I use fsl to process the functional MR data. It is a great > >>>>> software. > >>>>> To process the data, I first transform the EPI (subject image) > >>>>> data > >>>>> to T1 volume then to MNI_space with affine transformation. And > >>>>> I'll > >>>>> measure the absolute value from the images have been > >>>>> coregistered to > >>>>> MNI-space . I learned from the lectures and noticed the avscale > >>>>> for > >>>>> Inter-subject Registration. I wonder what's the scale mean. If the > >>>>> signal intensity of the subject image will change after affine > >>>>> transformation or global intra-subject transformation. > >>>>> > >>>>> > >>>>> > >>>>> Best regards. > >>>>> > >>>>> Li Jiang > >>>>> > >>>> > >>>> > >>>> ------------------------------------------------------------------- > >>>> -------- > >>>> Stephen M. Smith, Professor of Biomedical Engineering > >>>> Associate Director, Oxford University FMRIB Centre > >>>> > >>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > >>>> +44 (0) 1865 222726 (fax 222717) > >>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > >>>> ------------------------------------------------------------------- > >>>> -------- > >>>> > >>> > >> > >> > >> --------------------------------------------------------------------- > >> ------ > >> Stephen M. Smith, Professor of Biomedical Engineering > >> Associate Director, Oxford University FMRIB Centre > >> > >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > >> +44 (0) 1865 222726 (fax 222717) > >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > >> --------------------------------------------------------------------- > >> ------ > >> > > > ========================================================================= Date: Sat, 26 Jan 2008 21:29:55 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Pom Sailasuta <[log in to unmask]> Subject: fsl on window XP MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_5498_6486149.1201411795431" ------=_Part_5498_6486149.1201411795431 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, can I get someone to comment on fsl on window XP? I really like to install on window XP if it is wise to do so, i do not want to spend weeks or months debugging the problems. any input is greatly appreciated. thanks Pom ------=_Part_5498_6486149.1201411795431 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello,

can I get someone to comment on fsl on window XP?
I really like to install on window XP if it is wise to do so, i do not want to spend
weeks or months debugging the problems.

any input is greatly appreciated.

thanks
Pom
------=_Part_5498_6486149.1201411795431-- ========================================================================= Date: Sun, 27 Jan 2008 08:01:58 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: "=?ISO-8859-2?Q?Ji=F8=ED_Keller,_M.D.?=" <[log in to unmask]> Subject: Re: fsl on window XP In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, my recommendation is to install Linux if it is possible. If you can't get dedicated machine try vmware (it is much slower, but I have installed recent Debian without any problems). If you are about to have a dedicated machine, try Ubuntu live CD and you will see where are you going to ;-). It is possible to run FSL 3 on "Linux emulator" called Cygwin but 1) this is no longer true with FSL 4 and 2) configuration of Cygwin took me more time then Linux instalation. greetings George 2008/1/27, Pom Sailasuta <[log in to unmask]>: > Hello, > > can I get someone to comment on fsl on window XP? > I really like to install on window XP if it is wise to do so, i do not want > to spend > weeks or months debugging the problems. > > any input is greatly appreciated. > > thanks > Pom > ========================================================================= Date: Sun, 27 Jan 2008 11:54:34 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Juergen Haenggi <[log in to unmask]> Subject: Could not open matrix file Mime-version: 1.0 Content-type: multipart/mixed; boundary="B_3284279678_145963" > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3284279678_145963 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear FSL experts I tried to run DTIFIT but an error occurred. The bvals and bvecs file cannot be opened, although both are text files with plane text. Errors: Could not open matrix file /Users/.../bvecs Could not open matrix file /Users/.../bvals Terminate called after throwing an instance of `NEWMAT::ProgramException` Any idea what is wrong with these files? I attached my bvecs and bvals files! Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [log in to unmask] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- --B_3284279678_145963 Content-type: application/octet-stream; name="bvals.txt" Content-disposition: attachment; filename="bvals.txt" Content-transfer-encoding: base64 MTAwMCAxMDAwIDEwMDAgMTAwMCAxMDAwIDEwMDAgMTAwMCAxMDAwIDEwMDAgMTAwMCAxMDAw IDEwMDAgMTAwMCAxMDAwIDEwMDAgMTAwMCAxMDAwIDEwMDAgMTAwMCAxMDAwIDEwMDAgMTAw MCAxMDAwIDEwMDAg --B_3284279678_145963 Content-type: application/octet-stream; name="bvecs.txt" Content-disposition: attachment; filename="bvecs.txt" Content-transfer-encoding: base64 MCAwIDAgLTAuNTQ5NSAtMC4yMjkzIDAuMDUxNiAtMC44ODA2IDAuODc0NyAwLjQ2NDYgMC41 MTc3IC0wLjIxNDggMC4xNzg5IC0wLjUxNzggLTAuNTk0OSAwLjU4NjIgMC4yMTE2IDAuMTgw NCAwLjUxMTUgLTAuMzE4NyAtMC44OTMyIC0wLjI1NDkgLTAuODY0NSAwLjk0NjYgMC43OTM4 DTAgMCAwIC0wLjQ5OTUgMC43OTgyIC0wLjEyNjUgLTAuNDcyIDAuNDcyOCAwLjQ4NDYgMC42 Njg4IDAuMTYwMSAtMC43ODQzIC0wLjQ4MzcgMC43OTY5IC0wLjgwOTEgLTAuNjkwOSAwLjk2 OCAtMC4wMTU1IDAuNTI1OSAwLjE1MiAtMC45NjU3IDAuMjQ1NSAtMC4xODIzIC0wLjI0MzMN MCAwIDAgLTAuNjY5NyAwLjU1NyAtMC45OTA2IDAuMDQyNCAtMC4xMDYxIC0wLjc0MTEgMC41 MzM3IDAuOTYzNSAtMC41OTQgMC43MDU2IC0wLjEwNDggMC4wNDI1IDAuNjkxMyAtMC4xNzQ3 IDAuODU5MiAtMC43ODg2IC0wLjQyMzEgMC4wNDk1IDAuNDM4NiAwLjI2NTkgLTAuNTU3NA== --B_3284279678_145963-- ========================================================================= Date: Sun, 27 Jan 2008 12:38:34 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tom Johnstone <[log in to unmask]> Subject: Re: fsl on window XP In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: base64 Content-Disposition: inline WW91IGNhbiBydW4gRlNMIG9uIExpbnV4IGluc3RhbGxlZCBpbiBhIHZpcnR1YWwgbWFjaGluZSB3 aXRoIGVpdGhlcgpWTVdhcmUgb3IgVmlydHVhbEJveC4gSSBoYXZlIGFuIGluc3RhbGxhdGlvbiBy dW5uaW5nIG9uIFVidW50dSBydW5uaW5nCm9uIFZpcnR1YWxCb3ggb24gbXkgbGFwdG9wIGFuZCBp dCBydW5zIHByZXR0eSBtdWNoIHRoZSBzYW1lIHNwZWVkIGFzIGEKbmF0aXZlIGluc3RhbGxhdGlv bi4KCi1Ub20KCk9uIEphbiAyNywgMjAwOCA3OjAxIEFNLCBKafjtIEtlbGxlciwgTS5ELiA8a2Vs bGVyLmxpc3RzQGdtYWlsLmNvbT4gd3JvdGU6Cj4gSGksCj4gICBteSByZWNvbW1lbmRhdGlvbiBp cyB0byBpbnN0YWxsIExpbnV4IGlmIGl0IGlzIHBvc3NpYmxlLiBJZiB5b3UKPiBjYW4ndCBnZXQg ZGVkaWNhdGVkIG1hY2hpbmUgdHJ5IHZtd2FyZSAoaXQgaXMgbXVjaCBzbG93ZXIsIGJ1dCBJIGhh dmUKPiBpbnN0YWxsZWQgcmVjZW50IERlYmlhbiB3aXRob3V0IGFueSBwcm9ibGVtcykuIElmIHlv dSBhcmUgYWJvdXQgdG8KPiBoYXZlIGEgZGVkaWNhdGVkIG1hY2hpbmUsIHRyeSBVYnVudHUgbGl2 ZSBDRCBhbmQgeW91IHdpbGwgc2VlIHdoZXJlCj4gYXJlIHlvdSBnb2luZyB0byA7LSkuIEl0IGlz IHBvc3NpYmxlIHRvIHJ1biBGU0wgMyBvbiAiTGludXggZW11bGF0b3IiCj4gY2FsbGVkIEN5Z3dp biBidXQgMSkgdGhpcyBpcyBubyBsb25nZXIgdHJ1ZSB3aXRoIEZTTCA0IGFuZCAyKQo+IGNvbmZp Z3VyYXRpb24gb2YgQ3lnd2luIHRvb2sgbWUgbW9yZSB0aW1lIHRoZW4gTGludXggaW5zdGFsYXRp b24uCj4KPiAgICAgZ3JlZXRpbmdzCj4gICAgICAgICAgICBHZW9yZ2UKPgo+IDIwMDgvMS8yNywg UG9tIFNhaWxhc3V0YSA8c2FpbGFzdXRhQGhtcmkub3JnPjoKPgo+ID4gSGVsbG8sCj4gPgo+ID4g Y2FuIEkgZ2V0IHNvbWVvbmUgdG8gY29tbWVudCBvbiBmc2wgb24gd2luZG93IFhQPwo+ID4gSSBy ZWFsbHkgbGlrZSB0byBpbnN0YWxsIG9uIHdpbmRvdyBYUCBpZiBpdCBpcyB3aXNlIHRvIGRvIHNv LCBpIGRvIG5vdCB3YW50Cj4gPiB0byBzcGVuZAo+ID4gd2Vla3Mgb3IgbW9udGhzIGRlYnVnZ2lu ZyB0aGUgcHJvYmxlbXMuCj4gPgo+ID4gYW55IGlucHV0IGlzIGdyZWF0bHkgYXBwcmVjaWF0ZWQu Cj4gPgo+ID4gdGhhbmtzCj4gPiBQb20KPiA+Cj4KCgoKLS0gClNjaG9vbCBvZiBQc3ljaG9sb2d5 IGFuZCBDTFMKVW5pdmVyc2l0eSBvZiBSZWFkaW5nCjMgRWFybGV5IEdhdGUsIFdoaXRla25pZ2h0 cwpSZWFkaW5nIFJHNiA2QUwsIFVLClBoLiAgKzQ0ICgwKTExOCAzNzggNzUzMAppLnQuam9obnN0 b25lQHJlYWRpbmcuYWMudWsKaHR0cDovL3d3dy5wZXJzb25hbC5yZWFkaW5nLmFjLnVrL35zeHMw N2l0ai9pbmRleC5odG1sCmh0dHA6Ly9iZWNsYWIub3JnLnVrLwo= ========================================================================= Date: Sun, 27 Jan 2008 13:58:09 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Saad Jbabdi <[log in to unmask]> Subject: Re: Could not open matrix file In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-16--206810252 --Apple-Mail-16--206810252 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, If you're using the GUI, and just provide a directory name to dtifit, then the bvecs/bvals files should not have any file extension (such as .txt in your case) Saad. On 27 Jan 2008, at 11:54, Juergen Haenggi wrote: > Dear FSL experts > > I tried to run DTIFIT but an error occurred. The bvals and bvecs > file cannot > be opened, although both are text files with plane text. > > Errors: Could not open matrix file /Users/.../bvecs > Could not open matrix file /Users/.../bvals > Terminate called after throwing an instance of > `NEWMAT::ProgramException` > > Any idea what is wrong with these files? > I attached my bvecs and bvals files! > > Thanks in advance > Best regards > Juergen > > ----------------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > Division of Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > [log in to unmask] (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > ----------------------------------------------------------- > > > ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ --- --Apple-Mail-16--206810252 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
Hi,
If you're using the GUI, and just provide a directory = name to dtifit, then the bvecs/bvals files should not have any file = extension (such as .txt in your case)

Saad.


On 27 Jan 2008, = at 11:54, Juergen Haenggi wrote:

Dear FSL experts

I tried to run DTIFIT but an = error occurred. The bvals and bvecs file cannot
be opened, although both are text files with plane = text.

Errors: Could not open matrix file = /Users/.../bvecs
Could not open matrix file = /Users/.../bvals
Terminate called after throwing = an instance of `NEWMAT::ProgramException`

Any idea what = is wrong with these files?
I attached my = bvecs and bvals files!
Thanks in advance
Best regards=A0

Juergen Haenggi
Ph.D. (Dr. = des.)
Division of = Neuropsychology
Institute of = Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
[log in to unmask]<= /a> (email)
http://www.juergenhaenggi.ch = (private website)

Saad Jbabdi,=A0
Postdoctoral Research Assistant,=A0=A0
Oxford University FMRIB Centre

FMRIB, = JR Hospital, Headington, Oxford=A0=A0OX3 9DU, UK
+44 (0) 1865 222545=A0=A0(fax 222717)


=

= --Apple-Mail-16--206810252-- ========================================================================= Date: Sun, 27 Jan 2008 15:08:42 +0000 Reply-To: FSL - FMRIB's Software Library <
[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Steve Smith <[log in to unmask]> Subject: Re: Philips Scaling In-Reply-To: <[log in to unmask]> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Mime-Version: 1.0 (Apple Message framework v915) Hi, Depending on how your DTI images were produced/converted, you may need to adjust the intensity display range in FSLView (the Min and Max settings near the top). However, this intensity display issue won't affect any processing with tractography, etc. If the tractography is not working well then I suggest you go back and check the output of dtifit first to make sure your input data is ok, then once you've fixed that, rerun bedpostX. Cheers. On 27 Jan 2008, at 00:18, Anastasia Ford wrote: > Hello, > > We are trying to do tractography analysis on the Philips 3T Achieva > system. We have been able to > fit the tensors, generate the FA maps, as well as map out some > tracts. We are having difficulties > with the scaling imposed by the DICOM out from Philips. Do you have > any suggestions on how to > rescale the data for FSLview? Also, we were wondering if there is a > way to threshold the view of > tracts based on the probability threshold. Finally, we are working > on implementing the target > classification tractography using a specified list of targets and > applying the proj_thresh of the > output volumes, but the images do not contain any data. Could the > scaling issue be a problem for > this analysis? > > Thanks, > > Anastasia > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- ========================================================================= Date: Sun, 27 Jan 2008 15:11:46 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephen Smith <[log in to unmask]> Subject: Re: TBSS_4_prestats: Aborted Comments: To: Himachandra Chebrolu <[log in to unmask]> Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain Hi, seems most likely that either you're running a 64-bit flavour of Linu= x, or that you're not using a=20 64-bit version of FSL? Cheers. ========================================================================= Date: Sun, 27 Jan 2008 15:18:50 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephen Smith <[log in to unmask]> Subject: Re: Feat hang up Susan_smooth Comments: To: Li Sun <[log in to unmask]> Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain Hi - the fslerrorreport doesn't help with this - did you solve this issue= yet? If not, feel free to re- upload the semi-completed FEAT run - I'm afraid your original upload has = expired, as I was away=20 for a few weeks. Cheers, Steve. On Sat, 19 Jan 2008 12:18:52 -0000, Li Sun <[log in to unmask]> wrote= : >Steve, >Have you got time to look at the error report I sent a week ago? >Li > >Steve, >Please find attached file. >I wonder if it is due to memory. However, I can run the same data with >old version FSL 3.x without error. Regards,=20 >Li > > >-----Original Message----- >From: FSL - FMRIB's Software Library on behalf of Steve Smith >Sent: Tue 12/18/2007 7:55 AM >To: [log in to unmask] >Subject: Re: [FSL] Feat hang up Susan_smooth >=20 >Your logfile says: >Error: FILM did not complete - it probably ran out of memory > >What system are you running on? Please run fslerrorreport and send us=20= =20 >the output. > >Steve. > > >On 17 Dec 2007, at 14:28, Li Sun wrote: > >> Steve, >> I've just uploaded the tar file called "lidir.tar.gz", session is >> 735946. Thanks. >> Li >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf Of Steve Smith >> Sent: 17 December 2007 13:40 >> To: [log in to unmask] >> Subject: Re: [FSL] Feat hang up Susan_smooth >> >> >> Hi, >> >> In fact the reference to susan_smooth on the film_gls command line is >> not used, as susan is now called as a internal library call by=20 >> film_gls - that's why you don't see a binary called susan_smooth (it's= > >> now called susan). So this doesn't explain the problem.... >> >> If it's still not clear from the logfiles what the problem is here, >> please feel free to upload the whole (unfinished) FEAT directory for=20= >> us to take a quick look at. >> >> Please upload the files in a single compressed tarfile to >> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi >> And then email me the upload ID. >> >> Cheers, Steve. >> >> >> On 16 Dec 2007, at 09:54, Li Sun wrote: >> >>> Dear All, >>> I am trying FSL 4.0 after downloading it recently and installed it on= >>> Redhat WS 4. Feat hang up with a massage: Stats >>> /home/li/fsl/bin/film_gsl -rn stats -sa -ms 5 -sp >>> /home/li/fsl/bin/susan_smooth filtered_func_data design.mat 1000.0 >>> The data set worked well before with old version FSL 3. >>> I found there is not a fill called "susan_smooth" in .../bin of FSL >>> 4.0 >>> >>> Please help. >>> Li >>> >> >> >> ----------------------------------------------------------------------= >> -- >> --- >> Stephen M. Smith, Professor of Biomedical Engineering Associate=20 >> Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> ----------------------------------------------------------------------= >> -- >> --- >> > > >------------------------------------------------------------------------= >--- >Stephen M. Smith, Professor of Biomedical Engineering >Associate Director, Oxford University FMRIB Centre > >FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >+44 (0) 1865 222726 (fax 222717) >[log in to unmask] http://www.fmrib.ox.ac.uk/~steve >------------------------------------------------------------------------= >--- > > > > > ========================================================================= Date: Sun, 27 Jan 2008 08:34:18 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Pom Sailasuta <[log in to unmask]> Subject: Re: fsl on window XP In-Reply-To: <9f[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_6386_9884636.1201451658046" ------=_Part_6386_9884636.1201451658046 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: base64 Content-Disposition: inline dGhhbmsgeW91LCBJIHNoYWxsIHNlZSB3aGF0IGhhcHBlbiB3aXRoIGZzbHZtMzIgd2l0aCBWTVdh cmUuCgo+Cj4gcG9tCj4KPiAyMDA4LzEvMjcgVG9tIEpvaG5zdG9uZSA8aS50LmpvaG5zdG9uZUBy ZWFkaW5nLmFjLnVrPjoKPgo+IFlvdSBjYW4gcnVuIEZTTCBvbiBMaW51eCBpbnN0YWxsZWQgaW4g YSB2aXJ0dWFsIG1hY2hpbmUgd2l0aCBlaXRoZXIKPiA+IFZNV2FyZSBvciBWaXJ0dWFsQm94LiBJ IGhhdmUgYW4gaW5zdGFsbGF0aW9uIHJ1bm5pbmcgb24gVWJ1bnR1IHJ1bm5pbmcKPiA+IG9uIFZp cnR1YWxCb3ggb24gbXkgbGFwdG9wIGFuZCBpdCBydW5zIHByZXR0eSBtdWNoIHRoZSBzYW1lIHNw ZWVkIGFzIGEKPiA+IG5hdGl2ZSBpbnN0YWxsYXRpb24uCj4gPgo+ID4gLVRvbQo+ID4KPiA+IE9u IEphbiAyNywgMjAwOCA3OjAxIEFNLCBKafjtIEtlbGxlciwgTS5ELiA8a2VsbGVyLmxpc3RzQGdt YWlsLmNvbT4KPiA+IHdyb3RlOgo+ID4gPiBIaSwKPiA+ID4gICBteSByZWNvbW1lbmRhdGlvbiBp cyB0byBpbnN0YWxsIExpbnV4IGlmIGl0IGlzIHBvc3NpYmxlLiBJZiB5b3UKPiA+ID4gY2FuJ3Qg Z2V0IGRlZGljYXRlZCBtYWNoaW5lIHRyeSB2bXdhcmUgKGl0IGlzIG11Y2ggc2xvd2VyLCBidXQg SSBoYXZlCj4gPiA+IGluc3RhbGxlZCByZWNlbnQgRGViaWFuIHdpdGhvdXQgYW55IHByb2JsZW1z KS4gSWYgeW91IGFyZSBhYm91dCB0bwo+ID4gPiBoYXZlIGEgZGVkaWNhdGVkIG1hY2hpbmUsIHRy eSBVYnVudHUgbGl2ZSBDRCBhbmQgeW91IHdpbGwgc2VlIHdoZXJlCj4gPiA+IGFyZSB5b3UgZ29p bmcgdG8gOy0pLiBJdCBpcyBwb3NzaWJsZSB0byBydW4gRlNMIDMgb24gIkxpbnV4IGVtdWxhdG9y Igo+ID4gPiBjYWxsZWQgQ3lnd2luIGJ1dCAxKSB0aGlzIGlzIG5vIGxvbmdlciB0cnVlIHdpdGgg RlNMIDQgYW5kIDIpCj4gPiA+IGNvbmZpZ3VyYXRpb24gb2YgQ3lnd2luIHRvb2sgbWUgbW9yZSB0 aW1lIHRoZW4gTGludXggaW5zdGFsYXRpb24uCj4gPiA+Cj4gPiA+ICAgICBncmVldGluZ3MKPiA+ ID4gICAgICAgICAgICBHZW9yZ2UKPiA+ID4KPiA+ID4gMjAwOC8xLzI3LCBQb20gU2FpbGFzdXRh IDxzYWlsYXN1dGFAaG1yaS5vcmc+Ogo+ID4gPgo+ID4gPiA+IEhlbGxvLAo+ID4gPiA+Cj4gPiA+ ID4gY2FuIEkgZ2V0IHNvbWVvbmUgdG8gY29tbWVudCBvbiBmc2wgb24gd2luZG93IFhQPwo+ID4g PiA+IEkgcmVhbGx5IGxpa2UgdG8gaW5zdGFsbCBvbiB3aW5kb3cgWFAgaWYgaXQgaXMgd2lzZSB0 byBkbyBzbywgaSBkbwo+ID4gbm90IHdhbnQKPiA+ID4gPiB0byBzcGVuZAo+ID4gPiA+IHdlZWtz IG9yIG1vbnRocyBkZWJ1Z2dpbmcgdGhlIHByb2JsZW1zLgo+ID4gPiA+Cj4gPiA+ID4gYW55IGlu cHV0IGlzIGdyZWF0bHkgYXBwcmVjaWF0ZWQuCj4gPiA+ID4KPiA+ID4gPiB0aGFua3MKPiA+ID4g PiBQb20KPiA+ID4gPgo+ID4gPgo+ID4KPiA+Cj4gPgo+ID4gLS0KPiA+IFNjaG9vbCBvZiBQc3lj aG9sb2d5IGFuZCBDTFMKPiA+IFVuaXZlcnNpdHkgb2YgUmVhZGluZwo+ID4gMyBFYXJsZXkgR2F0 ZSwgV2hpdGVrbmlnaHRzCj4gPiBSZWFkaW5nIFJHNiA2QUwsIFVLCj4gPiBQaC4gICs0NCAoMCkx MTggMzc4IDc1MzAKPiA+IGkudC5qb2huc3RvbmVAcmVhZGluZy5hYy51awo+ID4gaHR0cDovL3d3 dy5wZXJzb25hbC5yZWFkaW5nLmFjLnVrL35zeHMwN2l0ai9pbmRleC5odG1sPGh0dHA6Ly93d3cu cGVyc29uYWwucmVhZGluZy5hYy51ay8lN0VzeHMwN2l0ai9pbmRleC5odG1sPgo+ID4gaHR0cDov L2JlY2xhYi5vcmcudWsvCj4gPgo+Cj4K ------=_Part_6386_9884636.1201451658046 Content-Type: text/html; 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boundary="----=_Part_4598_16403392.1201456188169" ------=_Part_4598_16403392.1201456188169 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I just want to make sure that I understand the outputs. The rendered image will only show clusters with a t-stat greater than the specified threshold, correct? Also, I ran the second option (easythresh ) and there was no thresh_root image created. Is this correct? Thanks! On Jan 24, 2008 7:25 PM, Stephane Jacobs <[log in to unmask]> wrote: > Yes - just use the easythresh command, something like: > > easythresh > > > It will generate cluster tables, thresholded image and rendered image > for you. > > Best, > > Stephane > > Brittany Copp wrote: > > I was wondering if there was any way of applying a cluster threshold to > the > > uncorrected t-stat image outputted by FSL. Thanks > > > > Brittany > > > > > > > ------=_Part_4598_16403392.1201456188169 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I just want to make sure that I understand the outputs.  The rendered image will only show clusters with a t-stat greater than the specified threshold, correct?  Also, I ran the second option (easythresh <stats> <threshold> <background image> <output>) and there was no thresh_root image created.  Is this correct?  Thanks!


On Jan 24, 2008 7:25 PM, Stephane Jacobs <[log in to unmask]> wrote:
Yes - just use the easythresh command, something like:

easythresh   <yourstats>  <yourmask>  <zthreshold>  <clusterthreshold>
<backgroundimage>  <output>

It will generate cluster tables, thresholded image and rendered image
for you.

Best,

Stephane

Brittany Copp wrote:
> I was wondering if there was any way of applying a cluster threshold to the
> uncorrected t-stat image outputted by FSL.  Thanks
>
> Brittany
>
>
>

------=_Part_4598_16403392.1201456188169-- ========================================================================= Date: Sun, 27 Jan 2008 18:35:44 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Mark Jenkinson <[log in to unmask]> Subject: Re: about flirt In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi, This still doesn't answer the important question: *HOW* are you measuring these intensities? Is it an average over an ROI? Is it from a single voxel? If it is a single voxel, is it a peak value surrounded by much smaller (even negative) values? If it is an ROI, how are you generating the ROIs and creating the average? All the best, Mark On 27 Jan 2008, at 05:11, Li Jiang wrote: > Hi, > > For example, with the methods I mentioned above, for one subject,the > intensity of the subjects data is 52.4554, but that of the subjects > data in MNI-space is only 36.1254. For another subject, the intensity > is 46.7794 and 43.8556, which is similar. I don't know how to explain > the different.I know that interpolation will affect a little. Compare > trilinear and nearest neighbour, which is better? > > Thank you! > > Li > > 2008/1/26, Mark Jenkinson <[log in to unmask]>: >> Hi, >> >> Those commands are fine for flirt. >> But how are you judging that the intensity is decreased? >> >> Could it be due to including slightly different voxels on the >> edge of your ROI mask? When you transform a binary >> mask you need to rethreshold it afterwards to decide >> whether to be inclusive of small partial volume overlap >> (of the mask and the new voxels) or exclusive. >> This could be the source of changes in average intensity >> over the ROI. In addition, trilinear interpolation will do >> some smoothing of the image a little - which affects sharp >> peaks particularly. >> >> All the best, >> Mark >> >> >> On 25 Jan 2008, at 17:24, Li Jiang wrote: >> >>> Hi, >>> >>> That's what I have done. >>> >>> * get the transformation matrix file (*.mat) that transforms >>> subject-space CBF >>> volume to MNI-space >>> * get ROI volume in subject-space >>> * transform ROI volume into MNI-space using the same *.mat file >>> * use flirt: >>> >>> flirt -in -ref -out -applyxfm >>> -init >>> >>> Thanks. >>> >>> Li >>> >>> 2008/1/25, Steve Smith <[log in to unmask]>: >>>> Hi, >>>> >>>> I'm still not sure you have a problem. How are you judging that the >>>> intensity is decreased? >>>> >>>> Cheers. >>>> >>>> >>>> On 22 Jan 2008, at 06:28, Li Jiang wrote: >>>> >>>>> Hi, >>>>> >>>>> Thank you very much. I still have a question. The original subject >>>>> image is epi sequence.After I transform this image to highres T1 >>>>> image >>>>> and then to MNI-space, the intensity of the transformed sub2mni >>>>> image >>>>> decreased compare to the original epi image. When transform, I use >>>>> trilinear interpolation and cost function is correlation ratio. >>>>> How >>>>> can I improve this problem? Which interpolation method and cost >>>>> function should I apply? >>>>> >>>>> Li >>>>> >>>>> 2008/1/21, Steve Smith <[log in to unmask]>: >>>>>> Hi, >>>>>> >>>>>> avscale gives you a whole set of different pieces of information >>>>>> about >>>>>> the spatial affine transform, including the average scaling >>>>>> (size) >>>>>> change. It does not tell you anything about intensities. On >>>>>> average, >>>>>> in general, intensities don't change upon resampling, though of >>>>>> course >>>>>> any given voxel will change! >>>>>> >>>>>> Cheers. >>>>>> >>>>>> >>>>>> On 19 Jan 2008, at 15:12, Li Jiang wrote: >>>>>> >>>>>>> Dear Steve Smith, >>>>>>> >>>>>>> I use fsl to process the functional MR data. It is a great >>>>>>> software. >>>>>>> To process the data, I first transform the EPI (subject image) >>>>>>> data >>>>>>> to T1 volume then to MNI_space with affine transformation. And >>>>>>> I'll >>>>>>> measure the absolute value from the images have been >>>>>>> coregistered to >>>>>>> MNI-space . I learned from the lectures and noticed the avscale >>>>>>> for >>>>>>> Inter-subject Registration. I wonder what's the scale mean. >>>>>>> If the >>>>>>> signal intensity of the subject image will change after affine >>>>>>> transformation or global intra-subject transformation. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Best regards. >>>>>>> >>>>>>> Li Jiang >>>>>>> >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> -- >>>>>> -------- >>>>>> Stephen M. Smith, Professor of Biomedical Engineering >>>>>> Associate Director, Oxford University FMRIB Centre >>>>>> >>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>>>> +44 (0) 1865 222726 (fax 222717) >>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>>>>> ----------------------------------------------------------------- >>>>>> -- >>>>>> -------- >>>>>> >>>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> -- >>>> ------ >>>> Stephen M. Smith, Professor of Biomedical Engineering >>>> Associate Director, Oxford University FMRIB Centre >>>> >>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>> +44 (0) 1865 222726 (fax 222717) >>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>>> ------------------------------------------------------------------- >>>> -- >>>> ------ >>>> >>> >> > ========================================================================= Date: Sun, 27 Jan 2008 16:09:24 -0600 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Dasa Zeithamova <[log in to unmask]> Subject: Re: easythresh vs feat cluster thresholding In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit I see, that makes sense. Thanks, this is very helpful. Dasa Steve Smith wrote: > Hi, the most likely difference is in the estimation of the data > spatial smoothness. > > When you run FEAT, it has access to the GLM residuals (res4d), which > is the most accurate thing to estimate the spatial smoothness from. > When you run easythresh, it doesn't have access to this (it could if > you knew where your residuals are and amended the script), so it > estimates the smoothness from the unthresholded input statistic image; > this is slightly less accurate than the former approach and will give > slightly different smoothness estimation, resulting in slightly > different p-values. > > Cheers, Steve. > > > On 26 Jan 2008, at 01:32, Dasa Zeithamova wrote: > >> Hi, >> >> I have noticed that cluster p-values provided by easythresh command >> and those that come from feat GUI when using cluster threshold in >> post-stats are different. This happens both when using BET-extracted >> whole brain ("mask.nii.gz") and when using a small volume mask (such >> as occipital cortex mask). The cluster locations and sizes are >> identical, but the associated p-values differ (are smaller, "more >> significant" from feat GUI). I was wondering what algorithms are used >> to estimate the cluster-associated p-values and what may account for >> this discrepancy. >> >> Thank you, >> Dasa >> > > > --------------------------------------------------------------------------- > > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > > ========================================================================= Date: Mon, 28 Jan 2008 10:18:26 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Juergen Haenggi <[log in to unmask]> Subject: Error message: NEWMAT::IndexException Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear FSL experts In the past I used DTIFIT and everything worked fine. Now I have a new project and tried to run DTIFIT again. But there is a problem (I think) with the reading of the bvecs and bvals files: [Macintosh-3:PreProc/AP/VP01_analyze] juergenhaenggi% dtifit -k data -o data -m nodif_brain_mask -r bvecs -b bvals -V data file data mask file nodif_brain_mask bvecs bvecs bvals bvals terminate called after throwing an instance of 'NEWMAT::IndexException' Abort [Macintosh-3:PreProc/AP/VP01_analyze] juergenhaenggi% What seems to be strange is the fact that we took the old files which worked fine and only changed the values inside the files and saved these files again. Is there any idea what can evoke such a problem? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [log in to unmask] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- ========================================================================= Date: Mon, 28 Jan 2008 17:51:30 +0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: WANG Bo <[log in to unmask]> In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Dear all, I am trying the FSL4.0.3. After I run the following two steps, I found the images created by FAST were in mirror orientation of x axial with the input BET image. bet anat anat_brain -o -e -v -f 0.5 -g 0 -m -s fast -v1 -t1 -c 3 -ov -od anat_brain anat_brain It's exactly same with what I had done with FSL3.2. Any suggestions? best wish! WANG Bo ------------------------------------------------ State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science Addr. : 15 Datun Road, Chaoyang District Beijing, 100101, PR China Tel. : ++8610-64888565/8431ext 808 Fax : ++8610-64838468 email: [log in to unmask] ========================================================================= Date: Mon, 28 Jan 2008 10:57:23 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Juergen Haenggi <[log in to unmask]> Subject: FW: Error message: NEWMAT::IndexException In-Reply-To: <[log in to unmask]> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit The problem is solved. Sorry Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [log in to unmask] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- ------ Forwarded Message From: Juergen Haenggi <[log in to unmask]> Date: Mon, 28 Jan 2008 10:18:26 +0100 To: FSL Mailinglist <[log in to unmask]> Conversation: Error message: NEWMAT::IndexException Subject: Error message: NEWMAT::IndexException Dear FSL experts In the past I used DTIFIT and everything worked fine. Now I have a new project and tried to run DTIFIT again. But there is a problem (I think) with the reading of the bvecs and bvals files: [Macintosh-3:PreProc/AP/VP01_analyze] juergenhaenggi% dtifit -k data -o data -m nodif_brain_mask -r bvecs -b bvals -V data file data mask file nodif_brain_mask bvecs bvecs bvals bvals terminate called after throwing an instance of 'NEWMAT::IndexException' Abort [Macintosh-3:PreProc/AP/VP01_analyze] juergenhaenggi% What seems to be strange is the fact that we took the old files which worked fine and only changed the values inside the files and saved these files again. Is there any idea what can evoke such a problem? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [log in to unmask] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- ------ End of Forwarded Message ========================================================================= Date: Mon, 28 Jan 2008 11:45:13 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Martin M Monti <[log in to unmask]> Subject: Re: fsl on window XP In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: quoted-printable I've ran FSL on cygwin successfully for quite a while -- and had minimal=20 trouble in installing it. Couldn't do the virtual machine because of the fake IPs it would create,=20 which got me booted out of my network for a while.. I've often heard complaints about the FSL-cygwin compatibility, however.=20 Plus, you'll be missing out on the new packages, which will not run on=20 cygwin; so you may be better off using something like Ubunto, which is a=20 really friendly and intuitive. cheers martin Tom Johnstone wrote: > You can run FSL on Linux installed in a virtual machine with either > VMWare or VirtualBox. I have an installation running on Ubuntu running > on VirtualBox on my laptop and it runs pretty much the same speed as a > native installation. > > -Tom > > On Jan 27, 2008 7:01 AM, Ji=F8=ED Keller, M.D. <[log in to unmask]>= wrote: > =20 >> Hi, >> my recommendation is to install Linux if it is possible. If you >> can't get dedicated machine try vmware (it is much slower, but I have >> installed recent Debian without any problems). If you are about to >> have a dedicated machine, try Ubuntu live CD and you will see where >> are you going to ;-). It is possible to run FSL 3 on "Linux emulator" >> called Cygwin but 1) this is no longer true with FSL 4 and 2) >> configuration of Cygwin took me more time then Linux instalation. >> >> greetings >> George >> >> 2008/1/27, Pom Sailasuta <[log in to unmask]>: >> >> =20 >>> Hello, >>> >>> can I get someone to comment on fsl on window XP? >>> I really like to install on window XP if it is wise to do so, i do no= t want >>> to spend >>> weeks or months debugging the problems. >>> >>> any input is greatly appreciated. >>> >>> thanks >>> Pom >>> >>> =20 > > > > =20 ========================================================================= Date: Mon, 28 Jan 2008 13:41:35 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Mark Woolrich <[log in to unmask]> Subject: Re: group differences in functional connectivity In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-84--117803342 --Apple-Mail-84--117803342 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi Phil, It sounds like you are wanting to do a group comparison on the X-Y correlation coefficients, and not on the "slope" of the relationship represented by the usual regression coefficient. Clearly it is true that these are not the same thing, e.g. you can get the same correlation coefficient for different slopes. So your ideal would be to calculate traditional X-Y correlation coefficients and then do some group test on those. But as I understand it - you are looking to avoid doing this and want to do the nearest equivalent thing using the GLM fitting in Feat. So it is the case that the correlation coefficient between X and Y is the same as the regression parameter obtained from fitting normalised (demeaned and divided by their std) X to normalised Y. Based on this it sounds to me as though Jeanette's suggestion is a good one. You normalise X, fit this to unnormalised Y, then rescale the resulting regression parameters (and their variances) to mimic as if you had normalised Y before fitting. Clearly, an alternative is to normalise filtered_func_data before film_gls is run. Cheers, Mark. ---- Dr Mark Woolrich EPSRC Advanced Research Fellow University Research Lecturer Oxford University Centre for Functional MRI of the Brain (FMRIB), John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich On 25 Jan 2008, at 19:01, Phil Reiss wrote: > Hello, > > I am interested in comparing two groups of subjects in terms of > functional connectivity with > respect to a seed voxel X. Evidently it would be in line with > common practice to perform this > comparison by > 1) running a general linear model with the voxel X time series as a > predictor, > and > 2) testing a 2nd-level contrast representing the difference between > the groups' average > coefficients for that predictor. > > However, this approach, by substituting regression coefficients for > correlations as the measure of > functional connectivity, appears to run into a serious problem: if, > say, the model finds a between- > groups difference at voxel Y, this could mean either that the > groups differ in terms of X-Y > correlation (i.e. the type of difference we're interested in), *or* > that the groups differ in terms > of the amount of signal at Y (but not in terms of X-Y correlation). > > It seems to me that this problem could be removed by scaling each > voxel's time series (including > that of the seed voxel) to a common variance, which would more or > less eliminate the difference > between regression coefficients and correlations. But I'm very > inexperienced with FSL, so I'd > appreciate it very much if anyone could comment on either my > diagnosis of the problem or my > proposed solution. > > Thanks very much! > > Regards, > Phil Reiss > > P.S. My much more FSL-savvy colleague Jeanette Mumford has proposed > the procedure below to > implement the above suggestion. If anyone has any thoughts on this > procedure's feasibility, or if > anyone has tried anything similar, I'd very much appreciate hearing > about it. > > ----------------------------- > [from JM:] > > First, simply fix the seed voxel time series in the design matrix > (divide by its sd), then estimate the > first level model the usual way. Before feeding the first level > copes into the second level you > could first copy the original copes and varcopes under a different > name and then create the > properly weighted cope/varcope images and save using the original > cope/varcope number. The > reason you'd have to be sneaky is because I think there are more > than just the cope/varcope files > that the next level of feat will be looking for. > > 1) Create the weighting image using avwmaths dir.feat/ > filtered_func_data -Tstd > sd_filtered_func_data > 2) Copy copes and varcopes cp cope# cope#_copy > 3) Create new cope/varcope avwmaths cope#_copy -div > ../sd_filtered_func_data cope# > avwmaths > varcope#_cope -div > ../sd_filtered_func_data -div ../sd_filtered_func_data varcope# > > I think simply dividing twice for the varcope should do the trick. > Oh, if you're using the newest > fsl, then avwmaths is fslmaths. > > I've never tried switching out the original cope/varcope files > before, but it seems like it would > work. > ------------------------------ > Philip Reiss, Ph.D. > Associate Research Scientist > New York University Child Study Center > 215 Lexington Ave., 16th floor > New York, NY 10016 > phone: 212-263-3669 > fax: 212-263-2476 > e-mail: [log in to unmask] > --Apple-Mail-84--117803342 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi Phil,

It sounds = like you are wanting to do a group comparison on the X-Y correlation = coefficients, and not on the "slope" of the relationship represented by = the usual regression coefficient. Clearly it is true that these are not = the same thing, e.g. you can get the same correlation coefficient for = different slopes. So your ideal would be to calculate traditional X-Y = correlation coefficients and then do some group test on those. But as I = understand it - you are looking to avoid doing this and want to do the = nearest equivalent thing using the GLM fitting in Feat.

So it is the case that the = correlation coefficient between X and Y is the same as the regression = parameter obtained from fitting normalised (demeaned and=A0divided=A0by = their std) X to normalised Y. Based on this it sounds to me as though = Jeanette's suggestion is a good one. You normalise X, fit this to = unnormalised Y, then
rescale the resulting regression = parameters (and their variances) to mimic as if you had normalised Y = before fitting. Clearly, an alternative is to normalise = filtered_func_data before film_gls is run.

Cheers, = Mark.

=
----
Dr Mark = Woolrich
EPSRC Advanced = Research Fellow=A0University Research Lecturer

Oxford = University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, = UK.

Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~wo= olrich



=

On 25 Jan 2008, at 19:01, Phil Reiss wrote:

Hello,

I am interested in comparing two = groups of subjects in terms of functional connectivity with=A0
respect = to a seed voxel X.=A0 = Evidently it would be in line with common practice to perform = this=A0
comparison by
1) running a = general linear model with the voxel X time series as a = predictor,
and
2) = testing a 2nd-level contrast representing the difference between the = groups' average=A0
coefficients for that predictor.

However, = this approach, by substituting regression coefficients for correlations = as the measure of=A0
functional connectivity, appears to run into a = serious problem: if, say, the model finds a between-
groups difference at voxel Y, this could mean either = that the groups differ in terms of X-Y=A0
of the amount = of signal at Y (but not in terms of X-Y correlation).

It seems = to me that this problem could be removed by scaling each voxel's time = series (including=A0
that of the seed voxel) to a common variance, which = would more or less eliminate the difference=A0
between = regression coefficients and correlations.=A0 But I'm very inexperienced = with FSL, so I'd=A0
appreciate it very much if anyone could comment on = either my diagnosis of the problem or my
proposed = solution.

Thanks very much!

Phil Reiss

P.S. My = much more FSL-savvy colleague Jeanette Mumford has proposed the = procedure below to=A0
implement the above suggestion.=A0 If anyone has any thoughts on = this procedure's feasibility, or if=A0
anyone = has tried anything similar, I'd very much appreciate hearing about = it.

-----------------------------
[from JM:]

First, simply fix the seed voxel = time series in the design matrix (divide by its sd), then estimate = the=A0
first level model the usual way.=A0 Before feeding the first = level copes into the second level you=A0
could = first copy the original copes and varcopes under a different name and = then create the=A0
properly weighted cope/varcope images and save using = the original cope/varcope number.=A0= The=A0
reason you'd have to be sneaky is because I think = there are more than just the cope/varcope files
that the next level of feat will be looking = for.

1)=A0 = Create the weighting image using avwmaths = dir.feat/filtered_func_data -Tstd=A0
2)=A0 Copy copes and varcopes=A0 cp cope# cope#_copy
3)=A0 = Create new cope/varcope=A0 = =A0 avwmaths cope#_copy -div
=A0 = cope#
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 avwmaths = varcope#_cope -div
../sd_filtered_func_data = -div ../sd_filtered_func_data varcope#

I think = simply dividing twice for the varcope should do the trick.=A0 Oh, if you're using the = newest=A0
fsl, then avwmaths is fslmaths.

I've = never tried switching out the original cope/varcope files before, but it = seems like it would=A0
Philip Reiss, = Ph.D.
Associate Research = Scientist
New York University Child Study = Center
215 Lexington Ave., 16th = floor
New York, NY 10016
phone: =A0 = 212-263-3669
fax: =A0 =A0 212-263-2476
e-mail:=A0 = [log in to unmask]

=
= --Apple-Mail-84--117803342-- ========================================================================= Date: Mon, 28 Jan 2008 16:45:10 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Hanne Lehn <[log in to unmask]> Subject: Re: within-subject effects of task performance In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hi, I see your point, I will drop the performance regressor at this level of the analysis. Thank you for helping me sort this out. Hanne Sitat Steve Smith <[log in to unmask]>: > Hi, > > If you have two regressors that are the same then the fitting > mathematics will be poorly conditioned and you will not be able to > run > such contrasts as: > [1 0] > [1 -1] > [0 1]. > > In this case you will have to drop the performace EV I suspect. > However, if the subject performs exacrtly the same for every task it > doesn't make sense to add it anyway. Maybe instead you maybe want to > be adding a performance regressor at the group level, in which case > you wouldn't need to have it like the in the first level. > > Cheers, Steve. > > > > On 24 Jan 2008, at 14:32, Hanne Lehn wrote: > > > Hi again, > > > > I have now run the first level analyses discussed in previous > e-mails, > > with an added regressor that models performance effects. For some > > subjects, I get a warning about my design being rank deficient. It > > seems > > it occurs whenever the performance regressor (EV2) is (too close to > > being) > > colinear to the main regressor (EV1). > > > > Example: The onsets and durations of EV1 and EV2 are always > > identical, as > > they model the same event; EV1=main effect, EV2= performance > > modulation. > > EV1 is always weighted with 1's (3rd column of onset file) > Sometimes > > EV2 > > is also weighted with only 1's (if performance equaled 1 point on > > every > > trial), or perhaps only 2's. In these cases my design is regarded > rank > > deficient, and the resulting statistics don't make any sense (EV2 > z- > > scores > >> 50). > > > > Does anyone know how to deal with this problem? > > > > From the past correspondence I understand there is no need to > demean > > the > > performance scores before entering them as weights for EV2, as long > > as EV2 > > is orthogonalized wrt EV1. What, then, could I do to get a proper > > design? > > > > Thanks a lot in advance! > > > > Hanne > > > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > -- ========================================================================= Date: Mon, 28 Jan 2008 08:39:24 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Jeanette Mumford <[log in to unmask]> Subject: Re: group differences in functional connectivity In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_11711_15439948.1201538364768" ------=_Part_11711_15439948.1201538364768 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Mark, Thanks for the response. Is there an easy way to normalise the filtered func data before film_gls is run? Thanks, Jeanette On Jan 28, 2008 5:41 AM, Mark Woolrich <[log in to unmask]> wrote: > Hi Phil, > It sounds like you are wanting to do a group comparison on the X-Y > correlation coefficients, and not on the "slope" of the relationship > represented by the usual regression coefficient. Clearly it is true that > these are not the same thing, e.g. you can get the same correlation > coefficient for different slopes. So your ideal would be to calculate > traditional X-Y correlation coefficients and then do some group test on > those. But as I understand it - you are looking to avoid doing this and want > to do the nearest equivalent thing using the GLM fitting in Feat. > So it is the case that the correlation coefficient between X and Y is the > same as the regression parameter obtained from fitting normalised (demeaned > and divided by their std) X to normalised Y. Based on this it sounds to me > as though Jeanette's suggestion is a good one. You normalise X, fit this to > unnormalised Y, then > rescale the resulting regression parameters (and their variances) to mimic > as if you had normalised Y before fitting. Clearly, an alternative is to > normalise filtered_func_data before film_gls is run. > > Cheers, Mark. > > ---- > Dr Mark Woolrich > EPSRC Advanced Research Fellow University Research Lecturer > > Oxford University Centre for Functional MRI of the Brain (FMRIB), > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. > > Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich > > > > > On 25 Jan 2008, at 19:01, Phil Reiss wrote: > > Hello, > > I am interested in comparing two groups of subjects in terms of functional > connectivity with > respect to a seed voxel X. Evidently it would be in line with common > practice to perform this > comparison by > 1) running a general linear model with the voxel X time series as a > predictor, > and > 2) testing a 2nd-level contrast representing the difference between the > groups' average > coefficients for that predictor. > > However, this approach, by substituting regression coefficients for > correlations as the measure of > functional connectivity, appears to run into a serious problem: if, say, > the model finds a between- > groups difference at voxel Y, this could mean either that the groups > differ in terms of X-Y > correlation (i.e. the type of difference we're interested in), *or* that > the groups differ in terms > of the amount of signal at Y (but not in terms of X-Y correlation). > > It seems to me that this problem could be removed by scaling each voxel's > time series (including > that of the seed voxel) to a common variance, which would more or less > eliminate the difference > between regression coefficients and correlations. But I'm very > inexperienced with FSL, so I'd > appreciate it very much if anyone could comment on either my diagnosis of > the problem or my > proposed solution. > > Thanks very much! > > Regards, > Phil Reiss > > P.S. My much more FSL-savvy colleague Jeanette Mumford has proposed the > procedure below to > implement the above suggestion. If anyone has any thoughts on this > procedure's feasibility, or if > anyone has tried anything similar, I'd very much appreciate hearing about > it. > > ----------------------------- > [from JM:] > > First, simply fix the seed voxel time series in the design matrix (divide > by its sd), then estimate the > first level model the usual way. Before feeding the first level copes > into the second level you > could first copy the original copes and varcopes under a different name > and then create the > properly weighted cope/varcope images and save using the original > cope/varcope number. The > reason you'd have to be sneaky is because I think there are more than just > the cope/varcope files > that the next level of feat will be looking for. > > 1) Create the weighting image using avwmaths dir.feat/filtered_func_data > -Tstd > sd_filtered_func_data > 2) Copy copes and varcopes cp cope# cope#_copy > 3) Create new cope/varcope avwmaths cope#_copy -div > ../sd_filtered_func_data cope# > avwmaths varcope#_cope -div > ../sd_filtered_func_data -div ../sd_filtered_func_data varcope# > > I think simply dividing twice for the varcope should do the trick. Oh, if > you're using the newest > fsl, then avwmaths is fslmaths. > > I've never tried switching out the original cope/varcope files before, but > it seems like it would > work. > ------------------------------ > Philip Reiss, Ph.D. > Associate Research Scientist > New York University Child Study Center > 215 Lexington Ave., 16th floor > New York, NY 10016 > phone: 212-263-3669 > fax: 212-263-2476 > e-mail: [log in to unmask] > > > ------=_Part_11711_15439948.1201538364768 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Mark,

Thanks for the response.  Is there an easy way to normali= se the filtered func data before film_gls is run?

Thanks,
Jeanett= e

On Jan 28, 2008 5:41 AM, Mark Woolrich = <[log in to unmask]&= gt; wrote:
Hi Phil,

It sounds like you are wanting to do a group co= mparison on the X-Y correlation coefficients, and not on the "slope&qu= ot; of the relationship represented by the usual regression coefficient. Cl= early it is true that these are not the same thing, e.g. you can get the sa= me correlation coefficient for different slopes. So your ideal would be to = calculate traditional X-Y correlation coefficients and then do some group t= est on those. But as I understand it - you are looking to avoid doing this = and want to do the nearest equivalent thing using the GLM fitting in Feat.<= div>
So it is the case that the correlation coefficient between X= and Y is the same as the regression parameter obtained from fitting normal= ised (demeaned and divided by their std) X to normalised Y. Based= on this it sounds to me as though Jeanette's suggestion is a good one.= You normalise X, fit this to unnormalised Y, then
rescale the resulting regression parameters (and their variances) to m= imic as if you had normalised Y before fitting. Clearly, an alternative is = to normalise filtered_func_data before film_gls is run.

Cheers, Mark.

----
Dr Mark Woolrich
EPSRC Advanced Research Fellow Universi= ty Research Lecturer
Oxford University Centre for Functional MRI of = the Brain (FMRIB),
John Radcliffe Hospital= , Headington, Oxford OX3 9DU, UK.

Tel: (+44)1865-222782 Homepage: http://www.f= mrib.ox.ac.uk/~woolrich



<= /span>

On 25 Jan 2008, at 19:0= 1, Phil Reiss wrote:

Hello,

I am interested in comparing two groups of subjects in terms of functional = connectivity with 
respe= ct to a seed voxel X.  Evidently it would be in line with= common practice to perform this 
comparison by
= 1) running a general linear model with the voxel X time series as a predict= or,
and
2= ) testing a 2nd-level contrast representing the difference between the grou= ps' average 
coefficients for that predictor.

= However, this approach, by substituting regression coefficients for correla= tions as the measure of 
functional connectivity, appears to run into a = serious problem: if, say, the model finds a between-
groups difference at voxel Y, this could mean either that the gr= oups differ in terms of X-Y 
correlation (i.e. the type of difference we'= ;re interested in), *or* that the groups differ in terms
of the amount of signal at Y (but not in terms of X-Y correl= ation).

It seems to me that this problem could be removed by scaling each = voxel's time series (including 
that of the seed voxel) to a common variance, which would more or less elim= inate the difference 
be= tween regression coefficients and correlations.  But I= 9;m very inexperienced with FSL, so I'd 
appreciate it very much if anyone could comment= on either my diagnosis of the problem or my
proposed solution.
Thanks very much!

Regards,<= /div>
Phil Reiss

P.S. My much more FSL-savvy colleague= Jeanette Mumford has proposed the procedure below to 
implement the above suggestion.  = If anyone has any thoughts on this procedure's feasibility, or i= f 
anyone has tried anything similar, I'd very= much appreciate hearing about it.

--------------------------= ---
[from JM:]

First, simply fix the = seed voxel time series in the design matrix (divide by its sd), then estima= te the 
first level model the usual way.  Before feeding the first level copes into the second level you&n= bsp;
could first copy the original = copes and varcopes under a different name and then create the 
properly weighted cope/varcope images and save = using the original cope/varcope number.  The <= /span>
reason you'd have to be sneaky = is because I think there are more than just the cope/varcope files
that the next level of feat will be looking for= .

1)  Create the weighting image using av= wmaths dir.feat/filtered_func_data -Tstd 
sd_filtered_func_data
2)  Copy copes and varcopes  cp= cope# cope#_copy
3)  Cr= eate new cope/varcope    avwmaths cope#_copy -div
../sd_filtered_func_data  cop= e#
         = ;                     &nb= sp;               avwmaths varcop= e#_cope -div
../sd_filtered_func_data -div= ../sd_filtered_func_data varcope#

I think simply dividing twice for the varcope should do the trick.=   Oh, if you're using the newest 
fsl, then avwmaths is fslmaths.

I've never tried switchin= g out the original cope/varcope files before, but it seems like it would 
work.
--------= ----------------------
Philip Reiss, Ph.D.=
Associate Research Scientist
New York University Child Study Center
215= Lexington Ave., 16th floor
New York, NY 1= 0016
phone:   212-263-36= 69
fax:     212-263-2476
e-mail:  [log in to unmask]" target=3D"_blank">[log in to unmask]



------=_Part_11711_15439948.1201538364768-- ========================================================================= Date: Mon, 28 Jan 2008 17:02:05 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Christopher Petty <[log in to unmask]> Subject: fslstats Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" is there an option with fslstats -V for grabbing only 1 volume of a 4D fi= le? for instance if i know R-amyg is the 10th volume of my results from run_first_all ... how can i only measure that volume? -chris ========================================================================= Date: Mon, 28 Jan 2008 17:05:06 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Mark Woolrich <[log in to unmask]> Subject: Re: group differences in functional connectivity In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-86--105593272 --Apple-Mail-86--105593272 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi Jeanette, No way to do it when running from the GUI. You would need to do this by inserting the filtered_func_data normalisation into a script of your first level feat run, something like: fslmaths filtered_func_data -Tstd sd_filtered_func_data -odt float fslmaths filtered_func_data -div sd_filtered_func_data filtered_func_data -odt float Otherwise, your suggested approach would be needed if you were using the GUI. Cheers, Mark. ---- Dr Mark Woolrich EPSRC Advanced Research Fellow University Research Lecturer Oxford University Centre for Functional MRI of the Brain (FMRIB), John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich On 28 Jan 2008, at 16:39, Jeanette Mumford wrote: > Mark, > > Thanks for the response. Is there an easy way to normalise the > filtered func data before film_gls is run? > > Thanks, > Jeanette > > On Jan 28, 2008 5:41 AM, Mark Woolrich <[log in to unmask]> > wrote: > Hi Phil, > > It sounds like you are wanting to do a group comparison on the X-Y > correlation coefficients, and not on the "slope" of the > relationship represented by the usual regression coefficient. > Clearly it is true that these are not the same thing, e.g. you can > get the same correlation coefficient for different slopes. So your > ideal would be to calculate traditional X-Y correlation > coefficients and then do some group test on those. But as I > understand it - you are looking to avoid doing this and want to do > the nearest equivalent thing using the GLM fitting in Feat. > > So it is the case that the correlation coefficient between X and Y > is the same as the regression parameter obtained from fitting > normalised (demeaned and divided by their std) X to normalised Y. > Based on this it sounds to me as though Jeanette's suggestion is a > good one. You normalise X, fit this to unnormalised Y, then > rescale the resulting regression parameters (and their variances) > to mimic as if you had normalised Y before fitting. Clearly, an > alternative is to normalise filtered_func_data before film_gls is run. > > Cheers, Mark. > > ---- > Dr Mark Woolrich > EPSRC Advanced Research Fellow University Research Lecturer > > Oxford University Centre for Functional MRI of the Brain (FMRIB), > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. > > Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich > > > > > On 25 Jan 2008, at 19:01, Phil Reiss wrote: > >> Hello, >> >> I am interested in comparing two groups of subjects in terms of >> functional connectivity with >> respect to a seed voxel X. Evidently it would be in line with >> common practice to perform this >> comparison by >> 1) running a general linear model with the voxel X time series as >> a predictor, >> and >> 2) testing a 2nd-level contrast representing the difference >> between the groups' average >> coefficients for that predictor. >> >> However, this approach, by substituting regression coefficients >> for correlations as the measure of >> functional connectivity, appears to run into a serious problem: >> if, say, the model finds a between- >> groups difference at voxel Y, this could mean either that the >> groups differ in terms of X-Y >> correlation (i.e. the type of difference we're interested in), >> *or* that the groups differ in terms >> of the amount of signal at Y (but not in terms of X-Y correlation). >> >> It seems to me that this problem could be removed by scaling each >> voxel's time series (including >> that of the seed voxel) to a common variance, which would more or >> less eliminate the difference >> between regression coefficients and correlations. But I'm very >> inexperienced with FSL, so I'd >> appreciate it very much if anyone could comment on either my >> diagnosis of the problem or my >> proposed solution. >> >> Thanks very much! >> >> Regards, >> Phil Reiss >> >> P.S. My much more FSL-savvy colleague Jeanette Mumford has >> proposed the procedure below to >> implement the above suggestion. If anyone has any thoughts on >> this procedure's feasibility, or if >> anyone has tried anything similar, I'd very much appreciate >> hearing about it. >> >> ----------------------------- >> [from JM:] >> >> First, simply fix the seed voxel time series in the design matrix >> (divide by its sd), then estimate the >> first level model the usual way. Before feeding the first level >> copes into the second level you >> could first copy the original copes and varcopes under a different >> name and then create the >> properly weighted cope/varcope images and save using the original >> cope/varcope number. The >> reason you'd have to be sneaky is because I think there are more >> than just the cope/varcope files >> that the next level of feat will be looking for. >> >> 1) Create the weighting image using avwmaths dir.feat/ >> filtered_func_data -Tstd >> sd_filtered_func_data >> 2) Copy copes and varcopes cp cope# cope#_copy >> 3) Create new cope/varcope avwmaths cope#_copy -div >> ../sd_filtered_func_data cope# >> avwmaths >> varcope#_cope -div >> ../sd_filtered_func_data -div ../sd_filtered_func_data varcope# >> >> I think simply dividing twice for the varcope should do the >> trick. Oh, if you're using the newest >> fsl, then avwmaths is fslmaths. >> >> I've never tried switching out the original cope/varcope files >> before, but it seems like it would >> work. >> ------------------------------ >> Philip Reiss, Ph.D. >> Associate Research Scientist >> New York University Child Study Center >> 215 Lexington Ave., 16th floor >> New York, NY 10016 >> phone: 212-263-3669 >> fax: 212-263-2476 >> e-mail: [log in to unmask] >> > > --Apple-Mail-86--105593272 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi Jeanette,

No way to do it when running from the = GUI.=A0You would need to do this by inserting the filtered_func_data = normalisation into a script of your first level feat run, something = like:
fslmaths filtered_func_data -Tstd=A0sd_filtered_func_data = -odt float
fslmaths filtered_func_data -div = sd_filtered_func_data=A0filtered_func_data=A0-odt float

Otherwise, your suggested = approach would be needed if you were using the GUI.

Cheers, = Mark.

=
----
Dr Mark = Woolrich
EPSRC Advanced = Research Fellow=A0University Research Lecturer

Oxford = University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, = UK.

Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~wo= olrich



=

On 28 Jan 2008, at 16:39, Jeanette Mumford = wrote:

Mark,

Thanks for the response.=A0 Is there an easy = way to normalise the filtered func data before film_gls is = run?

Thanks,
Jeanette

On Jan = 28, 2008 5:41 AM, Mark Woolrich <[log in to unmask]> = wrote:
Hi Phil,

It sounds like you = are wanting to do a group comparison on the X-Y correlation = coefficients, and not on the "slope" of the relationship represented by = the usual regression coefficient. Clearly it is true that these are not = the same thing, e.g. you can get the same correlation coefficient for = different slopes. So your ideal would be to calculate traditional X-Y = correlation coefficients and then do some group test on those. But as I = understand it - you are looking to avoid doing this and want to do the = nearest equivalent thing using the GLM fitting in Feat.
=
So it is the case that the correlation coefficient = between X and Y is the same as the regression parameter obtained from = fitting normalised (demeaned and=A0divided=A0by their std) X to = normalised Y. Based on this it sounds to me as though Jeanette's = suggestion is a good one. You normalise X, fit this to unnormalised Y, = then
rescale the resulting regression parameters (and their = variances) to mimic as if you had normalised Y before fitting. Clearly, = an alternative is to normalise filtered_func_data before film_gls is = run.

Cheers, = Mark.

----
Dr Mark Woolrich
EPSRC Advanced Research Fellow=A0University Research = Lecturer

=
Oxford University Centre for Functional MRI = of the Brain (FMRIB),
John Radcliffe = Hospital, Headington, Oxford OX3 9DU, UK.

Tel: = (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich



=

On 25 Jan 2008, at = 19:01, Phil Reiss wrote:

Hello,

I am = interested in comparing two groups of subjects in terms of functional = connectivity with=A0
respect to a seed voxel X.=A0 Evidently it would be = in line with common practice to perform this=A0
comparison by
1) = running a general linear model with the voxel X time series as a = predictor,
and
2) testing a 2nd-level contrast representing the difference = between the groups' average=A0
coefficients for that predictor.

However, this = approach, by substituting regression coefficients for correlations as = the measure of=A0
functional connectivity, appears to run into a serious problem: = if, say, the model finds a between-
groups difference at voxel Y, this could mean either that the = groups differ in terms of X-Y=A0
correlation (i.e. the type of difference we're interested in), = *or* that the groups differ in terms
of = the amount of signal at Y (but not in terms of X-Y correlation).
=

It seems to me that this problem could be removed = by scaling each voxel's time series (including=A0
that of the seed voxel) to a common variance, = which would more or less eliminate the = difference=A0
between = regression coefficients and correlations.=A0 But I'm very = inexperienced with FSL, so I'd=A0
appreciate it very much if anyone could comment on either my = diagnosis of the problem or my
proposed = solution.

=
Thanks very much!

Regards,
Phil Reiss

P.S. My much more FSL-savvy colleague Jeanette Mumford has = proposed the procedure below to=A0
implement the above suggestion.=A0 If anyone has any = thoughts on this procedure's feasibility, or if=A0
=
anyone has tried anything similar, I'd very = much appreciate hearing about it.

-----------------------------
[from JM:]

First, simply fix the seed = voxel time series in the design matrix (divide by its sd), then estimate = the=A0
first level model = the usual way.=A0 Before feeding the first level copes into = the second level you=A0
could first copy the original copes and varcopes under a different = name and then create the=A0
properly weighted cope/varcope images and save using the original = cope/varcope number.=A0 The=A0
reason you'd have to be sneaky is because I think = there are more than just the cope/varcope files
that the next level of feat will be looking = for.

1)=A0 Create the weighting image = using avwmaths dir.feat/filtered_func_data -Tstd=A0
=
sd_filtered_func_data
2)=A0 Copy copes and varcopes=A0= cp cope# cope#_copy
3)=A0 = Create new cope/varcope=A0 =A0 avwmaths cope#_copy = -div
../sd_filtered_func_data=A0 = cope#
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = avwmaths varcope#_cope -div
../sd_filtered_func_data -div ../sd_filtered_func_data = varcope#

I think simply dividing = twice for the varcope should do the trick.=A0 Oh, if you're = using the newest=A0
fsl, = then avwmaths is fslmaths.

I've never tried switching = out the original cope/varcope files before, but it seems like it = would=A0
work.
------------------------------
Philip Reiss, Ph.D.
Associate Research Scientist
New = York University Child Study Center
215 = Lexington Ave., 16th floor
New York, NY = 10016
phone: =A0 = 212-263-3669
fax: =A0 =A0 = 212-263-2476
e-mail:=A0 = [log in to unmask]

=


= --Apple-Mail-86--105593272-- ========================================================================= Date: Tue, 29 Jan 2008 01:07:19 +0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: WANG Bo <[log in to unmask]> Subject: FAST changing orientation of BETed image Mime-Version: 1.0 (Apple Message framework v753) Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear all, I am trying the FSL4.0.3. After I run the following two steps, I found the images created by FAST were in mirror orientation of x axial with the input BET image. bet anat anat_brain -o -e -v -f 0.5 -g 0 -m -s fast -v1 -t1 -c 3 -ov -od anat_brain anat_brain It's exactly same with what I had done with FSL3.2. Any suggestions? Sorry for resending this mail instead of last one without title. best wish! WANG Bo ------------------------------------------------ State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science Addr. : 15 Datun Road, Chaoyang District Beijing, 100101, PR China Tel. : ++8610-64888565/8431ext 808 Fax : ++8610-64838468 email: [log in to unmask] ========================================================================= Date: Mon, 28 Jan 2008 09:01:37 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Pom Sailasuta <[log in to unmask]> Subject: Re: fsl on window XP In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_10929_26724413.1201539697932" ------=_Part_10929_26724413.1201539697932 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: base64 Content-Disposition: inline aGVsbG8gbWFydGluLAoKbWF5IGkgYXNrIHdoaWNoIHZlcnNpb24gZnNsIHlvdSBhcmUgcnVubmlu ZyBvbiBjeWd3aW4/Cgp0aGFua3MKCjIwMDgvMS8yOCBNYXJ0aW4gTSBNb250aSA8bWFydGluLm0u bW9udGlAZ21haWwuY29tPjoKCj4gSSd2ZSByYW4gRlNMIG9uIGN5Z3dpbiBzdWNjZXNzZnVsbHkg Zm9yIHF1aXRlIGEgd2hpbGUgLS0gYW5kIGhhZCBtaW5pbWFsCj4gdHJvdWJsZSBpbiBpbnN0YWxs aW5nIGl0Lgo+IENvdWxkbid0IGRvIHRoZSB2aXJ0dWFsIG1hY2hpbmUgYmVjYXVzZSBvZiB0aGUg ZmFrZSBJUHMgaXQgd291bGQgY3JlYXRlLAo+IHdoaWNoIGdvdCBtZSBib290ZWQgb3V0IG9mIG15 IG5ldHdvcmsgZm9yIGEgd2hpbGUuLgo+Cj4gSSd2ZSBvZnRlbiBoZWFyZCBjb21wbGFpbnRzIGFi b3V0IHRoZSBGU0wtY3lnd2luIGNvbXBhdGliaWxpdHksIGhvd2V2ZXIuCj4gUGx1cywgeW91J2xs IGJlIG1pc3Npbmcgb3V0IG9uIHRoZSBuZXcgcGFja2FnZXMsIHdoaWNoIHdpbGwgbm90IHJ1biBv bgo+IGN5Z3dpbjsgc28geW91IG1heSBiZSBiZXR0ZXIgb2ZmIHVzaW5nIHNvbWV0aGluZyBsaWtl IFVidW50bywgd2hpY2ggaXMgYQo+IHJlYWxseSBmcmllbmRseSBhbmQgaW50dWl0aXZlLgo+Cj4g Y2hlZXJzCj4KPiAgbWFydGluCj4KPiBUb20gSm9obnN0b25lIHdyb3RlOgo+ID4gWW91IGNhbiBy dW4gRlNMIG9uIExpbnV4IGluc3RhbGxlZCBpbiBhIHZpcnR1YWwgbWFjaGluZSB3aXRoIGVpdGhl cgo+ID4gVk1XYXJlIG9yIFZpcnR1YWxCb3guIEkgaGF2ZSBhbiBpbnN0YWxsYXRpb24gcnVubmlu ZyBvbiBVYnVudHUgcnVubmluZwo+ID4gb24gVmlydHVhbEJveCBvbiBteSBsYXB0b3AgYW5kIGl0 IHJ1bnMgcHJldHR5IG11Y2ggdGhlIHNhbWUgc3BlZWQgYXMgYQo+ID4gbmF0aXZlIGluc3RhbGxh dGlvbi4KPiA+Cj4gPiAtVG9tCj4gPgo+ID4gT24gSmFuIDI3LCAyMDA4IDc6MDEgQU0sIEpp+O0g S2VsbGVyLCBNLkQuIDxrZWxsZXIubGlzdHNAZ21haWwuY29tPgo+IHdyb3RlOgo+ID4KPiA+PiBI aSwKPiA+PiAgIG15IHJlY29tbWVuZGF0aW9uIGlzIHRvIGluc3RhbGwgTGludXggaWYgaXQgaXMg cG9zc2libGUuIElmIHlvdQo+ID4+IGNhbid0IGdldCBkZWRpY2F0ZWQgbWFjaGluZSB0cnkgdm13 YXJlIChpdCBpcyBtdWNoIHNsb3dlciwgYnV0IEkgaGF2ZQo+ID4+IGluc3RhbGxlZCByZWNlbnQg RGViaWFuIHdpdGhvdXQgYW55IHByb2JsZW1zKS4gSWYgeW91IGFyZSBhYm91dCB0bwo+ID4+IGhh dmUgYSBkZWRpY2F0ZWQgbWFjaGluZSwgdHJ5IFVidW50dSBsaXZlIENEIGFuZCB5b3Ugd2lsbCBz ZWUgd2hlcmUKPiA+PiBhcmUgeW91IGdvaW5nIHRvIDstKS4gSXQgaXMgcG9zc2libGUgdG8gcnVu IEZTTCAzIG9uICJMaW51eCBlbXVsYXRvciIKPiA+PiBjYWxsZWQgQ3lnd2luIGJ1dCAxKSB0aGlz IGlzIG5vIGxvbmdlciB0cnVlIHdpdGggRlNMIDQgYW5kIDIpCj4gPj4gY29uZmlndXJhdGlvbiBv ZiBDeWd3aW4gdG9vayBtZSBtb3JlIHRpbWUgdGhlbiBMaW51eCBpbnN0YWxhdGlvbi4KPiA+Pgo+ ID4+ICAgICBncmVldGluZ3MKPiA+PiAgICAgICAgICAgIEdlb3JnZQo+ID4+Cj4gPj4gMjAwOC8x LzI3LCBQb20gU2FpbGFzdXRhIDxzYWlsYXN1dGFAaG1yaS5vcmc+Ogo+ID4+Cj4gPj4KPiA+Pj4g SGVsbG8sCj4gPj4+Cj4gPj4+IGNhbiBJIGdldCBzb21lb25lIHRvIGNvbW1lbnQgb24gZnNsIG9u IHdpbmRvdyBYUD8KPiA+Pj4gSSByZWFsbHkgbGlrZSB0byBpbnN0YWxsIG9uIHdpbmRvdyBYUCBp ZiBpdCBpcyB3aXNlIHRvIGRvIHNvLCBpIGRvIG5vdAo+IHdhbnQKPiA+Pj4gdG8gc3BlbmQKPiA+ Pj4gd2Vla3Mgb3IgbW9udGhzIGRlYnVnZ2luZyB0aGUgcHJvYmxlbXMuCj4gPj4+Cj4gPj4+IGFu eSBpbnB1dCBpcyBncmVhdGx5IGFwcHJlY2lhdGVkLgo+ID4+Pgo+ID4+PiB0aGFua3MKPiA+Pj4g UG9tCj4gPj4+Cj4gPj4+Cj4gPgo+ID4KPiA+Cj4gPgo+Cg== ------=_Part_10929_26724413.1201539697932 Content-Type: text/html; 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charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, There's no way just to do this with fslstats. However, with fslroi you can easily extract the single volume and then run fslstats on that. All the best, Mark Christopher Petty wrote: > is there an option with fslstats -V for grabbing only 1 volume of a 4D file? > > for instance if i know R-amyg is the 10th volume of my results from > run_first_all ... how can i only measure that volume? > > -chris > > ========================================================================= Date: Mon, 28 Jan 2008 09:58:52 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Pom Sailasuta <[log in to unmask]> Subject: Re: fsl on window XP In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_11244_4215599.1201543132912" ------=_Part_11244_4215599.1201543132912 Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: base64 Content-Disposition: inline aGVsbG8sCgpjYW4gSSBzdGlsbCBnZXQgb2xkZXIgZnNsIHZlcnNpb24gdGhhdCBpcyBjb21wYXRp 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MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear FSLers, I seem to keep having an error as I finish setting up the stats fr a first level analysis, and I keep on getting the following error, which seems to relate to the balloon-help bad window path name ".dialog1.f.viewport.f.btn" bad window path name ".dialog1.f.viewport.f.btn" while executing "winfo rootx $win" (procedure "balloonhelp_show" line 7) invoked from within "balloonhelp_show .dialog1.f.viewport.f.btn" ("after" script) it seems to me to be a completely benign error -- that has to do with the GUI, not with the contents of the analysis. Is this the case? Is there an obvious way to avoid it (errors always give me chills.. :)) other than turning off the balloon help I presume? cheers martin ========================================================================= Date: Mon, 28 Jan 2008 10:31:44 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Pom Sailasuta <[log in to unmask]> Subject: older version of fsl for cygwin MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_11413_15526046.1201545104854" ------=_Part_11413_15526046.1201545104854 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, Can I still get an older fsl version compatible with cygwin? thanks ------=_Part_11413_15526046.1201545104854 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi,

Can I still get an older fsl version compatible with cygwin?

thanks

------=_Part_11413_15526046.1201545104854-- ========================================================================= Date: Mon, 28 Jan 2008 20:41:27 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: EV Setup, just need verification Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I am setting EVs and just wanted to make sure I am doing this correctly. The study consists of an OSPAN (working memory task) portion), an arithme= tic portion, and a baseline. It goes as follows. -----------I------------I ---------I ---------------= OSPAN 30s Response 15s Arith 30s Repeat=20 ----------I ---------I Base 30s Base 30s So, the task w/ the response and the arithmetic are done 3 times total, a= nd baseline is done 6 times. I am not interested in including the response condition in the analysis (this is just to verify they are paying attenti= on, at least for now). I have setup the EVs as follows: For the OSPAN: Skip =3D 0s, Off =3D 105s, On =3D 30s, Phase =3D 105s, Sto= p =3D -1. For Baseline, I set up two EVs because the intervals vary, so the Baselin= e after the OSPAN is: Skip =3D 0, Off=3D 105, On =3D 30, Phase =3D 60, Stop= =3D -1. Baseline after Arithemtic is: Skip =3D 0, Off =3D 105, On =3D 30, Phase =3D= 0, Stop =3D -1. Arithemtic =3D Skip =3D 0, Off =3D 105, On =3D 30, Phase =3D 30, Stop =3D= -1. Is this correct? Also, when I set up my contrast for OSPAN vs. Baseline, = I choose OSPAN =3D 1, Baseline 1 =3D -.5, and Baseline 2 =3D -.5. This shou= ld make it as if there was just one baseline, correct? Or are the statistics affected differently somehow? Lastly, I am setting the highpass filter at 135; this is the total time f= or one cycle. Is this too high though? Thanks. ========================================================================= Date: Mon, 28 Jan 2008 14:36:11 -0600 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Jeffrey Spielberg <[log in to unmask]> Subject: Re: Fsl-vbm and First In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_10929_295653.1201552571975" ------=_Part_10929_295653.1201552571975 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, great, thanks. I have another question about Fsl-vbm/Randomise usage. Are there some designs that are appropriate for use in Feat but not in Randomise (in Fsl-vbm in particular)? Specifically, we want to use a one group design correlating two questionnaire scores with grey-matter. We set this up similarly to the example on the Feat webpage, for example, Group Mean Quest_1 Quest_2 1 1 2.6 9.4 1 1 7.3 5.7 1 1 4.9 4.3 1 1 4.6 3.6 1 1 9.2 8.6 with one cope for the mean, one for each questionnaire, and one for the difference between the two questionnaires. Is this design appropriate for Randomise/Fsl-vbm? Thanks, Jeff On Jan 26, 2008 1:21 AM, Steve Smith <[log in to unmask]> wrote: > Hi, > > On 24 Jan 2008, at 21:57, Jeff Spielberg wrote: > > > Hi, I have a couple of questions regarding Fsl-vbm and First. The > > scans we > > have been using for both have some signal loss superiorly and > > inferiorly. > > Due to this we do not get a good extraction with Bet (brain is > > excluded top > > and bottom). We have been dealing with this issue by correcting for > > the > > bias field with Fast and have gotten good results. Since Fsl-vbm > > applies > > Bet we have entered bias-corrected scans into our Vbm analyses. > > However, > > will this cause problems when segmentation is done in > > fslvbm_2_template (or > > anywhere else in Fsl-vbm)? > > The bias correction is fine, but if you have already run BET that > might compromise the FSL-VBM when you feed the already-betted image > into FSL-VBM. The simple solution is to apply the bias field > correction to the original image and feed that into FSL-VBM. That > should be fine then. > > > Also, is it best to use the bias-corrected scans in First as well? > > It seems > > possible that not correcting scan intensities for the bias field will > > interfere with the identification of structures (since First uses > > intensities in this process), thanks, > > If it looks like the bias field correction has improved the image then > it should be better to feed the corrected image into FIRST than the > original. > > Cheers, Steve. > > > > > > Jeff > > > > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > --------------------------------------------------------------------------- > ------=_Part_10929_295653.1201552571975 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, great, thanks.  I have another question about Fsl-vbm/Randomise usage.  Are there some designs that are appropriate for use in Feat but not in Randomise (in Fsl-vbm in particular)?  Specifically, we want to use a one group design correlating two questionnaire scores with grey-matter.  We set this up similarly to the example on the Feat webpage, for example,

Group    Mean    Quest_1    Quest_2
1           1          2.6            9.4
1           1          7.3            5.7
1           1          4.9            4.3
1           1          4.6            3.6
1           1          9.2            8.6

with one cope for the mean, one for each questionnaire, and one for the difference between the two questionnaires.  Is this design appropriate for Randomise/Fsl-vbm?  Thanks,
Jeff

On Jan 26, 2008 1:21 AM, Steve Smith <[log in to unmask]> wrote:
Hi,

On 24 Jan 2008, at 21:57, Jeff Spielberg wrote:

> Hi, I have a couple of questions regarding Fsl-vbm and First.  The
> scans we
> have been using for both have some signal loss superiorly and
> inferiorly.
> Due to this we do not get a good extraction with Bet (brain is
> excluded top
> and bottom).  We have been dealing with this issue by correcting for
> the
> bias field with Fast and have gotten good results.  Since Fsl-vbm
> applies
> Bet we have entered bias-corrected scans into our Vbm analyses.
> However,
> will this cause problems when segmentation is done in
> fslvbm_2_template (or
> anywhere else in Fsl-vbm)?

The bias correction is fine, but if you have already run BET that
might compromise the FSL-VBM when you feed the already-betted image
into FSL-VBM. The simple solution is to apply the bias field
correction to the original image and feed that into FSL-VBM. That
should be fine then.

> Also, is it best to use the bias-corrected scans in First as well?
> It seems
> possible that not correcting scan intensities for the bias field will
> interfere with the identification of structures (since First uses
> intensities in this process), thanks,

If it looks like the bias field correction has improved the image then
it should be better to feed the corrected image into FIRST than the
original.

Cheers, Steve.


>
> Jeff
>


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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------=_Part_10929_295653.1201552571975-- ========================================================================= Date: Mon, 28 Jan 2008 15:16:46 -0600 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Paul Geha <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear FSL users, I ran a TBSS t-test between 2 groups and found a significant FA difference between them. I would like to see where does it come from L1 or L2+L3/2? How do I do that? L1, L2, and L3 do I have to repeat Tbss for each alone i.e L1 and L2 and L3?? thanks Paul Geha M.D. Northwestern University The Feinberg School of Medicine Department of Physiology M211 303 E. Chicago Ave. Chicago, IL 60611 Tel:312-503 2886 Fax: 312-503-5101 ========================================================================= Date: Mon, 28 Jan 2008 16:53:33 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Chris Petty <[log in to unmask]> Subject: Re: fslstats MIME-Version: 1.0 Content-Type: text/plain Thanks, How/why will the volume measure with fslstats differ from the output of first_utils (.vol)? - assuming I'm using native reconstruction, and no boundary correction I can't seem to make these match, regardless of the options I've tried. Thanks, chris -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson Sent: Monday, January 28, 2008 12:33 PM To: [log in to unmask] Subject: Re: [FSL] fslstats Hi, There's no way just to do this with fslstats. However, with fslroi you can easily extract the single volume and then run fslstats on that. All the best, Mark Christopher Petty wrote: > is there an option with fslstats -V for grabbing only 1 volume of a 4D file? > > for instance if i know R-amyg is the 10th volume of my results from > run_first_all ... how can i only measure that volume? > > -chris > > ========================================================================= Date: Mon, 28 Jan 2008 18:05:14 -0700 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Dianne Patterson <[log in to unmask]> Subject: tbss_3_postreg produces empty images?? MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_11327_22883122.1201568714787" ------=_Part_11327_22883122.1201568714787 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello All, I apologize if I've simply overlooked the answer to my questions in the archives or the FAQ. I am working on an Intel Power Mac with 4 cores and 16 gb of ram. I'm running tiger, FSL 4.0.3 (updated last week from 4.0.1). I have plenty of space on my hard drive. ================================== I have been using the probtrack pipeline for several months now, and thought I would try the tbss pipeline. I have 14 subjects with identical acquisition parameters that were run through dtifit (that data all seems to be in good shape and has been used and examined pretty extensively). I've put their fa images in a separate TBSS_ERP directory and run tbss_1_preproc after making sure the range of values was roughly 0-1. tbss_2_reg seems to have run successfully (but I'm not sure how to assess this, as I'm not sure what files ought to be created). The following is what I found on my screen at the end of the tbss_2_reg run: [Data/dti_erp/TBSS_ERP] dpat% tbss_2_reg -T ecc3131_FA_FAi_to_target ecc3393_FA_FAi_to_target ecc3472_FA_FAi_to_target ecc3515_FA_FAi_to_target ecc3559_FA_FAi_to_target ecc3591_FA_FAi_to_target ecc3647_FA_FAi_to_target ecc3717_FA_FAi_to_target ecc3740_FA_FAi_to_target ecc3824_FA_FAi_to_target ecc3835_FA_FAi_to_target ecc3888_FA_FAi_to_target ecc3936_FA_FAi_to_target ecc3956_FA_FAi_to_target 14636 =================== So, I tried tbss_3_postreg -S This seems to produce the stats directory and files predicted: In the FAi directory, there are a couple of new image files for each subject: ecc3824_FA_FAi_to_target_nonlinear.nii.gz ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz I've checked several of them, and they contain stuff...so that seems good. However, only the MNI image in the stats directory appears to contain anything. The other images in the stats directory display as black and give me a mean of 0 when I run >fslstats image -M [dti_erp/TBSS_ERP/stats] dpat% ls -l total 21824 -rw-r--r-- 1 dpat admin 10917429 Jan 28 16:01 MNI152.nii.gz -rw-r--r-- 1 dpat admin 196651 Jan 28 16:04 all_FA.nii.gz -rw-r--r-- 1 dpat admin 14174 Jan 28 16:04 mean_FA.nii.gz -rw-r--r-- 1 dpat admin 7152 Jan 28 16:04 mean_FA_mask.nii.gz -rw-r--r-- 1 dpat admin 28207 Jan 28 16:05 mean_FA_skeleton.nii.gz BTW, it seemed to take only about 5 minutes for tbss_3_postreg to run. Thankyou for your time, Dianne ============================= For what it is worth, here are the files in the FAi directory: [dti_erp/TBSS_ERP/FAi] dpat% ls -l total 2059304 -rw-r--r-- 1 dpat admin 7 Jan 28 16:01 best.msf -rw-r--r-- 1 dpat admin 348 Jan 24 15:47 ecc3131_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:47 ecc3131_FA_FAi.img -rw-r--r-- 1 dpat admin 211 Jan 25 15:19 ecc3131_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18367 Jan 25 18:14 ecc3131_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 25 18:14 ecc3131_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 71360428 Jan 25 18:15 ecc3131_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2674985 Jan 28 16:02 ecc3131_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:47 ecc3393_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:47 ecc3393_FA_FAi.img -rw-r--r-- 1 dpat admin 208 Jan 25 18:24 ecc3393_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18364 Jan 25 21:15 ecc3393_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 25 21:16 ecc3393_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 71222937 Jan 25 21:17 ecc3393_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2722194 Jan 28 16:02 ecc3393_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3472_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3472_FA_FAi.img -rw-r--r-- 1 dpat admin 203 Jan 25 21:23 ecc3472_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18359 Jan 26 00:14 ecc3472_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 00:14 ecc3472_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 68257531 Jan 26 00:15 ecc3472_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2826240 Jan 28 16:02 ecc3472_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3515_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3515_FA_FAi.img -rw-r--r-- 1 dpat admin 194 Jan 26 00:19 ecc3515_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18350 Jan 26 03:11 ecc3515_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 03:12 ecc3515_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 69756191 Jan 26 03:13 ecc3515_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2746299 Jan 28 16:02 ecc3515_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3559_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3559_FA_FAi.img -rw-r--r-- 1 dpat admin 211 Jan 26 03:20 ecc3559_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18367 Jan 26 06:11 ecc3559_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 06:12 ecc3559_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 71794848 Jan 26 06:13 ecc3559_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2749851 Jan 28 16:02 ecc3559_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3591_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3591_FA_FAi.img -rw-r--r-- 1 dpat admin 214 Jan 26 06:21 ecc3591_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18370 Jan 26 09:12 ecc3591_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 09:13 ecc3591_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 70797764 Jan 26 09:13 ecc3591_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2718995 Jan 28 16:02 ecc3591_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3647_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3647_FA_FAi.img -rw-r--r-- 1 dpat admin 211 Jan 26 09:22 ecc3647_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18367 Jan 26 12:13 ecc3647_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 12:14 ecc3647_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 72127885 Jan 26 12:15 ecc3647_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2789331 Jan 28 16:02 ecc3647_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3717_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3717_FA_FAi.img -rw-r--r-- 1 dpat admin 211 Jan 26 12:22 ecc3717_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18367 Jan 26 15:14 ecc3717_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 15:15 ecc3717_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 61316401 Jan 26 15:16 ecc3717_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 14139 Jan 28 16:02 ecc3717_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3740_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3740_FA_FAi.img -rw-r--r-- 1 dpat admin 206 Jan 26 15:24 ecc3740_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18362 Jan 26 18:16 ecc3740_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 18:17 ecc3740_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 72341839 Jan 26 18:17 ecc3740_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2669134 Jan 28 16:02 ecc3740_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3824_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3824_FA_FAi.img -rw-r--r-- 1 dpat admin 196 Jan 26 18:26 ecc3824_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18352 Jan 26 21:17 ecc3824_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 26 21:18 ecc3824_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 67623887 Jan 26 21:19 ecc3824_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2714604 Jan 28 16:02 ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3835_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3835_FA_FAi.img -rw-r--r-- 1 dpat admin 198 Jan 26 21:25 ecc3835_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18354 Jan 27 00:17 ecc3835_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 27 00:18 ecc3835_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 68614776 Jan 27 00:18 ecc3835_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2670394 Jan 28 16:03 ecc3835_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3888_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3888_FA_FAi.img -rw-r--r-- 1 dpat admin 206 Jan 27 00:26 ecc3888_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18362 Jan 27 03:18 ecc3888_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 27 03:19 ecc3888_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 70673036 Jan 27 03:19 ecc3888_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2687060 Jan 28 16:03 ecc3888_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 ecc3936_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 ecc3936_FA_FAi.img -rw-r--r-- 1 dpat admin 215 Jan 27 03:27 ecc3936_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18371 Jan 27 06:18 ecc3936_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 27 06:18 ecc3936_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 72270981 Jan 27 06:19 ecc3936_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2977842 Jan 28 16:03 ecc3936_FA_FAi_to_target_nonlinear_hr.nii.gz -rw-r--r-- 1 dpat admin 348 Jan 24 15:49 ecc3956_FA_FAi.hdr -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:49 ecc3956_FA_FAi.img -rw-r--r-- 1 dpat admin 210 Jan 27 06:26 ecc3956_FA_FAi_to_target_affine.dof -rw-r--r-- 1 dpat admin 18366 Jan 27 09:18 ecc3956_FA_FAi_to_target_nonlinear.dof -rw-r--r-- 1 dpat admin 21 Jan 27 09:18 ecc3956_FA_FAi_to_target_nonlinear.msf -rw-r--r-- 1 dpat admin 70852363 Jan 27 09:19 ecc3956_FA_FAi_to_target_nonlinear.nii.gz -rw-r--r-- 1 dpat admin 2624975 Jan 28 16:03 ecc3956_FA_FAi_to_target_nonlinear_hr.nii.gz drwxr-xr-x 26 dpat admin 884 Jan 24 15:49 slicesdir -rw-r--r-- 1 dpat admin 348 Jan 25 15:14 target.hdr -rw-r--r-- 1 dpat admin 14442064 Jan 25 15:14 target.img -rw-r--r-- 1 dpat admin 0 Jan 24 15:52 tbss_2_reg.e13383.1 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.10 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.11 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.12 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.13 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.14 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.2 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.3 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.4 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.5 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.6 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.7 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.8 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.e13383.9 -rw-r--r-- 1 dpat admin 0 Jan 24 15:53 tbss_2_reg.e13804 -rw-r--r-- 1 dpat admin 0 Jan 25 15:14 tbss_2_reg.e14636.1 -rw-r--r-- 1 dpat admin 0 Jan 26 18:17 tbss_2_reg.e14636.10 -rw-r--r-- 1 dpat admin 0 Jan 26 21:19 tbss_2_reg.e14636.11 -rw-r--r-- 1 dpat admin 0 Jan 27 00:18 tbss_2_reg.e14636.12 -rw-r--r-- 1 dpat admin 0 Jan 27 03:19 tbss_2_reg.e14636.13 -rw-r--r-- 1 dpat admin 0 Jan 27 06:19 tbss_2_reg.e14636.14 -rw-r--r-- 1 dpat admin 0 Jan 25 18:15 tbss_2_reg.e14636.2 -rw-r--r-- 1 dpat admin 0 Jan 25 21:17 tbss_2_reg.e14636.3 -rw-r--r-- 1 dpat admin 0 Jan 26 00:15 tbss_2_reg.e14636.4 -rw-r--r-- 1 dpat admin 0 Jan 26 03:13 tbss_2_reg.e14636.5 -rw-r--r-- 1 dpat admin 0 Jan 26 06:13 tbss_2_reg.e14636.6 -rw-r--r-- 1 dpat admin 0 Jan 26 09:13 tbss_2_reg.e14636.7 -rw-r--r-- 1 dpat admin 337 Jan 26 15:15 tbss_2_reg.e14636.8 -rw-r--r-- 1 dpat admin 0 Jan 26 15:16 tbss_2_reg.e14636.9 -rw-r--r-- 1 dpat admin 20186 Jan 24 18:51 tbss_2_reg.o13383.1 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.10 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.11 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.12 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.13 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.14 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.2 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.3 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.4 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.5 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.6 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.7 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.8 -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 tbss_2_reg.o13383.9 -rw-r--r-- 1 dpat admin 0 Jan 24 15:53 tbss_2_reg.o13804 -rw-r--r-- 1 dpat admin 20186 Jan 25 18:14 tbss_2_reg.o14636.1 -rw-r--r-- 1 dpat admin 18915 Jan 26 21:18 tbss_2_reg.o14636.10 -rw-r--r-- 1 dpat admin 18263 Jan 27 00:17 tbss_2_reg.o14636.11 -rw-r--r-- 1 dpat admin 19090 Jan 27 03:19 tbss_2_reg.o14636.12 -rw-r--r-- 1 dpat admin 19256 Jan 27 06:18 tbss_2_reg.o14636.13 -rw-r--r-- 1 dpat admin 20077 Jan 27 09:18 tbss_2_reg.o14636.14 -rw-r--r-- 1 dpat admin 21212 Jan 25 21:16 tbss_2_reg.o14636.2 -rw-r--r-- 1 dpat admin 21080 Jan 26 00:14 tbss_2_reg.o14636.3 -rw-r--r-- 1 dpat admin 15853 Jan 26 03:11 tbss_2_reg.o14636.4 -rw-r--r-- 1 dpat admin 20175 Jan 26 06:12 tbss_2_reg.o14636.5 -rw-r--r-- 1 dpat admin 18050 Jan 26 09:12 tbss_2_reg.o14636.6 -rw-r--r-- 1 dpat admin 20453 Jan 26 12:14 tbss_2_reg.o14636.7 -rw-r--r-- 1 dpat admin 18650 Jan 26 15:15 tbss_2_reg.o14636.8 -rw-r--r-- 1 dpat admin 20916 Jan 26 18:17 tbss_2_reg.o14636.9 -- Dianne Patterson, Ph.D. [log in to unmask] ERP Lab University of Arizona 621-3256 (Office) ------=_Part_11327_22883122.1201568714787 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello All,

I apologize if I've simply overlooked the answer to my questions in the archives or the FAQ.

I am working on an Intel Power Mac with 4 cores and 16 gb of ram.  I'm running tiger, FSL 4.0.3 (updated last week from 4.0.1).
I have plenty of space on my hard drive.
==================================
I have been using the probtrack pipeline for several months now, and thought I would try the tbss pipeline.
I have 14 subjects with identical acquisition parameters that were run through dtifit (that data all seems to be in good shape and has been used and examined pretty extensively).
I've put their fa images in a separate TBSS_ERP directory and run tbss_1_preproc after making sure the range of values was roughly 0-1.

tbss_2_reg seems to have run successfully (but I'm not sure how to assess this, as I'm not sure what files ought to be created).

The following is what I found on my screen at the end of the tbss_2_reg run:
[Data/dti_erp/TBSS_ERP] dpat% tbss_2_reg -T
ecc3131_FA_FAi_to_target
ecc3393_FA_FAi_to_target
ecc3472_FA_FAi_to_target
ecc3515_FA_FAi_to_target
ecc3559_FA_FAi_to_target
ecc3591_FA_FAi_to_target
ecc3647_FA_FAi_to_target
ecc3717_FA_FAi_to_target
ecc3740_FA_FAi_to_target
ecc3824_FA_FAi_to_target
ecc3835_FA_FAi_to_target
ecc3888_FA_FAi_to_target
ecc3936_FA_FAi_to_target
ecc3956_FA_FAi_to_target
14636
===================
So, I tried tbss_3_postreg -S
This seems to produce the stats directory and files predicted:
In the FAi directory, there are a couple of new image files for each subject:
ecc3824_FA_FAi_to_target_nonlinear.nii.gz
ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz

I've checked several of them, and they contain stuff...so that seems good.
However, only the MNI image in the stats directory appears to contain anything.
The other images in the stats directory display as black and give me a mean of 0
when I run
>fslstats image -M

[dti_erp/TBSS_ERP/stats] dpat% ls -l
total 21824
-rw-r--r--   1 dpat  admin  10917429 Jan 28 16:01 MNI152.nii.gz
-rw-r--r--   1 dpat  admin    196651 Jan 28 16:04 all_FA.nii.gz
-rw-r--r--   1 dpat  admin     14174 Jan 28 16:04 mean_FA.nii.gz
-rw-r--r--   1 dpat  admin      7152 Jan 28 16:04 mean_FA_mask.nii.gz
-rw-r--r--   1 dpat  admin     28207 Jan 28 16:05 mean_FA_skeleton.nii.gz

BTW, it seemed to take only about 5 minutes for tbss_3_postreg to run.

Thankyou for your time,

Dianne
=============================
For what it is worth, here are the files in the FAi directory:

[dti_erp/TBSS_ERP/FAi] dpat% ls -l
total 2059304
-rw-r--r--    1 dpat  admin         7 Jan 28 16:01 best.msf
-rw-r--r--    1 dpat  admin       348 Jan 24 15:47 ecc3131_FA_FAi.hdr
-rw-r--r--    1 dpat  admin   1746360 Jan 24 15:47 ecc3131_FA_FAi.img
-rw-r--r--    1 dpat  admin       211 Jan 25 15:19 ecc3131_FA_FAi_to_target_affine.dof
-rw-r--r--    1 dpat  admin     18367 Jan 25 18:14 ecc3131_FA_FAi_to_target_nonlinear.dof
-rw-r--r--    1 dpat  admin        21 Jan 25 18:14 ecc3131_FA_FAi_to_target_nonlinear.msf
-rw-r--r--    1 dpat  admin  71360428 Jan 25 18:15 ecc3131_FA_FAi_to_target_nonlinear.nii.gz
-rw-r--r--    1 dpat  admin   2674985 Jan 28 16:02 ecc3131_FA_FAi_to_target_nonlinear_hr.nii.gz
-rw-r--r--    1 dpat  admin       348 Jan 24 15:47 ecc3393_FA_FAi.hdr
-rw-r--r--    1 dpat  admin   1746360 Jan 24 15:47 ecc3393_FA_FAi.img
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--
Dianne Patterson, Ph.D.
[log in to unmask]
ERP Lab
University of Arizona
621-3256 (Office) ------=_Part_11327_22883122.1201568714787-- ========================================================================= Date: Tue, 29 Jan 2008 01:37:26 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Brittany Copp <[log in to unmask]> Subject: easythresh output Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Hey group, I was hoping someone would be willing to tell me exactly what each of the= outputs from easythresh (with both a stat threshold and a significance le= vel specified) means. I am getting cluster_root, thresh_root, and rendered_r= oot files. Thanks! Brittany ========================================================================= Date: Mon, 28 Jan 2008 17:52:44 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephane Jacobs <[log in to unmask]> Subject: Re: easythresh output In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Brittany, The "cluster_root" image is a mask of your significant clusters, which containing cluster indexes (ordered by size I think) rather than z values. "thresh_root" is the thresholded zstat map produced by the thresholds (Z threshold and cluster-extent significance threshold p) your chose. "rendered_root" is the same zstat map, only overlayed on the background image you specified. Best Stephane Brittany Copp wrote: > Hey group, > > I was hoping someone would be willing to tell me exactly what each of the > outputs from easythresh (with both a stat threshold and a significance level > specified) means. I am getting cluster_root, thresh_root, and rendered_root > files. Thanks! > > Brittany > > > ========================================================================= Date: Mon, 28 Jan 2008 18:00:40 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephane Jacobs <[log in to unmask]> Subject: Re: featquery on a second level analysis In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Steve, Steve Smith wrote: >> My question was: is this correct in this case to go back to the first >> level design.con file, and selectively average the ppheight value for >> each contrast separately, and have featquery use those instead? > > I think what FEAT/Featquery are doing should be right - it should be > averaging the effective ppheight across all the relevant first-level > contrasts, and as far as I can see this should be correct. > > Cheers, Steve. > I'm probably missing something here. I did not check into details for FEAT, but I have looked into the Featquery script, and here is what I understood: when calculating the scaling factor, it determines whether it's a first or higher level analysis just by looking whether a design.lcon file exists within the feat directory. If not (first level), it uses the ppheight from the design.con file, which specifies a ppheight value for each EV. If it does find design.lcon (higher level), however, then it uses the single value contained in this file to scale all the copes contained in the feat directory - which, in my case, come from different 1st level copes. If this is right, then I don't see how this ppheight is related only to the relevant 1st level contrasts... Could you tell me where I'm getting lost here? Thanks again Best Stephane > >> Thanks again for your time! >> >> Stephane >> >> >> >> Steve Smith wrote: >>> Hi, >>> >>> Yes, this should work fine; FEAT should extract the correct ppheight >>> values from the correct contrast specification files, according to the >>> copes that you have selected. It should appropriately estimate the >>> right average ppheight for each of your second-level contrasts. >>> >>> Cheers, Steve. >>> >>> >>> >>> On 15 Jan 2008, at 19:39, Stephane Jacobs wrote: >>> >>>> Hello, >>>> >>>> I had a question about the way the model peak-to-peak height was >>>> computed for a second level analysis of which input were cope images >>>> rather than feat directories, and about running featquery on it. I had >>>> forgotten to mention that I am interested in percent signal change for >>>> contrasts (condition vs. modeled rest), which explains why I'm looking >>>> at the ppheight values in design.lcon. Also, I'm looking at contrasts >>>> that have been set at the first level already, then I have ppheight >>>> values for each of those and for each first level run. >>>> >>>> Can anybody tell me whether I'm doing the right thing here? >>>> >>>> Thanks a lot, >>>> >>>> Stephane >>>> >>>> >>>> Stephane Jacobs wrote: >>>>> Hello, >>>>> >>>>> I would like to run featquery on a second level analysis (cross >>>>> session - >>>>> within subject level) to compute percent change of COPEs within a >>>>> given ROI. >>>>> I understand that featquery is using the average ppheight found in >>>>> the >>>>> design.lcon file in the copeX.feat directory as a scale factor to >>>>> compute >>>>> percent change. >>>>> However, I am wondering whether this is still correct to do so in my >>>>> case. >>>>> Indeed, I have fed cope images into my second level analysis, >>>>> instead of >>>>> .feat directories, as I needed to contrast EVs coming from different >>>>> runs. >>>>> Then, I end up with one single cope1.feat directory at the output >>>>> of my >>>>> second level analysis, which contains as many cope images as I >>>>> have set >>>>> contrasts at the 2nd level (4), rather than getting >>>>> cope1.feat..cope4.feat >>>>> as when you feed feat directories containing all the same EVs. >>>>> >>>>> Therefore, it seems that the value contained in design.lcon is the >>>>> average >>>>> of the ppheight across all my contrasts. I wonder if I rather should >>>>> compute >>>>> an average ppheight for each of my 2nd level contrast separately, to >>>>> be more >>>>> accurate? >>>>> >>>>> Thanks in advance for all your thoughts and advice, >>>>> >>>>> Best, >>>>> >>>>> Stephane >>>>> >>>>> >>>>> >>>> >>> >>> >>> --------------------------------------------------------------------------- >>> >>> >>> Stephen M. Smith, Professor of Biomedical Engineering >>> Associate Director, Oxford University FMRIB Centre >>> >>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>> +44 (0) 1865 222726 (fax 222717) >>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>> --------------------------------------------------------------------------- >>> >>> >>> >>> >> > > > --------------------------------------------------------------------------- > > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > > > ========================================================================= Date: Tue, 29 Jan 2008 08:01:33 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Juergen Haenggi <[log in to unmask]> Subject: Tbss_2_reg on a cluster Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear FSL experts We intent to run tbss_2_reg on a grid computer. Are there any examples how to edit $FSLDIR/bin/fsl_sub and to set up the SGE commands to submit jobs to the cluster? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [log in to unmask] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- ========================================================================= Date: Tue, 29 Jan 2008 16:04:13 +0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Li Jiang <[log in to unmask]> Subject: Re: about flirt In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, It is an average over an ROI. First I genarate a ROI mask on the subject image. Then apply the subject to MNI transformation matrix (.mat) to the ROI-to-MNI volume.Then measure the intensity of ROI on the subject image and that of ROI-to-MNI on the subject-to-MNI image with Matlab. Thanks. Li 2008/1/28, Mark Jenkinson <[log in to unmask]>: > Hi, > > This still doesn't answer the important question: > > *HOW* are you measuring these intensities? > > Is it an average over an ROI? > Is it from a single voxel? > > If it is a single voxel, is it a peak value surrounded by > much smaller (even negative) values? > > If it is an ROI, how are you generating the ROIs and > creating the average? > > All the best, > Mark > > > On 27 Jan 2008, at 05:11, Li Jiang wrote: > > > Hi, > > > > For example, with the methods I mentioned above, for one subject,the > > intensity of the subjects data is 52.4554, but that of the subjects > > data in MNI-space is only 36.1254. For another subject, the intensity > > is 46.7794 and 43.8556, which is similar. I don't know how to explain > > the different.I know that interpolation will affect a little. Compare > > trilinear and nearest neighbour, which is better? > > > > Thank you! > > > > Li > > > > 2008/1/26, Mark Jenkinson <[log in to unmask]>: > >> Hi, > >> > >> Those commands are fine for flirt. > >> But how are you judging that the intensity is decreased? > >> > >> Could it be due to including slightly different voxels on the > >> edge of your ROI mask? When you transform a binary > >> mask you need to rethreshold it afterwards to decide > >> whether to be inclusive of small partial volume overlap > >> (of the mask and the new voxels) or exclusive. > >> This could be the source of changes in average intensity > >> over the ROI. In addition, trilinear interpolation will do > >> some smoothing of the image a little - which affects sharp > >> peaks particularly. > >> > >> All the best, > >> Mark > >> > >> > >> On 25 Jan 2008, at 17:24, Li Jiang wrote: > >> > >>> Hi, > >>> > >>> That's what I have done. > >>> > >>> * get the transformation matrix file (*.mat) that transforms > >>> subject-space CBF > >>> volume to MNI-space > >>> * get ROI volume in subject-space > >>> * transform ROI volume into MNI-space using the same *.mat file > >>> * use flirt: > >>> > >>> flirt -in -ref -out -applyxfm > >>> -init > >>> > >>> Thanks. > >>> > >>> Li > >>> > >>> 2008/1/25, Steve Smith <[log in to unmask]>: > >>>> Hi, > >>>> > >>>> I'm still not sure you have a problem. How are you judging that the > >>>> intensity is decreased? > >>>> > >>>> Cheers. > >>>> > >>>> > >>>> On 22 Jan 2008, at 06:28, Li Jiang wrote: > >>>> > >>>>> Hi, > >>>>> > >>>>> Thank you very much. I still have a question. The original subject > >>>>> image is epi sequence.After I transform this image to highres T1 > >>>>> image > >>>>> and then to MNI-space, the intensity of the transformed sub2mni > >>>>> image > >>>>> decreased compare to the original epi image. When transform, I use > >>>>> trilinear interpolation and cost function is correlation ratio. > >>>>> How > >>>>> can I improve this problem? Which interpolation method and cost > >>>>> function should I apply? > >>>>> > >>>>> Li > >>>>> > >>>>> 2008/1/21, Steve Smith <[log in to unmask]>: > >>>>>> Hi, > >>>>>> > >>>>>> avscale gives you a whole set of different pieces of information > >>>>>> about > >>>>>> the spatial affine transform, including the average scaling > >>>>>> (size) > >>>>>> change. It does not tell you anything about intensities. On > >>>>>> average, > >>>>>> in general, intensities don't change upon resampling, though of > >>>>>> course > >>>>>> any given voxel will change! > >>>>>> > >>>>>> Cheers. > >>>>>> > >>>>>> > >>>>>> On 19 Jan 2008, at 15:12, Li Jiang wrote: > >>>>>> > >>>>>>> Dear Steve Smith, > >>>>>>> > >>>>>>> I use fsl to process the functional MR data. It is a great > >>>>>>> software. > >>>>>>> To process the data, I first transform the EPI (subject image) > >>>>>>> data > >>>>>>> to T1 volume then to MNI_space with affine transformation. And > >>>>>>> I'll > >>>>>>> measure the absolute value from the images have been > >>>>>>> coregistered to > >>>>>>> MNI-space . I learned from the lectures and noticed the avscale > >>>>>>> for > >>>>>>> Inter-subject Registration. I wonder what's the scale mean. > >>>>>>> If the > >>>>>>> signal intensity of the subject image will change after affine > >>>>>>> transformation or global intra-subject transformation. > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> Best regards. > >>>>>>> > >>>>>>> Li Jiang > >>>>>>> > >>>>>> > >>>>>> > >>>>>> ----------------------------------------------------------------- > >>>>>> -- > >>>>>> -------- > >>>>>> Stephen M. Smith, Professor of Biomedical Engineering > >>>>>> Associate Director, Oxford University FMRIB Centre > >>>>>> > >>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > >>>>>> +44 (0) 1865 222726 (fax 222717) > >>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > >>>>>> ----------------------------------------------------------------- > >>>>>> -- > >>>>>> -------- > >>>>>> > >>>>> > >>>> > >>>> > >>>> ------------------------------------------------------------------- > >>>> -- > >>>> ------ > >>>> Stephen M. Smith, Professor of Biomedical Engineering > >>>> Associate Director, Oxford University FMRIB Centre > >>>> > >>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > >>>> +44 (0) 1865 222726 (fax 222717) > >>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > >>>> ------------------------------------------------------------------- > >>>> -- > >>>> ------ > >>>> > >>> > >> > > > ========================================================================= Date: Tue, 29 Jan 2008 08:40:29 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Nicholas P Holmes <[log in to unmask]> Subject: 2nd level fixed effects won't run (on latest ubuntu gutsy: 4.0.3-1) Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1252" Hi all (but this may be one for Michale Hanke), for some reason, my higher-level across-session fixed effects analysis=20= won't work: rather than taking the usual 10 minutes, it takes FOREVER and seems to ru= n=20 the FLAME 1+2 instead (i re-ran previous analyses which all worked fine=20= until now) during the last fsl release update (4.0.3-1), the feat.tcl file was=20 overwritten while feat was open and I now have a feat.tcl.dkpg-old file a= s=20 well - could this have caused a problem (is it defaulting to run FLAME=20= 1+2) or is something else to blame? thanks for any input, nick ========================================================================= Date: Tue, 29 Jan 2008 09:13:05 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Mark Woolrich <[log in to unmask]> Subject: Re: 2nd level fixed effects won't run (on latest ubuntu gutsy: 4.0.3-1) In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-93--47513851 --Apple-Mail-93--47513851 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi nick, Take a look in the log file and find the flame call. It should have a --fe or a --fixed option if it is doing fixed effects. Cheers, Mark. ---- Dr Mark Woolrich EPSRC Advanced Research Fellow University Research Lecturer Oxford University Centre for Functional MRI of the Brain (FMRIB), John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich On 29 Jan 2008, at 08:40, Nicholas P Holmes wrote: > Hi all (but this may be one for Michale Hanke), > > for some reason, my higher-level across-session fixed effects analysis > won't work: > > rather than taking the usual 10 minutes, it takes FOREVER and seems > to run > the FLAME 1+2 instead (i re-ran previous analyses which all worked > fine > until now) > > during the last fsl release update (4.0.3-1), the feat.tcl file was > overwritten while feat was open and I now have a feat.tcl.dkpg-old > file as > well - could this have caused a problem (is it defaulting to run FLAME > 1+2) or is something else to blame? > > thanks for any input, > nick > --Apple-Mail-93--47513851 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi nick,

Take a = look in the log file and find the flame call. It should have a --fe or a = --fixed option if it is doing fixed effects.

Cheers, = Mark.

=
----
Dr Mark = Woolrich
EPSRC Advanced = Research Fellow=A0University Research Lecturer

Oxford = University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, = UK.

Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~wo= olrich



=

On 29 Jan 2008, at 08:40, Nicholas P Holmes = wrote:

Hi all (but this may be one for = Michale Hanke),

for some reason, my higher-level across-session = fixed effects analysis=A0
won't = work:

rather than taking the usual 10 minutes, it takes = FOREVER and seems to run=A0
the = FLAME 1+2 instead (i re-ran previous analyses which all worked fine=A0
until = now)

during the last fsl release update (4.0.3-1), the = feat.tcl file was=A0
overwritten while feat was open and I now have a = feat.tcl.dkpg-old file as=A0
well - = could this have caused a problem (is it defaulting to run FLAME=A0
1+2) or = is something else to blame?

thanks for any input,
nick


= --Apple-Mail-93--47513851-- ========================================================================= Date: Tue, 29 Jan 2008 10:44:56 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?iso-8859-1?q?Gwena=EBlle=20DOUAUD?= <[log in to unmask]> Subject: RE : [FSL] In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Paul, you can either run separately L1, L2 and L3 or consider L1 and the mean of L2 and L3. Then, all you need to do is to create a separate directory for each type of image (so, say, Lparralel and Lperpendicular) and make sure that the images in their corresponding directory are named *exactly* the same as the original FA images are (please see the manual: http://www.fmrib.ox.ac.uk/fsl/tbss/index.html, section "Using non-FA Images in TBSS"). Hope this helps, Gwenaelle --- Paul Geha <[log in to unmask]> a =E9crit : > Dear FSL users, >=20 >=20 > I ran a TBSS t-test between 2 groups and found a > significant FA difference > between them. I would like to see where does it > come from L1 or L2+L3/2? > How do I do that? L1, L2, and L3 do I have to > repeat Tbss for each alone > i.e L1 and L2 and L3?? > thanks >=20 > Paul Geha M.D. > Northwestern University > The Feinberg School of Medicine > Department of Physiology M211 > 303 E. Chicago Ave. > Chicago, IL 60611 > Tel:312-503 2886 > Fax: 312-503-5101 >=20 ___________________________________________________________________= __________=20 Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! M= ail http://mail.yahoo.fr ========================================================================= Date: Tue, 29 Jan 2008 11:00:15 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?iso-8859-1?q?Gwena=EBlle=20DOUAUD?= <[log in to unmask]> Subject: RE : [FSL] tbss_3_postreg produces empty images?? In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Dianne, it seems that at least a part of tbss_3_postreg has run properly. It should be quick indeed as it only applies the non-linear transformations (that you can see in the 4D images *_to_target_nonlinear.nii.gz) calculated at the tbss_2 stage to the corresponding images (*_to_target_nonlinear_hr.nii.gz). Then, it concatenates all the *_hr.nii.gz images in the big 4D file called all_FA.nii.gz. If this one is really empty, this is where the process failed. Have you got any error message running tbss_3? Maybe try running it again to see if the problem remains, and if this is the case, I'll give you the few command lines that will allow you to finish the tbss_3 stage and continue to the tbss_4 one. Hope this helps, Gwenaelle --- Dianne Patterson <[log in to unmask]> a =E9crit : > Hello All, >=20 > I apologize if I've simply overlooked the answer to > my questions in the > archives or the FAQ. >=20 > I am working on an Intel Power Mac with 4 cores and > 16 gb of ram. I'm > running tiger, FSL 4.0.3 (updated last week from > 4.0.1). > I have plenty of space on my hard drive. > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > I have been using the probtrack pipeline for several > months now, and thought > I would try the tbss pipeline. > I have 14 subjects with identical acquisition > parameters that were run > through dtifit (that data all seems to be in good > shape and has been used > and examined pretty extensively). > I've put their fa images in a separate TBSS_ERP > directory and run > tbss_1_preproc after making sure the range of values > was roughly 0-1. >=20 > tbss_2_reg seems to have run successfully (but I'm > not sure how to assess > this, as I'm not sure what files ought to be > created). >=20 > The following is what I found on my screen at the > end of the tbss_2_reg run: > [Data/dti_erp/TBSS_ERP] dpat% tbss_2_reg -T > ecc3131_FA_FAi_to_target > ecc3393_FA_FAi_to_target > ecc3472_FA_FAi_to_target > ecc3515_FA_FAi_to_target > ecc3559_FA_FAi_to_target > ecc3591_FA_FAi_to_target > ecc3647_FA_FAi_to_target > ecc3717_FA_FAi_to_target > ecc3740_FA_FAi_to_target > ecc3824_FA_FAi_to_target > ecc3835_FA_FAi_to_target > ecc3888_FA_FAi_to_target > ecc3936_FA_FAi_to_target > ecc3956_FA_FAi_to_target > 14636 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > So, I tried tbss_3_postreg -S > This seems to produce the stats directory and files > predicted: > In the FAi directory, there are a couple of new > image files for each > subject: > ecc3824_FA_FAi_to_target_nonlinear.nii.gz > ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz >=20 > I've checked several of them, and they contain > stuff...so that seems good. > However, only the MNI image in the stats directory > appears to contain > anything. > The other images in the stats directory display as > black and give me a mean > of 0 > when I run > >fslstats image -M >=20 > [dti_erp/TBSS_ERP/stats] dpat% ls -l > total 21824 > -rw-r--r-- 1 dpat admin 10917429 Jan 28 16:01 > MNI152.nii.gz > -rw-r--r-- 1 dpat admin 196651 Jan 28 16:04 > all_FA.nii.gz > -rw-r--r-- 1 dpat admin 14174 Jan 28 16:04 > mean_FA.nii.gz > -rw-r--r-- 1 dpat admin 7152 Jan 28 16:04 > mean_FA_mask.nii.gz > -rw-r--r-- 1 dpat admin 28207 Jan 28 16:05 > mean_FA_skeleton.nii.gz >=20 > BTW, it seemed to take only about 5 minutes for > tbss_3_postreg to run. >=20 > Thankyou for your time, >=20 > Dianne > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D > For what it is worth, here are the files in the FAi > directory: >=20 > [dti_erp/TBSS_ERP/FAi] dpat% ls -l > total 2059304 > -rw-r--r-- 1 dpat admin 7 Jan 28 16:01 > best.msf > -rw-r--r-- 1 dpat admin 348 Jan 24 15:47 > ecc3131_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:47 > ecc3131_FA_FAi.img > -rw-r--r-- 1 dpat admin 211 Jan 25 15:19 > ecc3131_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18367 Jan 25 18:14 > ecc3131_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 25 18:14 > ecc3131_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 71360428 Jan 25 18:15 > ecc3131_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2674985 Jan 28 16:02 > ecc3131_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:47 > ecc3393_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:47 > ecc3393_FA_FAi.img > -rw-r--r-- 1 dpat admin 208 Jan 25 18:24 > ecc3393_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18364 Jan 25 21:15 > ecc3393_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 25 21:16 > ecc3393_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 71222937 Jan 25 21:17 > ecc3393_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2722194 Jan 28 16:02 > ecc3393_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3472_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3472_FA_FAi.img > -rw-r--r-- 1 dpat admin 203 Jan 25 21:23 > ecc3472_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18359 Jan 26 00:14 > ecc3472_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 00:14 > ecc3472_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 68257531 Jan 26 00:15 > ecc3472_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2826240 Jan 28 16:02 > ecc3472_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3515_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3515_FA_FAi.img > -rw-r--r-- 1 dpat admin 194 Jan 26 00:19 > ecc3515_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18350 Jan 26 03:11 > ecc3515_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 03:12 > ecc3515_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 69756191 Jan 26 03:13 > ecc3515_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2746299 Jan 28 16:02 > ecc3515_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3559_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3559_FA_FAi.img > -rw-r--r-- 1 dpat admin 211 Jan 26 03:20 > ecc3559_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18367 Jan 26 06:11 > ecc3559_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 06:12 > ecc3559_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 71794848 Jan 26 06:13 > ecc3559_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2749851 Jan 28 16:02 > ecc3559_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3591_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3591_FA_FAi.img > -rw-r--r-- 1 dpat admin 214 Jan 26 06:21 > ecc3591_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18370 Jan 26 09:12 > ecc3591_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 09:13 > ecc3591_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 70797764 Jan 26 09:13 > ecc3591_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2718995 Jan 28 16:02 > ecc3591_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3647_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3647_FA_FAi.img > -rw-r--r-- 1 dpat admin 211 Jan 26 09:22 > ecc3647_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18367 Jan 26 12:13 > ecc3647_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 12:14 > ecc3647_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 72127885 Jan 26 12:15 > ecc3647_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2789331 Jan 28 16:02 > ecc3647_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3717_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3717_FA_FAi.img > -rw-r--r-- 1 dpat admin 211 Jan 26 12:22 > ecc3717_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18367 Jan 26 15:14 > ecc3717_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 15:15 > ecc3717_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 61316401 Jan 26 15:16 > ecc3717_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 14139 Jan 28 16:02 > ecc3717_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3740_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3740_FA_FAi.img > -rw-r--r-- 1 dpat admin 206 Jan 26 15:24 > ecc3740_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18362 Jan 26 18:16 > ecc3740_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 18:17 > ecc3740_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 72341839 Jan 26 18:17 > ecc3740_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2669134 Jan 28 16:02 > ecc3740_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3824_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3824_FA_FAi.img > -rw-r--r-- 1 dpat admin 196 Jan 26 18:26 > ecc3824_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18352 Jan 26 21:17 > ecc3824_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 26 21:18 > ecc3824_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 67623887 Jan 26 21:19 > ecc3824_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2714604 Jan 28 16:02 > ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3835_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3835_FA_FAi.img > -rw-r--r-- 1 dpat admin 198 Jan 26 21:25 > ecc3835_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18354 Jan 27 00:17 > ecc3835_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 27 00:18 > ecc3835_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 68614776 Jan 27 00:18 > ecc3835_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2670394 Jan 28 16:03 > ecc3835_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3888_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3888_FA_FAi.img > -rw-r--r-- 1 dpat admin 206 Jan 27 00:26 > ecc3888_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18362 Jan 27 03:18 > ecc3888_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 27 03:19 > ecc3888_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 70673036 Jan 27 03:19 > ecc3888_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2687060 Jan 28 16:03 > ecc3888_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > ecc3936_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > ecc3936_FA_FAi.img > -rw-r--r-- 1 dpat admin 215 Jan 27 03:27 > ecc3936_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18371 Jan 27 06:18 > ecc3936_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 27 06:18 > ecc3936_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 72270981 Jan 27 06:19 > ecc3936_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2977842 Jan 28 16:03 > ecc3936_FA_FAi_to_target_nonlinear_hr.nii.gz > -rw-r--r-- 1 dpat admin 348 Jan 24 15:49 > ecc3956_FA_FAi.hdr > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:49 > ecc3956_FA_FAi.img > -rw-r--r-- 1 dpat admin 210 Jan 27 06:26 > ecc3956_FA_FAi_to_target_affine.dof > -rw-r--r-- 1 dpat admin 18366 Jan 27 09:18 > ecc3956_FA_FAi_to_target_nonlinear.dof > -rw-r--r-- 1 dpat admin 21 Jan 27 09:18 > ecc3956_FA_FAi_to_target_nonlinear.msf > -rw-r--r-- 1 dpat admin 70852363 Jan 27 09:19 > ecc3956_FA_FAi_to_target_nonlinear.nii.gz > -rw-r--r-- 1 dpat admin 2624975 Jan 28 16:03 > ecc3956_FA_FAi_to_target_nonlinear_hr.nii.gz > drwxr-xr-x 26 dpat admin 884 Jan 24 15:49 > slicesdir > -rw-r--r-- 1 dpat admin 348 Jan 25 15:14 > target.hdr > -rw-r--r-- 1 dpat admin 14442064 Jan 25 15:14 > target.img > -rw-r--r-- 1 dpat admin 0 Jan 24 15:52 > tbss_2_reg.e13383.1 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.10 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.11 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.12 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.13 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.14 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.2 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.3 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.4 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.5 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.6 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.7 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.8 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.e13383.9 > -rw-r--r-- 1 dpat admin 0 Jan 24 15:53 > tbss_2_reg.e13804 > -rw-r--r-- 1 dpat admin 0 Jan 25 15:14 > tbss_2_reg.e14636.1 > -rw-r--r-- 1 dpat admin 0 Jan 26 18:17 > tbss_2_reg.e14636.10 > -rw-r--r-- 1 dpat admin 0 Jan 26 21:19 > tbss_2_reg.e14636.11 > -rw-r--r-- 1 dpat admin 0 Jan 27 00:18 > tbss_2_reg.e14636.12 > -rw-r--r-- 1 dpat admin 0 Jan 27 03:19 > tbss_2_reg.e14636.13 > -rw-r--r-- 1 dpat admin 0 Jan 27 06:19 > tbss_2_reg.e14636.14 > -rw-r--r-- 1 dpat admin 0 Jan 25 18:15 > tbss_2_reg.e14636.2 > -rw-r--r-- 1 dpat admin 0 Jan 25 21:17 > tbss_2_reg.e14636.3 > -rw-r--r-- 1 dpat admin 0 Jan 26 00:15 > tbss_2_reg.e14636.4 > -rw-r--r-- 1 dpat admin 0 Jan 26 03:13 > tbss_2_reg.e14636.5 > -rw-r--r-- 1 dpat admin 0 Jan 26 06:13 > tbss_2_reg.e14636.6 > -rw-r--r-- 1 dpat admin 0 Jan 26 09:13 > tbss_2_reg.e14636.7 > -rw-r--r-- 1 dpat admin 337 Jan 26 15:15 > tbss_2_reg.e14636.8 > -rw-r--r-- 1 dpat admin 0 Jan 26 15:16 > tbss_2_reg.e14636.9 > -rw-r--r-- 1 dpat admin 20186 Jan 24 18:51 > tbss_2_reg.o13383.1 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.10 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.11 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.12 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.13 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.14 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.2 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.3 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.4 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.5 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.6 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.7 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.8 > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > tbss_2_reg.o13383.9 > -rw-r--r-- 1 dpat admin 0 Jan 24 15:53 > tbss_2_reg.o13804 > -rw-r--r-- 1 dpat admin 20186 Jan 25 18:14 > tbss_2_reg.o14636.1 > -rw-r--r-- 1 dpat admin 18915 Jan 26 21:18 > tbss_2_reg.o14636.10 > -rw-r--r-- 1 dpat admin 18263 Jan 27 00:17 > tbss_2_reg.o14636.11 > -rw-r--r-- 1 dpat admin 19090 Jan 27 03:19 > tbss_2_reg.o14636.12 > -rw-r--r-- 1 dpat admin 19256 Jan 27 06:18 > tbss_2_reg.o14636.13 > -rw-r--r-- 1 dpat admin 20077 Jan 27 09:18 > tbss_2_reg.o14636.14 > -rw-r--r-- 1 dpat admin 21212 Jan 25 21:16 > tbss_2_reg.o14636.2 > -rw-r--r-- 1 dpat admin 21080 Jan 26 00:14 > tbss_2_reg.o14636.3 > -rw-r--r-- 1 dpat admin 15853 Jan 26 03:11 > tbss_2_reg.o14636.4 > -rw-r--r-- 1 dpat admin 20175 Jan 26 06:12 > tbss_2_reg.o14636.5 > -rw-r--r-- 1 dpat admin 18050 Jan 26 09:12 > tbss_2_reg.o14636.6 > -rw-r--r-- 1 dpat admin 20453 Jan 26 12:14 > tbss_2_reg.o14636.7 > -rw-r--r-- 1 dpat admin 18650 Jan 26 15:15 > tbss_2_reg.o14636.8 > -rw-r--r-- 1 dpat admin 20916 Jan 26 18:17 > tbss_2_reg.o14636.9 >=20 > --=20 > Dianne Patterson, Ph.D. > [log in to unmask] > ERP Lab > University of Arizona > 621-3256 (Office) >=20 ___________________________________________________________________= __________=20 Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! M= ail http://mail.yahoo.fr ========================================================================= Date: Tue, 29 Jan 2008 09:53:18 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?utf-8?q?=22Nicholas=20P=20Holmes=22?= <[log in to unmask]> Subject: Re: 2nd level fixed effects won't run (on latest ubuntu gutsy: 4.0.3-1) MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Mark, Yes, that's the funny thing - i checked a few times, and each time the --fe was always in the log files, but still the FLAME 1+2 seemed to be run. a mystery! also, there is an oft-repeated: ndtri domain error and the FLAME 1 and 2 results are 'abnormally different' any other ideas? many thanks, nick here are some of logs from the last attempt:
Higher-level stats
cat ../design.lcon | awk '{ print  }' > design.lcon
/usr/share/fsl/bin/flame --cope=3Dltered_func_data --vc=3Dr_filtered_func_data
--dvc=3Dof_filtered_func_data --mask=3Dsk --ld=3Dats --dmsign.mat --cssign.grp
--tcsign.con  --fe


/bin/sh: line 1:  9503 Killed                  /usr/share/fsl/bin/flame
--cope=3Dltered_func_data --vc=3Dr_filtered_func_data
--dvc=3Dof_filtered_func_data --mask=3Dsk --ld=3Dats --dmsign.mat --cssign.grp
--tcsign.con --fe

Log directory is: stats
Setting up:
ntptsing=3D000000

No f contrasts
nevs=3D
ntpts=3D
ngs=3D
nvoxels=194988
Running:

ndtri domain error [repeats this a lot...]

maskvoxels=194988
njumps =3D000
burnin =3D00
sampleevery =3D
nsamples =3D500

Metropolis Hasting Sampling
Number of voxels=194988
Percentage done:
 1
WARNING: FLAME stage 2 has given an abnormally large difference to stage 1
x=10,yC,z0
vox=184
zts[0](vox)=3D.15594
zemlowerts[0](vox)=3Dnf
beta_mean[0](vox)=3D45854e-05
beta_b[0](vox)/beta_c[0](vox)=3D00022e-10






----- Original Message -----
From: Mark Woolrich
To: [log in to unmask]
Sent: Tuesday, January 29, 2008 11:13 AM
Subject: Re: [FSL] 2nd level fixed effects won't run (on latest ubuntu
gutsy: 4.0.3-1)


Hi nick,


Take a look in the log file and find the flame call. It should have a --fe
or a --fixed option if it is doing fixed effects.


Cheers, Mark.


----
Dr Mark Woolrich
EPSRC Advanced Research Fellow University Research Lecturer


Oxford University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.


Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich








On 29 Jan 2008, at 08:40, Nicholas P Holmes wrote:


Hi all (but this may be one for Michale Hanke),


for some reason, my higher-level across-session fixed effects analysis
won't work:


rather than taking the usual 10 minutes, it takes FOREVER and seems to run
the FLAME 1+2 instead (i re-ran previous analyses which all worked fine
until now)


during the last fsl release update (4.0.3-1), the feat.tcl file was
overwritten while feat was open and I now have a feat.tcl.dkpg-old file as
well - could this have caused a problem (is it defaulting to run FLAME
1+2) or is something else to blame?


thanks for any input,
nick
=========================================================================
Date:         Tue, 29 Jan 2008 10:14:22 +0000
Reply-To:     FSL - FMRIB's Software Library <[log in to unmask]>
Sender:       FSL - FMRIB's Software Library <[log in to unmask]>
From:         Brian Patenaude <[log in to unmask]>
Subject:      Re: fslstats
In-Reply-To:  <[log in to unmask]>
Mime-Version: 1.0 (Apple Message framework v753)
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Content-Transfer-Encoding: 7bit

Hi,

Following fslroi, you need to se first_utils to boundary correct the  
structure:

first_utils --singleBoundaryCorr -i subject1-R_Amyg -r subject1_T1 -p  
3 -o subject1-R_Amyg_bcorr_p3

Alternatively, instead of using fslroi you could regenerate the  
single volume for just the amygdala from the surface output by using  
(this is a fast operation):

first_utils --meshToVol -i subject1.nii.gz -m subject1-R_Amyg.vtk  -o  
subject1-R_Amyg_image

You would then still apply the boundary correction before using  
fslstats.

Cheers,

Brian

On 28 Jan 2008, at 21:53, Chris Petty wrote:

> Thanks,
>
> How/why will the volume measure with fslstats differ from the  
> output of
> first_utils (.vol)?
>  - assuming I'm using native reconstruction, and no boundary  
> correction
>
> I can't seem to make these match, regardless of the options I've  
> tried.
>
> Thanks,
> chris
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf
> Of Mark Jenkinson
> Sent: Monday, January 28, 2008 12:33 PM
> To: [log in to unmask]
> Subject: Re: [FSL] fslstats
>
> Hi,
>
> There's no way just to do this with fslstats.
> However, with fslroi you can easily extract the single volume and  
> then run
> fslstats on that.
>
> All the best,
>     Mark
>
>
> Christopher Petty wrote:
>> is there an option with fslstats -V for grabbing only 1 volume of  
>> a 4D
> file?
>>
>> for instance if i know R-amyg is the 10th volume of my results from
>> run_first_all ... how can i only measure that volume?
>>
>> -chris
>>
>>
>
=========================================================================
Date:         Tue, 29 Jan 2008 08:29:57 -0500
Reply-To:     FSL - FMRIB's Software Library <[log in to unmask]>
Sender:       FSL - FMRIB's Software Library <[log in to unmask]>
From:         Jiansong Xu <[log in to unmask]>
Subject:      TBSS:    tbss_2_reg
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Content-Transfer-Encoding: 7bit
Mime-Version: 1.0 (Apple Message framework v915)

Dear Friends:

I'm running tbss_2_reg -T using one processor on my Mac with dural  
processors.  I used Top to check the usage of processors.  At first  
few days, about 50% of processor was used, and about two subjects were  
processed every day.
Since yesterday, I found about 30% of processor was used, and the  
whole night did not finish one subject.  I noticed one process called  
nreg uses about 15% of processor.  Is nreg a function in tbss_2_reg?  
Is the slowdown normal?


Best

Jiansong Xu, M.D., Ph.D.
Associate Research Scientist
Dept. of Psychiatry
Yale School of Medicine

Connecticut Mental Health Center, Room S-100
34 Park St.
New Haven, CT 06519
=========================================================================
Date:         Tue, 29 Jan 2008 13:42:49 +0000
Reply-To:     FSL - FMRIB's Software Library <[log in to unmask]>
Sender:       FSL - FMRIB's Software Library <[log in to unmask]>
From:         Suzanna Laycock <[log in to unmask]>
Subject:      Re: TBSS:    tbss_2_reg
In-Reply-To:  <[log in to unmask]>
Mime-Version: 1.0 (Apple Message framework v752.3)
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Content-Transfer-Encoding: 7bit

Hi,

I ran 20 subjects on my Mac using only 1 of the 2 processors,  
probably like you (and 2Gb RAM).  It took the best part of 5 days.  I  
think nreg is a part of tbss...at least it came up on my list of  
active tasks and I had no other programmes running on the computer.   
Also, there's areg.

I guess the FSL team can advise you better, but I think you just have  
to be patient with tbss_2.

Suzanna

On 29 Jan 2008, at 13:29, Jiansong Xu wrote:

> Dear Friends:
>
> I'm running tbss_2_reg -T using one processor on my Mac with dural  
> processors.  I used Top to check the usage of processors.  At first  
> few days, about 50% of processor was used, and about two subjects  
> were processed every day.
> Since yesterday, I found about 30% of processor was used, and the  
> whole night did not finish one subject.  I noticed one process  
> called nreg uses about 15% of processor.  Is nreg a function in  
> tbss_2_reg? Is the slowdown normal?
>
>
> Best
>
> Jiansong Xu, M.D., Ph.D.
> Associate Research Scientist
> Dept. of Psychiatry
> Yale School of Medicine
>
> Connecticut Mental Health Center, Room S-100
> 34 Park St.
> New Haven, CT 06519
=========================================================================
Date:         Tue, 29 Jan 2008 14:00:17 +0000
Reply-To:     FSL - FMRIB's Software Library <[log in to unmask]>
Sender:       FSL - FMRIB's Software Library <[log in to unmask]>
From:         Saad Jbabdi <[log in to unmask]>
Subject:      Re: FSL -Source Programs
In-Reply-To:  <[log in to unmask]>
Mime-Version: 1.0 (Apple Message framework v753)
Content-Type: multipart/alternative; boundary=Apple-Mail-44--30281821

--Apple-Mail-44--30281821
Content-Transfer-Encoding: 7bit
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	charset=US-ASCII;
	delsp=yes;
	format=flowed

Dear Nagulan,

There is no documentation on the FDT code, apart from the old  
fashioned comments throughout the source code :-)

You can certainly use probtrackx for streamlining, if you convert the  
principal tensor orientation (as calculated by dtifit) into theta/phi  
angles, and call them merged_thsamples and merged_phsamples.  
probtrackx will always sample the same direction, so you can run it  
once for each voxel.
Note that this will not be the exact same thing as FACT because of  
the probabilistic interpolation (see Behrens et al MRM 2003)

Cheers,
Saad.


On 24 Jan 2008, at 11:48, R Nagulan wrote:

> Dear All
> I am a PhD student  at University of Kent, UK I am working on on DT- 
> MRI.. I
> am using FSL for my DTI Analysis..
> I have to develop some programs in C++ based on FSL to implement  
> our algorithm..
> Is there any helps or detail description available about FSL source  
> code ( I
> downloaded and build it) specially in FDT..
> is there any Stream line, FACT fiber tracking programs available  
> for FSL...
> FSL used Probabilistic tracking..
>
> Please let me know any contact persons or sites to help me..
>
> Thanks
> Nagulan
>

------------------------------------------------------------------------ 
---
Saad Jbabdi,
Postdoctoral Research Assistant,
Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222545  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
------------------------------------------------------------------------ 
---





--Apple-Mail-44--30281821
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=ISO-8859-1


Dear Nagulan,

There is no documentation = on the FDT code, apart from the old fashioned comments throughout the = source code :-)

You can certainly use = probtrackx for streamlining, if you convert the principal tensor = orientation (as calculated by dtifit) into theta/phi angles, and call = them merged_thsamples and merged_phsamples. probtrackx will always = sample the same direction, so you can run it once for each = voxel.=A0
Note that this will not be the exact same thing as = FACT because of the probabilistic interpolation (see Behrens et al MRM = 2003)

Cheers,
Saad.


On 24 = Jan 2008, at 11:48, R Nagulan wrote:

Dear All
I am a PhD = student=A0 at University of = Kent, UK I am working on on DT-MRI.. I
am using = FSL for my DTI Analysis..
I have to = develop some programs in C++ based on FSL to implement our = algorithm..
Is there any helps or detail = description available about FSL source code ( I
downloaded and build it) specially in = FDT..
is there any Stream line, FACT = fiber tracking programs available for FSL...
FSL used Probabilistic tracking..

Please = let me know any contact persons or sites to help me..

Nagulan

=

Saad Jbabdi,=A0
Postdoctoral Research Assistant,=A0=A0
Oxford University FMRIB Centre

FMRIB, = JR Hospital, Headington, Oxford=A0=A0OX3 9DU, UK
+44 (0) 1865 222545=A0=A0(fax 222717)


=

= --Apple-Mail-44--30281821-- ========================================================================= Date: Tue, 29 Jan 2008 16:17:06 +0000 Reply-To: FSL - FMRIB's Software Library <
[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Brittany Copp <[log in to unmask]> Subject: easythresh Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I am still a bit confused about the difference between the two options fo= r easythresh. How do these two options differ when interpreting data? Usage: easythresh [--mm] e.g.: easythresh stats/zstat1 mask 2.3 0.01 example_func grot Or: easythresh e.g.: easythresh stats/zstat1 2.3 example_func grot Is there anywhere to specify how many voxels constitute a cluster? Thanks! Brittany ========================================================================= Date: Tue, 29 Jan 2008 10:59:00 -0600 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Paul Geha <[log in to unmask]> Subject: Re: RE : [FSL] In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thank you Gwenaelle, for the mean of L1+L2 should I just do it with avwmaths? in fsl and feed = the result to TBSS? thanks a lot Paul -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On Behalf Of Gwena=EBlle DOUAUD Sent: Tuesday, January 29, 2008 3:45 AM To: [log in to unmask] Subject: [FSL] RE : [FSL] Hi Paul, you can either run separately L1, L2 and L3 or consider L1 and the mean of L2 and L3. Then, all you need to do is to create a separate directory for each type of image (so, say, Lparralel and Lperpendicular) and make sure that the images in their corresponding directory are named *exactly* the same as the original FA images are (please see the manual: http://www.fmrib.ox.ac.uk/fsl/tbss/index.html, section "Using non-FA Images in TBSS"). Hope this helps, Gwenaelle --- Paul Geha <[log in to unmask]> a =E9crit : > Dear FSL users, > > > I ran a TBSS t-test between 2 groups and found a > significant FA difference > between them. I would like to see where does it > come from L1 or L2+L3/2? > How do I do that? L1, L2, and L3 do I have to > repeat Tbss for each alone > i.e L1 and L2 and L3?? > thanks > > Paul Geha M.D. > Northwestern University > The Feinberg School of Medicine > Department of Physiology M211 > 303 E. Chicago Ave. > Chicago, IL 60611 > Tel:312-503 2886 > Fax: 312-503-5101 > _________________________________________________________________________= ___ _ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! M= ail http://mail.yahoo.fr ========================================================================= Date: Tue, 29 Jan 2008 18:15:18 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?iso-8859-1?q?Gwena=EBlle=20DOUAUD?= <[log in to unmask]> Subject: RE : Re: [FSL] RE : [FSL] In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Paul, you rather mean the average of L2 and L3 I guess? Yes, just create it with avwmaths (or fslmaths if you have the latest version of FSL) and feed it in tbss. Don't forget to rename the new images as the FA ones BUT in a different, parallel, directory. Cheers, Gwen --- Paul Geha <[log in to unmask]> a =E9crit : > Thank you Gwenaelle, >=20 > for the mean of L1+L2 should I just do it with > avwmaths? in fsl and feed the > result to TBSS? > thanks a lot > Paul >=20 >=20 >=20 >=20 > -----Original Message----- > From: FSL - FMRIB's Software Library > [mailto:[log in to unmask]]On > Behalf Of Gwena=EBlle DOUAUD > Sent: Tuesday, January 29, 2008 3:45 AM > To: [log in to unmask] > Subject: [FSL] RE : [FSL] >=20 >=20 > Hi Paul, >=20 > you can either run separately L1, L2 and L3 or > consider L1 and the mean of L2 and L3. Then, all you > need to do is to create a separate directory for > each > type of image (so, say, Lparralel and > Lperpendicular) > and make sure that the images in their corresponding > directory are named *exactly* the same as the > original > FA images are (please see the manual: > http://www.fmrib.ox.ac.uk/fsl/tbss/index.html, > section > "Using non-FA Images in TBSS"). >=20 > Hope this helps, > Gwenaelle >=20 >=20 > --- Paul Geha <[log in to unmask]> a =E9crit : >=20 > > Dear FSL users, > > > > > > I ran a TBSS t-test between 2 groups and found a > > significant FA difference > > between them. I would like to see where does it > > come from L1 or L2+L3/2? > > How do I do that? L1, L2, and L3 do I have to > > repeat Tbss for each alone > > i.e L1 and L2 and L3?? > > thanks > > > > Paul Geha M.D. > > Northwestern University > > The Feinberg School of Medicine > > Department of Physiology M211 > > 303 E. Chicago Ave. > > Chicago, IL 60611 > > Tel:312-503 2886 > > Fax: 312-503-5101 > > >=20 >=20 >=20 >=20 > _________________________________________________________________________= ___ > _ > Ne gardez plus qu'une seule adresse mail ! Copiez > vos mails vers Yahoo! Mail > http://mail.yahoo.fr >=20 ___________________________________________________________________= __________=20 Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! M= ail http://mail.yahoo.fr ========================================================================= Date: Tue, 29 Jan 2008 09:48:37 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephane Jacobs <[log in to unmask]> Subject: Re: easythresh In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, The first command applies a mask to your statistical map. This can be the whole brain mask, or an ROI that you specify. It also applies 2 thresholds: a Z threshold that determines which voxels are considered significant, and a cluster extent threshold (the p value in the GUI), which determines the minimum size a cluster must have to be considered significant. You must use this threshold to determine the minimum size for a cluster. The second command is run without applying a mask, and does not specify any cluster extent threshold, which I assume means that it runs voxelwise on the whole brain. I don't think you can specify directly how many voxels a cluster should be to be considered significant. Rather, you use the cluster extent threshold (p threshold) to specify a maximum probability of type I error that you consider acceptable. For example, setting p<0.05 means that there is a probability < 5% that the clusters appearing in your resulting stat map are due to chance. This takes in account the properties of your data, i.e. spatial resolution, smoothness, etc..., to determine the minimum size a cluster should be to meet these criteria. There has been several more detailed discussions about how thresholding works - have a look in the archives. And of course, if I'm forgetting anything or getting something wrong, please someone correct me! Best, Stephane Brittany Copp wrote: > I am still a bit confused about the difference between the two options for > easythresh. How do these two options differ when interpreting data? > > Usage: easythresh > [--mm] > e.g.: easythresh stats/zstat1 mask 2.3 0.01 example_func grot > > Or: easythresh > e.g.: easythresh stats/zstat1 2.3 example_func grot > > Is there anywhere to specify how many voxels constitute a cluster? > > Thanks! > > Brittany > > > ========================================================================= Date: Tue, 29 Jan 2008 18:01:01 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Jonathan Hakun <[log in to unmask]> Subject: Re: Mixed Anova 2x2 Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I see this is a popular question -- and have tried to apply the help give= n to other folks, but I keep hitting a wall... I've used the 2x2 ANOVA design in the FEAT manual with success. (my model= =3D Gender x Stimulus type (2 types, A and B); 4 subjects for sake of argumen= t). If I assume independent measures for both factors and use the example mod= el (below, a 4 sj example of the model I used) I encounter no errors: EV1 EV2 EV3 EV4 input COPE Group Stim Gender Interaction Mn Female_sj1_stimA 1 -1 -1 1 1 Female_sj2_stimA 1 -1 -1 1 1 Male_sj3_stimA 1 -1 1 -1 1 Male_sj4_stimA 1 -1 1 -1 1 Female_sj1_stimB 1 1 -1 -1 1 Female_sj2_stimB 1 1 -1 -1 1 Male_sj3_stimB 1 1 1 1 1 Male_sj4_stimB 1 1 1 1 1 The issue is, as you may have noticed -- my group is not 8 independent subjects, rather 4 subjects with a repeated measure (stimulus) and an independent factor (gender). I'd like to model out within subject variability: i.e. like the paired t-test. I see this was recommended to several people asking a similar question. This model looks like: EV1 EV2 EV3 EV4 EV5 EV6 EV7=20=20= inputCOPE Group Stim Gender Interaction sj1 sj2 sj3 sj4=20=20= Fem_sj1_stimA 1 -1 -1 1 1 0 0 0=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Fem_sj2_stimA 1 -1 -1 1 0 1 0 0=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Male_sj3_stimA 1 -1 1 -1 0 0 1 0=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Male_sj4_stimA 1 -1 1 -1 0 0 0 1=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Fem_sj1_stimB 1 1 -1 -1 1 0 0 0=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Fem_sj2_stimB 1 1 -1 -1 0 1 0 0=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Male_sj3_stimB 1 1 1 1 0 0 1 0=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 Male_sj4_stimB 1 1 1 1 0 0 0 1=20=20=20= =20=20=20=20=20=20 =20=20=20=20=20=20=20=20=20=20=20 I assume that this accounts for the dependence of inputs 1 and 5, 2 and 6= , and so on. Problem I run into is everytime I try and use this model it reports a ran= k deficient error.=20=20 Any ideas on what might I be missing? Thank you, ~Jonathan ========================================================================= Date: Tue, 29 Jan 2008 18:02:28 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: FSLView timeseries, combined runs Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I was just wondering how to interpet the linear function presented for th= e timeseries of combined runs for one subject? In other words, higher-level= stats for the runs using FE. Thanks. ========================================================================= Date: Tue, 29 Jan 2008 18:22:30 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: Smoothing SPM vs FSL Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I am wondering is there is a way to specify the smoothing kernel as is do= ne in SPM? For example, can I specify a 5 x 7.5 x 7.5 kernel, instead of jus= t 5?=20 I know there is suppossed to be a command line smoothing option, ip, but = I cannot find it in my install (4.0.3, CentOS4-32bit) and from what I've re= ad here, it does not appear able to do the above. Thanks, Carlos ========================================================================= Date: Tue, 29 Jan 2008 18:47:18 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Anastasia Ford <[log in to unmask]> Subject: Re: Philips Scaling Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Hello, I have checked the output of dtifit and the tensor fit looks correct. The= tractography images generated using waypoint seed masks look anatomically= correct. However, the output of the tract connectivity analysis (classification targets) does not contain the seeds_to_target volumes, on= ly the seeds_to_target masks and the fdt_paths image.=20 Any help will be greatly appreciated. Sincerely, Anastasia ========================================================================= Date: Tue, 29 Jan 2008 18:53:38 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Saad Jbabdi <[log in to unmask]> Subject: Re: Philips Scaling In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-52--12680888 --Apple-Mail-52--12680888 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hello Anastasia, I wonder what you mean by seeds_to_target volumes vs masks? This option in probtrackx produces files that are named seeds_to_target{i} where the only non-zero voxels are the _seed_ voxels for which some sample tracts reached target {i}. If you are thinking of isolated tracts that reach each of the different targets, this is not an output of probtrackx. Cheers, Saad. On 29 Jan 2008, at 18:47, Anastasia Ford wrote: > Hello, > > I have checked the output of dtifit and the tensor fit looks > correct. The > tractography images generated using waypoint seed masks look > anatomically > correct. However, the output of the tract connectivity analysis > (classification targets) does not contain the seeds_to_target > volumes, only > the seeds_to_target masks and the fdt_paths image. > Any help will be greatly appreciated. > > Sincerely, > Anastasia > ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ --- --Apple-Mail-52--12680888 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
Hello Anastasia,

I wonder what you mean by = seeds_to_target volumes vs masks?

This option in probtrackx = produces files that are named seeds_to_target{i}
where the = only non-zero voxels are the _seed_ voxels for which some sample tracts = reached target {i}.
If you are thinking of isolated tracts = that reach each of the different targets, this is not an output of = probtrackx.

Cheers,
Saad.


On 29 = Jan 2008, at 18:47, Anastasia Ford wrote:

Hello,

I have checked the output of = dtifit and the tensor fit looks correct. The
tractography images generated using waypoint seed = masks look anatomically
correct. = However, the output of the tract connectivity analysis
(classification targets) does not contain the = seeds_to_target volumes, only
the = seeds_to_target masks and the fdt_paths image.=A0
Any help = will be greatly appreciated.

Sincerely,
Anastasia


Saad Jbabdi,=A0
Postdoctoral Research Assistant,=A0=A0
Oxford University FMRIB Centre

FMRIB, = JR Hospital, Headington, Oxford=A0=A0OX3 9DU, UK
+44 (0) 1865 222545=A0=A0(fax 222717)


=

= --Apple-Mail-52--12680888-- ========================================================================= Date: Tue, 29 Jan 2008 19:09:06 +0000 Reply-To: FSL - FMRIB's Software Library <
[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Anastasia Ford <[log in to unmask]> Subject: Re: Philips Scaling Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Saad, You are right, the seeds_to_target files are generated, but they do not contain any data, as seen from fslview. Sincerely, Anastasia ========================================================================= Date: Tue, 29 Jan 2008 12:31:39 -0700 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Dianne Patterson <[log in to unmask]> Subject: Re: RE : [FSL] tbss_3_postreg produces empty images?? In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_15895_11037336.1201635099116" ------=_Part_15895_11037336.1201635099116 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks Gwenaelle for your suggestions. I removed the stats directory and reran tbss_3_postreg. I get 14 empty volumes in all_FA.nii.gz...and, as you can see, no obvious error messages. I'm going to go dig around in the scripts a little and the existing images, to see if I can identify any problems that I've missed so far. Any other thoughts? Thankyou, Dianne [Data/dti_erp/TBSS_ERP] dpat% rm -fr stats [Data/dti_erp/TBSS_ERP] dpat% tbss_3_postreg -S using pre-chosen target for registration transforming all FA images into MNI152 space ecc3131_FA_FAi ecc3393_FA_FAi ecc3472_FA_FAi ecc3515_FA_FAi ecc3559_FA_FAi ecc3591_FA_FAi ecc3647_FA_FAi ecc3717_FA_FAi ecc3740_FA_FAi ecc3824_FA_FAi ecc3835_FA_FAi ecc3888_FA_FAi ecc3936_FA_FAi ecc3956_FA_FAi merging all upsampled FA images into single 4D image creating valid mask and mean FA skeletonising mean FA now view mean_FA_skeleton to check whether the default threshold of 2000 needs changing, when running: tbss_4_prestats [threshold] [Data/dti_erp/TBSS_ERP] dpat% cd stats [dti_erp/TBSS_ERP/stats] dpat% fv [dti_erp/TBSS_ERP/stats] dpat% fslstats all_FA.nii.gz -V 0 0.000000 [dti_erp/TBSS_ERP/stats] dpat% fslstats all_FA.nii.gz -M 0.000000 On Jan 29, 2008 3:00 AM, Gwena=EBlle DOUAUD <[log in to unmask]> wrot= e: > Hi Dianne, > > it seems that at least a part of tbss_3_postreg has > run properly. It should be quick indeed as it only > applies the non-linear transformations (that you can > see in the 4D images *_to_target_nonlinear.nii.gz) > calculated at the tbss_2 stage to the corresponding > images (*_to_target_nonlinear_hr.nii.gz). Then, it > concatenates all the *_hr.nii.gz images in the big 4D > file called all_FA.nii.gz. If this one is really > empty, this is where the process failed. Have you got > any error message running tbss_3? Maybe try running it > again to see if the problem remains, and if this is > the case, I'll give you the few command lines that > will allow you to finish the tbss_3 stage and continue > to the tbss_4 one. > > Hope this helps, > Gwenaelle > > > > > --- Dianne Patterson <[log in to unmask]> a =E9crit : > > > Hello All, > > > > I apologize if I've simply overlooked the answer to > > my questions in the > > archives or the FAQ. > > > > I am working on an Intel Power Mac with 4 cores and > > 16 gb of ram. I'm > > running tiger, FSL 4.0.3 (updated last week from > > 4.0.1). > > I have plenty of space on my hard drive. > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > I have been using the probtrack pipeline for several > > months now, and thought > > I would try the tbss pipeline. > > I have 14 subjects with identical acquisition > > parameters that were run > > through dtifit (that data all seems to be in good > > shape and has been used > > and examined pretty extensively). > > I've put their fa images in a separate TBSS_ERP > > directory and run > > tbss_1_preproc after making sure the range of values > > was roughly 0-1. > > > > tbss_2_reg seems to have run successfully (but I'm > > not sure how to assess > > this, as I'm not sure what files ought to be > > created). > > > > The following is what I found on my screen at the > > end of the tbss_2_reg run: > > [Data/dti_erp/TBSS_ERP] dpat% tbss_2_reg -T > > ecc3131_FA_FAi_to_target > > ecc3393_FA_FAi_to_target > > ecc3472_FA_FAi_to_target > > ecc3515_FA_FAi_to_target > > ecc3559_FA_FAi_to_target > > ecc3591_FA_FAi_to_target > > ecc3647_FA_FAi_to_target > > ecc3717_FA_FAi_to_target > > ecc3740_FA_FAi_to_target > > ecc3824_FA_FAi_to_target > > ecc3835_FA_FAi_to_target > > ecc3888_FA_FAi_to_target > > ecc3936_FA_FAi_to_target > > ecc3956_FA_FAi_to_target > > 14636 > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > So, I tried tbss_3_postreg -S > > This seems to produce the stats directory and files > > predicted: > > In the FAi directory, there are a couple of new > > image files for each > > subject: > > ecc3824_FA_FAi_to_target_nonlinear.nii.gz > > ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz > > > > I've checked several of them, and they contain > > stuff...so that seems good. > > However, only the MNI image in the stats directory > > appears to contain > > anything. > > The other images in the stats directory display as > > black and give me a mean > > of 0 > > when I run > > >fslstats image -M > > > > [dti_erp/TBSS_ERP/stats] dpat% ls -l > > total 21824 > > -rw-r--r-- 1 dpat admin 10917429 Jan 28 16:01 > > MNI152.nii.gz > > -rw-r--r-- 1 dpat admin 196651 Jan 28 16:04 > > all_FA.nii.gz > > -rw-r--r-- 1 dpat admin 14174 Jan 28 16:04 > > mean_FA.nii.gz > > -rw-r--r-- 1 dpat admin 7152 Jan 28 16:04 > > mean_FA_mask.nii.gz > > -rw-r--r-- 1 dpat admin 28207 Jan 28 16:05 > > mean_FA_skeleton.nii.gz > > > > BTW, it seemed to take only about 5 minutes for > > tbss_3_postreg to run. > > > > Thankyou for your time, > > > > Dianne > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D > > For what it is worth, here are the files in the FAi > > directory: > > > > [dti_erp/TBSS_ERP/FAi] dpat% ls -l > > total 2059304 > > -rw-r--r-- 1 dpat admin 7 Jan 28 16:01 > > best.msf > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:47 > > ecc3131_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:47 > > ecc3131_FA_FAi.img > > -rw-r--r-- 1 dpat admin 211 Jan 25 15:19 > > ecc3131_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18367 Jan 25 18:14 > > ecc3131_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 25 18:14 > > ecc3131_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 71360428 Jan 25 18:15 > > ecc3131_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2674985 Jan 28 16:02 > > ecc3131_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:47 > > ecc3393_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:47 > > ecc3393_FA_FAi.img > > -rw-r--r-- 1 dpat admin 208 Jan 25 18:24 > > ecc3393_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18364 Jan 25 21:15 > > ecc3393_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 25 21:16 > > ecc3393_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 71222937 Jan 25 21:17 > > ecc3393_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2722194 Jan 28 16:02 > > ecc3393_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3472_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3472_FA_FAi.img > > -rw-r--r-- 1 dpat admin 203 Jan 25 21:23 > > ecc3472_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18359 Jan 26 00:14 > > ecc3472_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 00:14 > > ecc3472_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 68257531 Jan 26 00:15 > > ecc3472_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2826240 Jan 28 16:02 > > ecc3472_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3515_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3515_FA_FAi.img > > -rw-r--r-- 1 dpat admin 194 Jan 26 00:19 > > ecc3515_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18350 Jan 26 03:11 > > ecc3515_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 03:12 > > ecc3515_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 69756191 Jan 26 03:13 > > ecc3515_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2746299 Jan 28 16:02 > > ecc3515_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3559_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3559_FA_FAi.img > > -rw-r--r-- 1 dpat admin 211 Jan 26 03:20 > > ecc3559_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18367 Jan 26 06:11 > > ecc3559_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 06:12 > > ecc3559_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 71794848 Jan 26 06:13 > > ecc3559_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2749851 Jan 28 16:02 > > ecc3559_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3591_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3591_FA_FAi.img > > -rw-r--r-- 1 dpat admin 214 Jan 26 06:21 > > ecc3591_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18370 Jan 26 09:12 > > ecc3591_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 09:13 > > ecc3591_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 70797764 Jan 26 09:13 > > ecc3591_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2718995 Jan 28 16:02 > > ecc3591_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3647_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3647_FA_FAi.img > > -rw-r--r-- 1 dpat admin 211 Jan 26 09:22 > > ecc3647_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18367 Jan 26 12:13 > > ecc3647_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 12:14 > > ecc3647_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 72127885 Jan 26 12:15 > > ecc3647_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2789331 Jan 28 16:02 > > ecc3647_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3717_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3717_FA_FAi.img > > -rw-r--r-- 1 dpat admin 211 Jan 26 12:22 > > ecc3717_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18367 Jan 26 15:14 > > ecc3717_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 15:15 > > ecc3717_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 61316401 Jan 26 15:16 > > ecc3717_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 14139 Jan 28 16:02 > > ecc3717_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3740_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3740_FA_FAi.img > > -rw-r--r-- 1 dpat admin 206 Jan 26 15:24 > > ecc3740_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18362 Jan 26 18:16 > > ecc3740_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 18:17 > > ecc3740_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 72341839 Jan 26 18:17 > > ecc3740_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2669134 Jan 28 16:02 > > ecc3740_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3824_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3824_FA_FAi.img > > -rw-r--r-- 1 dpat admin 196 Jan 26 18:26 > > ecc3824_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18352 Jan 26 21:17 > > ecc3824_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 26 21:18 > > ecc3824_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 67623887 Jan 26 21:19 > > ecc3824_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2714604 Jan 28 16:02 > > ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3835_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3835_FA_FAi.img > > -rw-r--r-- 1 dpat admin 198 Jan 26 21:25 > > ecc3835_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18354 Jan 27 00:17 > > ecc3835_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 27 00:18 > > ecc3835_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 68614776 Jan 27 00:18 > > ecc3835_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2670394 Jan 28 16:03 > > ecc3835_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3888_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3888_FA_FAi.img > > -rw-r--r-- 1 dpat admin 206 Jan 27 00:26 > > ecc3888_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18362 Jan 27 03:18 > > ecc3888_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 27 03:19 > > ecc3888_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 70673036 Jan 27 03:19 > > ecc3888_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2687060 Jan 28 16:03 > > ecc3888_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:48 > > ecc3936_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:48 > > ecc3936_FA_FAi.img > > -rw-r--r-- 1 dpat admin 215 Jan 27 03:27 > > ecc3936_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18371 Jan 27 06:18 > > ecc3936_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 27 06:18 > > ecc3936_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 72270981 Jan 27 06:19 > > ecc3936_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2977842 Jan 28 16:03 > > ecc3936_FA_FAi_to_target_nonlinear_hr.nii.gz > > -rw-r--r-- 1 dpat admin 348 Jan 24 15:49 > > ecc3956_FA_FAi.hdr > > -rw-r--r-- 1 dpat admin 1746360 Jan 24 15:49 > > ecc3956_FA_FAi.img > > -rw-r--r-- 1 dpat admin 210 Jan 27 06:26 > > ecc3956_FA_FAi_to_target_affine.dof > > -rw-r--r-- 1 dpat admin 18366 Jan 27 09:18 > > ecc3956_FA_FAi_to_target_nonlinear.dof > > -rw-r--r-- 1 dpat admin 21 Jan 27 09:18 > > ecc3956_FA_FAi_to_target_nonlinear.msf > > -rw-r--r-- 1 dpat admin 70852363 Jan 27 09:19 > > ecc3956_FA_FAi_to_target_nonlinear.nii.gz > > -rw-r--r-- 1 dpat admin 2624975 Jan 28 16:03 > > ecc3956_FA_FAi_to_target_nonlinear_hr.nii.gz > > drwxr-xr-x 26 dpat admin 884 Jan 24 15:49 > > slicesdir > > -rw-r--r-- 1 dpat admin 348 Jan 25 15:14 > > target.hdr > > -rw-r--r-- 1 dpat admin 14442064 Jan 25 15:14 > > target.img > > -rw-r--r-- 1 dpat admin 0 Jan 24 15:52 > > tbss_2_reg.e13383.1 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.10 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.11 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.12 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.13 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.14 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.2 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.3 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.4 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.5 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.6 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.7 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.8 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.e13383.9 > > -rw-r--r-- 1 dpat admin 0 Jan 24 15:53 > > tbss_2_reg.e13804 > > -rw-r--r-- 1 dpat admin 0 Jan 25 15:14 > > tbss_2_reg.e14636.1 > > -rw-r--r-- 1 dpat admin 0 Jan 26 18:17 > > tbss_2_reg.e14636.10 > > -rw-r--r-- 1 dpat admin 0 Jan 26 21:19 > > tbss_2_reg.e14636.11 > > -rw-r--r-- 1 dpat admin 0 Jan 27 00:18 > > tbss_2_reg.e14636.12 > > -rw-r--r-- 1 dpat admin 0 Jan 27 03:19 > > tbss_2_reg.e14636.13 > > -rw-r--r-- 1 dpat admin 0 Jan 27 06:19 > > tbss_2_reg.e14636.14 > > -rw-r--r-- 1 dpat admin 0 Jan 25 18:15 > > tbss_2_reg.e14636.2 > > -rw-r--r-- 1 dpat admin 0 Jan 25 21:17 > > tbss_2_reg.e14636.3 > > -rw-r--r-- 1 dpat admin 0 Jan 26 00:15 > > tbss_2_reg.e14636.4 > > -rw-r--r-- 1 dpat admin 0 Jan 26 03:13 > > tbss_2_reg.e14636.5 > > -rw-r--r-- 1 dpat admin 0 Jan 26 06:13 > > tbss_2_reg.e14636.6 > > -rw-r--r-- 1 dpat admin 0 Jan 26 09:13 > > tbss_2_reg.e14636.7 > > -rw-r--r-- 1 dpat admin 337 Jan 26 15:15 > > tbss_2_reg.e14636.8 > > -rw-r--r-- 1 dpat admin 0 Jan 26 15:16 > > tbss_2_reg.e14636.9 > > -rw-r--r-- 1 dpat admin 20186 Jan 24 18:51 > > tbss_2_reg.o13383.1 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.10 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.11 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.12 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.13 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.14 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.2 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.3 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.4 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.5 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.6 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.7 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.8 > > -rw-r--r-- 1 dpat admin 0 Jan 24 18:52 > > tbss_2_reg.o13383.9 > > -rw-r--r-- 1 dpat admin 0 Jan 24 15:53 > > tbss_2_reg.o13804 > > -rw-r--r-- 1 dpat admin 20186 Jan 25 18:14 > > tbss_2_reg.o14636.1 > > -rw-r--r-- 1 dpat admin 18915 Jan 26 21:18 > > tbss_2_reg.o14636.10 > > -rw-r--r-- 1 dpat admin 18263 Jan 27 00:17 > > tbss_2_reg.o14636.11 > > -rw-r--r-- 1 dpat admin 19090 Jan 27 03:19 > > tbss_2_reg.o14636.12 > > -rw-r--r-- 1 dpat admin 19256 Jan 27 06:18 > > tbss_2_reg.o14636.13 > > -rw-r--r-- 1 dpat admin 20077 Jan 27 09:18 > > tbss_2_reg.o14636.14 > > -rw-r--r-- 1 dpat admin 21212 Jan 25 21:16 > > tbss_2_reg.o14636.2 > > -rw-r--r-- 1 dpat admin 21080 Jan 26 00:14 > > tbss_2_reg.o14636.3 > > -rw-r--r-- 1 dpat admin 15853 Jan 26 03:11 > > tbss_2_reg.o14636.4 > > -rw-r--r-- 1 dpat admin 20175 Jan 26 06:12 > > tbss_2_reg.o14636.5 > > -rw-r--r-- 1 dpat admin 18050 Jan 26 09:12 > > tbss_2_reg.o14636.6 > > -rw-r--r-- 1 dpat admin 20453 Jan 26 12:14 > > tbss_2_reg.o14636.7 > > -rw-r--r-- 1 dpat admin 18650 Jan 26 15:15 > > tbss_2_reg.o14636.8 > > -rw-r--r-- 1 dpat admin 20916 Jan 26 18:17 > > tbss_2_reg.o14636.9 > > > > -- > > Dianne Patterson, Ph.D. > > [log in to unmask] > > ERP Lab > > University of Arizona > > 621-3256 (Office) > > > > > > > ________________________________________________________________________= _____ > Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! > Mail http://mail.yahoo.fr > > --=20 Dianne Patterson, Ph.D. [log in to unmask] ERP Lab University of Arizona 621-3256 (Office) ------=_Part_15895_11037336.1201635099116 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks Gwenaelle for your suggestions.

I removed the stats directory= and reran tbss_3_postreg.
I get 14 empty volumes in all_FA.nii.gz...and= , as you can see, no obvious error messages.
I'm going to go dig aro= und in the scripts a little and the existing images, to see if I can identi= fy any problems
that I've missed so far.

Any other thoughts?

Thankyou,
Dianne

[Data/dti_erp/TBSS_ERP] dpat% rm -fr stats
[Data/dti_= erp/TBSS_ERP] dpat% tbss_3_postreg -S
using pre-chosen target for regist= ration
transforming all FA images into MNI152 space
ecc3131_FA_FAi
ecc3393_F= A_FAi
ecc3472_FA_FAi
ecc3515_FA_FAi
ecc3559_FA_FAi
ecc3591_FA_F= Ai
ecc3647_FA_FAi
ecc3717_FA_FAi
ecc3740_FA_FAi
ecc3824_FA_FAi<= br> ecc3835_FA_FAi
ecc3888_FA_FAi
ecc3936_FA_FAi
ecc3956_FA_FAi
mer= ging all upsampled FA images into single 4D image
creating valid mask an= d mean FA
skeletonising mean FA
now view mean_FA_skeleton to check wh= ether the default threshold of 2000 needs changing, when running:
tbss_4_prestats [threshold]
[Data/dti_erp/TBSS_ERP] dpat% cd stats
[d= ti_erp/TBSS_ERP/stats] dpat% fv
[dti_erp/TBSS_ERP/stats] dpat% fslstats = all_FA.nii.gz -V
0 0.000000
[dti_erp/TBSS_ERP/stats] dpat% fslstats = all_FA.nii.gz -M
0.000000

On Jan 29, 2008 3:00 AM, Gwena= =EBlle DOUAUD <gwenaelledoua= [log in to unmask]> wrote:
Hi Dianne,

it seems that at least a part of tbss_3_postreg has
ru= n properly. It should be quick indeed as it only
applies the non-linear = transformations (that you can
see in the 4D images *_to_target_nonlinear= .nii.gz)
calculated at the tbss_2 stage to the corresponding
images (*_to_target_= nonlinear_hr.nii.gz). Then, it
concatenates all the *_hr.nii.gz images i= n the big 4D
file called all_FA.nii.gz. If this one is really
empty, = this is where the process failed. Have you got
any error message running tbss_3? Maybe try running it
again to see if t= he problem remains, and if this is
the case, I'll give you the few c= ommand lines that
will allow you to finish the tbss_3 stage and continue=
to the tbss_4 one.

Hope this helps,
Gwenaelle




= --- Dianne Patterson <dkp@EMAIL= .ARIZONA.EDU> a =E9crit :
<= br> > Hello All,
>
> I apologize if I've simply overlooked t= he answer to
> my questions in the
> archives or the FAQ.
&g= t;
> I am working on an Intel Power Mac with 4 cores and
> 16 g= b of ram.  I'm
> running tiger, FSL 4.0.3 (updated last week from
> 4.0.1).
&g= t; I have plenty of space on my hard drive.
> =3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D
> I have been using the probtrack pipeline for several
> months now, and thought
> I would try the tbss pipeline.
>= I have 14 subjects with identical acquisition
> parameters that were= run
> through dtifit (that data all seems to be in good
> shap= e and has been used
> and examined pretty extensively).
> I've put their fa images= in a separate TBSS_ERP
> directory and run
> tbss_1_preproc af= ter making sure the range of values
> was roughly 0-1.
>
> tbss_2_reg seems to have run successfully (but I'm
> not sur= e how to assess
> this, as I'm not sure what files ought to be> created).
>
> The following is what I found on my screen = at the
> end of the tbss_2_reg run:
> [Data/dti_erp/TBSS_ERP] dpat% tbss_= 2_reg -T
> ecc3131_FA_FAi_to_target
> ecc3393_FA_FAi_to_target<= br>> ecc3472_FA_FAi_to_target
> ecc3515_FA_FAi_to_target
> e= cc3559_FA_FAi_to_target
> ecc3591_FA_FAi_to_target
> ecc3647_FA_FAi_to_target
> ecc3= 717_FA_FAi_to_target
> ecc3740_FA_FAi_to_target
> ecc3824_FA_FA= i_to_target
> ecc3835_FA_FAi_to_target
> ecc3888_FA_FAi_to_targ= et
> ecc3936_FA_FAi_to_target
> ecc3956_FA_FAi_to_target
> 1463= 6
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>= So, I tried tbss_3_postreg -S
> This seems to produce the stats dire= ctory and files
> predicted:
> In the FAi directory, there are a couple of new
> image files fo= r each
> subject:
> ecc3824_FA_FAi_to_target_nonlinear.nii.gz> ecc3824_FA_FAi_to_target_nonlinear_hr.nii.gz
>
> I'v= e checked several of them, and they contain
> stuff...so that seems good.
> However, only the MNI image in the= stats directory
> appears to contain
> anything.
> The o= ther images in the stats directory display as
> black and give me a m= ean
> of 0
> when I run
> >fslstats image -M
>
> = [dti_erp/TBSS_ERP/stats] dpat% ls -l
> total 21824
> -rw-r--r--=   1 dpat  admin  10917429 Jan 28 16:01
> MNI152.nii.g= z
> -rw-r--r--   1 dpat  admin    196651 Jan 28 1= 6:04
> all_FA.nii.gz
> -rw-r--r--   1 dpat  admin   &nbs= p; 14174 Jan 28 16:04
> mean_FA.nii.gz
> -rw-r--r--   1 dp= at  admin      7152 Jan 28 16:04
> mean_FA_mask.n= ii.gz
> -rw-r--r--   1 dpat  admin     28207 Jan = 28 16:05
> mean_FA_skeleton.nii.gz
>
> BTW, it seemed to take only ab= out 5 minutes for
> tbss_3_postreg to run.
>
> Thankyou f= or your time,
>
> Dianne
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> For what it is worth, here are the files in the FAi
> directory:=
>
> [dti_erp/TBSS_ERP/FAi] dpat% ls -l
> total 2059304> -rw-r--r--    1 dpat  admin       &nbs= p; 7 Jan 28 16:01
> best.msf
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:47
> ecc3131_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:47
> ecc3131_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       211 Jan 2= 5 15:19
> ecc3131_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18367 Jan 25 18:14
> ecc3131_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 25 18:14
> ecc3131_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  71360428 Jan 25 18:15=
> ecc3131_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2674985 Jan 28 16:02
> ecc3131_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:47
> ecc3393_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:47
> ecc3393_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       208 Jan 2= 5 18:24
> ecc3393_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18364 Jan 25 21:15
> ecc3393_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 25 21:16
> ecc3393_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  71222937 Jan 25 21:17=
> ecc3393_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2722194 Jan 28 16:02
> ecc3393_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3472_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3472_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       203 Jan 2= 5 21:23
> ecc3472_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18359 Jan 26 00:14
> ecc3472_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 00:14
> ecc3472_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  68257531 Jan 26 00:15=
> ecc3472_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2826240 Jan 28 16:02
> ecc3472_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3515_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3515_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       194 Jan 2= 6 00:19
> ecc3515_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18350 Jan 26 03:11
> ecc3515_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 03:12
> ecc3515_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  69756191 Jan 26 03:13=
> ecc3515_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2746299 Jan 28 16:02
> ecc3515_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3559_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3559_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       211 Jan 2= 6 03:20
> ecc3559_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18367 Jan 26 06:11
> ecc3559_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 06:12
> ecc3559_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  71794848 Jan 26 06:13=
> ecc3559_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2749851 Jan 28 16:02
> ecc3559_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3591_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3591_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       214 Jan 2= 6 06:21
> ecc3591_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18370 Jan 26 09:12
> ecc3591_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 09:13
> ecc3591_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  70797764 Jan 26 09:13=
> ecc3591_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2718995 Jan 28 16:02
> ecc3591_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3647_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3647_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       211 Jan 2= 6 09:22
> ecc3647_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18367 Jan 26 12:13
> ecc3647_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 12:14
> ecc3647_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  72127885 Jan 26 12:15=
> ecc3647_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2789331 Jan 28 16:02
> ecc3647_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3717_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3717_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       211 Jan 2= 6 12:22
> ecc3717_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18367 Jan 26 15:14
> ecc3717_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 15:15
> ecc3717_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  61316401 Jan 26 15:16=
> ecc3717_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin     14139 Jan 28 16:02
> ecc3717= _FA_FAi_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3740_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3740_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       206 Jan 2= 6 15:24
> ecc3740_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18362 Jan 26 18:16
> ecc3740_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 18:17
> ecc3740_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  72341839 Jan 26 18:17=
> ecc3740_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2669134 Jan 28 16:02
> ecc3740_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3824_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3824_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       196 Jan 2= 6 18:26
> ecc3824_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18352 Jan 26 21:17
> ecc3824_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 26 21:18
> ecc3824_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  67623887 Jan 26 21:19=
> ecc3824_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2714604 Jan 28 16:02
> ecc3824_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3835_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3835_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       198 Jan 2= 6 21:25
> ecc3835_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18354 Jan 27 00:17
> ecc3835_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 27 00:18
> ecc3835_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  68614776 Jan 27 00:18=
> ecc3835_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2670394 Jan 28 16:03
> ecc3835_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3888_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3888_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       206 Jan 2= 7 00:26
> ecc3888_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18362 Jan 27 03:18
> ecc3888_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 27 03:19
> ecc3888_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  70673036 Jan 27 03:19=
> ecc3888_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2687060 Jan 28 16:03
> ecc3888_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:48
> ecc3936_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:48
> ecc3936_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       215 Jan 2= 7 03:27
> ecc3936_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18371 Jan 27 06:18
> ecc3936_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 27 06:18
> ecc3936_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  72270981 Jan 27 06:19=
> ecc3936_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2977842 Jan 28 16:03
> ecc3936_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> -rw-r--r--    1 dpat  admin       348 Ja= n 24 15:49
> ecc3956_FA_FAi.hdr
> -rw-r--r--    1 dpa= t  admin   1746360 Jan 24 15:49
> ecc3956_FA_FAi.img
>= ; -rw-r--r--    1 dpat  admin       210 Jan 2= 7 06:26
> ecc3956_FA_FAi_to_target_affine.dof
> -rw-r--r--    1 = dpat  admin     18366 Jan 27 09:18
> ecc3956_FA_FAi_to= _target_nonlinear.dof
> -rw-r--r--    1 dpat  admin &n= bsp;      21 Jan 27 09:18
> ecc3956_FA_FAi_to_target_n= onlinear.msf
> -rw-r--r--    1 dpat  admin  70852363 Jan 27 09:19=
> ecc3956_FA_FAi_to_target_nonlinear.nii.gz
> -rw-r--r--  = ;  1 dpat  admin   2624975 Jan 28 16:03
> ecc3956_FA_F= Ai_to_target_nonlinear_hr.nii.gz
> drwxr-xr-x   26 dpat  admin       884 Jan 24 = 15:49
> slicesdir
> -rw-r--r--    1 dpat  admin =       348 Jan 25 15:14
> target.hdr
> -rw-r--r--=    1 dpat  admin  14442064 Jan 25 15:14
> target= .img
> -rw-r--r--    1 dpat  admin        = 0 Jan 24 15:52
> tbss_2_reg.e13383.1
> -rw-r--r--    = ;1 dpat  admin         0 Jan 24 18:52
> tbss= _2_reg.e13383.10
> -rw-r--r--    1 dpat  admin   =       0 Jan 24 18:52
> tbss_2_reg.e13383.11
> -rw-r--r--    1 dpat  admi= n         0 Jan 24 18:52
> tbss_2_reg.e13383.12> -rw-r--r--    1 dpat  admin       &nbs= p; 0 Jan 24 18:52
> tbss_2_reg.e13383.13
> -rw-r--r--   &n= bsp;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.e13383.14
> -rw-r--r--    1 dpat  admi= n         0 Jan 24 18:52
> tbss_2_reg.e13383.2> -rw-r--r--    1 dpat  admin        = ; 0 Jan 24 18:52
> tbss_2_reg.e13383.3
> -rw-r--r--   &nbs= p;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.e13383.4
> -rw-r--r--    1 dpat  admin=         0 Jan 24 18:52
> tbss_2_reg.e13383.5
= > -rw-r--r--    1 dpat  admin        = 0 Jan 24 18:52
> tbss_2_reg.e13383.6
> -rw-r--r--    = ;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.e13383.7
> -rw-r--r--    1 dpat  admin=         0 Jan 24 18:52
> tbss_2_reg.e13383.8
= > -rw-r--r--    1 dpat  admin        = 0 Jan 24 18:52
> tbss_2_reg.e13383.9
> -rw-r--r--    = ;1 dpat  admin         0 Jan 24 15:53
> tbss_2_reg.e13804
> -rw-r--r--    1 dpat  admin &= nbsp;       0 Jan 25 15:14
> tbss_2_reg.e14636.1
&g= t; -rw-r--r--    1 dpat  admin         0= Jan 26 18:17
> tbss_2_reg.e14636.10
> -rw-r--r--    = 1 dpat  admin         0 Jan 26 21:19
> tbss_2_reg.e14636.11
> -rw-r--r--    1 dpat  admi= n         0 Jan 27 00:18
> tbss_2_reg.e14636.12> -rw-r--r--    1 dpat  admin       &nbs= p; 0 Jan 27 03:19
> tbss_2_reg.e14636.13
> -rw-r--r--   &n= bsp;1 dpat  admin         0 Jan 27 06:19
> tbss_2_reg.e14636.14
> -rw-r--r--    1 dpat  admi= n         0 Jan 25 18:15
> tbss_2_reg.e14636.2> -rw-r--r--    1 dpat  admin        = ; 0 Jan 25 21:17
> tbss_2_reg.e14636.3
> -rw-r--r--   &nbs= p;1 dpat  admin         0 Jan 26 00:15
> tbss_2_reg.e14636.4
> -rw-r--r--    1 dpat  admin=         0 Jan 26 03:13
> tbss_2_reg.e14636.5
= > -rw-r--r--    1 dpat  admin        = 0 Jan 26 06:13
> tbss_2_reg.e14636.6
> -rw-r--r--    = ;1 dpat  admin         0 Jan 26 09:13
> tbss_2_reg.e14636.7
> -rw-r--r--    1 dpat  admin=       337 Jan 26 15:15
> tbss_2_reg.e14636.8
> = -rw-r--r--    1 dpat  admin         0 Ja= n 26 15:16
> tbss_2_reg.e14636.9
> -rw-r--r--    1 dp= at  admin     20186 Jan 24 18:51
> tbss_2_reg.o13383.1
> -rw-r--r--    1 dpat  admin=         0 Jan 24 18:52
> tbss_2_reg.o13383.10> -rw-r--r--    1 dpat  admin        = ; 0 Jan 24 18:52
> tbss_2_reg.o13383.11
> -rw-r--r--   &nb= sp;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.o13383.12
> -rw-r--r--    1 dpat  admi= n         0 Jan 24 18:52
> tbss_2_reg.o13383.13> -rw-r--r--    1 dpat  admin       &nbs= p; 0 Jan 24 18:52
> tbss_2_reg.o13383.14
> -rw-r--r--   &n= bsp;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.o13383.2
> -rw-r--r--    1 dpat  admin=         0 Jan 24 18:52
> tbss_2_reg.o13383.3
= > -rw-r--r--    1 dpat  admin        = 0 Jan 24 18:52
> tbss_2_reg.o13383.4
> -rw-r--r--    = ;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.o13383.5
> -rw-r--r--    1 dpat  admin=         0 Jan 24 18:52
> tbss_2_reg.o13383.6
= > -rw-r--r--    1 dpat  admin        = 0 Jan 24 18:52
> tbss_2_reg.o13383.7
> -rw-r--r--    = ;1 dpat  admin         0 Jan 24 18:52
> tbss_2_reg.o13383.8
> -rw-r--r--    1 dpat  admin=         0 Jan 24 18:52
> tbss_2_reg.o13383.9
= > -rw-r--r--    1 dpat  admin        = 0 Jan 24 15:53
> tbss_2_reg.o13804
> -rw-r--r--    1= dpat  admin     20186 Jan 25 18:14
> tbss_2_reg.o14636.1
> -rw-r--r--    1 dpat  admin=     18915 Jan 26 21:18
> tbss_2_reg.o14636.10
> -rw-= r--r--    1 dpat  admin     18263 Jan 27 00:17
= > tbss_2_reg.o14636.11
> -rw-r--r--    1 dpat  admi= n     19090 Jan 27 03:19
> tbss_2_reg.o14636.12
> -rw-r--r--    1 dpat  admi= n     19256 Jan 27 06:18
> tbss_2_reg.o14636.13
> -rw= -r--r--    1 dpat  admin     20077 Jan 27 09:18> tbss_2_reg.o14636.14
> -rw-r--r--    1 dpat  adm= in     21212 Jan 25 21:16
> tbss_2_reg.o14636.2
> -rw-r--r--    1 dpat  admin=     21080 Jan 26 00:14
> tbss_2_reg.o14636.3
> -rw-r= --r--    1 dpat  admin     15853 Jan 26 03:11
&= gt; tbss_2_reg.o14636.4
> -rw-r--r--    1 dpat  admin =     20175 Jan 26 06:12
> tbss_2_reg.o14636.5
> -rw-r--r--    1 dpat  admin=     18050 Jan 26 09:12
> tbss_2_reg.o14636.6
> -rw-r= --r--    1 dpat  admin     20453 Jan 26 12:14
&= gt; tbss_2_reg.o14636.7
> -rw-r--r--    1 dpat  admin =     18650 Jan 26 15:15
> tbss_2_reg.o14636.8
> -rw-r--r--    1 dpat  admin=     20916 Jan 26 18:17
> tbss_2_reg.o14636.9
>
&g= t; --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> ERP Lab
> University of Arizona
> 621-3256 (Office)
>= ;



     ___= __________________________________________________________________________<= br>Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yah= oo! Mail http://mail.yah= oo.fr




--
Dianne Patter= son, Ph.D.
[log in to unmask]ERP Lab
University of Arizona
621-3256 (Office) ------=_Part_15895_11037336.1201635099116-- ========================================================================= Date: Tue, 29 Jan 2008 13:15:26 -0700 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Dianne Patterson <[log in to unmask]> Subject: tbss_3_postreg produces empty images: an insight MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_16067_25294634.1201637727208" ------=_Part_16067_25294634.1201637727208 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Group, Aha...I found the proximate cause of my problem. The *hr.nii.gz image for one subject (one in the middle, not at the beginning or end of the processing) was empty. When I moved his files out of the FAi directory and reran tbss_3_postreg, I get all_FA and the skeleton image and they look fine. Now, that one subject looks fine in the *.png in slicesdir...(the brain is right way around and looks to be sliced in roughly the same places as everyone else's brains. His other *.nii.gz image looks okay, and the original img and hdr look okay... Is there some way for me to determine why this fellow's *hr.nii.gz image wa= s empty? Thankyou, Dianne On Jan 29, 2008 12:31 PM, Dianne Patterson <[log in to unmask]> wrote: Thanks Gwenaelle for your suggestions. I removed the stats directory and reran tbss_3_postreg. I get 14 empty volumes in all_FA.nii.gz...and, as you can see, no obvious error messages. I'm going to go dig around in the scripts a little and the existing images, to see if I can identify any problems that I've missed so far. Any other thoughts? Thankyou, Dianne [Data/dti_erp/TBSS_ERP] dpat% rm -fr stats [Data/dti_erp/TBSS_ERP] dpat% tbss_3_postreg -S using pre-chosen target for registration transforming all FA images into MNI152 space ecc3131_FA_FAi ecc3393_FA_FAi ecc3472_FA_FAi ecc3515_FA_FAi ecc3559_FA_FAi ecc3591_FA_FAi ecc3647_FA_FAi ecc3717_FA_FAi ecc3740_FA_FAi ecc3824_FA_FAi ecc3835_FA_FAi ecc3888_FA_FAi ecc3936_FA_FAi ecc3956_FA_FAi merging all upsampled FA images into single 4D image creating valid mask and mean FA skeletonising mean FA now view mean_FA_skeleton to check whether the default threshold of 2000 needs changing, when running: tbss_4_prestats [threshold] [Data/dti_erp/TBSS_ERP] dpat% cd stats [dti_erp/TBSS_ERP/stats] dpat% fv [dti_erp/TBSS_ERP/stats] dpat% fslstats all_FA.nii.gz -V 0 0.000000 [dti_erp/TBSS_ERP/stats] dpat% fslstats all_FA.nii.gz -M 0.000000 On Jan 29, 2008 3:00 AM, Gwena=EBlle DOUAUD <[log in to unmask]> wrot= e: Hi Dianne, it seems that at least a part of tbss_3_postreg has run properly. It should be quick indeed as it only applies the non-linear transformations (that you can see in the 4D images *_to_target_nonlinear.nii.gz) calculated at the tbss_2 stage to the corresponding images (*_to_target_nonlinear_hr.nii > > .gz). Then, it > concatenates all the *_hr.nii.gz images in the big 4D > file called all_FA.nii.gz. If this one is really > empty, this is where the process failed. Have you got > any error message running tbss_3? Maybe try running it > again to see if the problem remains, and if this is > the case, I'll give you the few command lines that > will allow you to finish the tbss_3 stage and continue > to the tbss_4 one. > > Hope this helps, > Gwenaelle > --=20 Dianne Patterson, Ph.D. [log in to unmask] ERP Lab University of Arizona 621-3256 (Office) ------=_Part_16067_25294634.1201637727208 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Group,
Aha...I found the proximate cause of my problem.
The *hr.= nii.gz image for one subject (one in the middle, not at the beginning or en= d of the processing) was empty.
When I moved his files out of the FAi directory and reran tbss_3_postreg, I get all_FA and the skeleton image and they look fine.

Now, that one subject looks fine in the *.png in slicesdir...(the brain is right way around and looks to be sliced in roughly the same places as everyone else's brains.
His other  *.nii.gz image loo= ks okay, and the original img and hdr look okay...

Is there some way for me to determine why this fellow's *hr.nii.gz = image was empty?

Thankyou,

Dianne


On Jan 29, 2008 = 12:31 PM, Dianne Patterson <[log in to unmask]> wrote:
Thanks Gwenaelle for your suggestions.

I removed the stats directory= and reran tbss_3_postreg.
I get 14 empty volumes in all_FA.nii.gz...and, as you can see, no obvious e= rror messages.
I'm going to go dig around in the scripts a little an= d the existing images, to see if I can identify any problems
that I've missed so far.

Any other thoughts?

Thankyou,
Dianne

[Data/dti_erp/TBSS_ERP] dpat% rm -fr stats
[Data/dti_= erp/TBSS_ERP] dpat% tbss_3_postreg -S
using pre-chosen target for regist= ration
transforming all FA images into MNI152 space
ecc3131_FA_FAi
ecc3393_F= A_FAi
ecc3472_FA_FAi
ecc3515_FA_FAi
ecc3559_FA_FAi
ecc3591_FA_F= Ai
ecc3647_FA_FAi
ecc3717_FA_FAi
ecc3740_FA_FAi
ecc3824_FA_FAi<= br> ecc3835_FA_FAi
ecc3888_FA_FAi
ecc3936_FA_FAi
ecc3956_FA_FAi
mer= ging all upsampled FA images into single 4D image
creating valid mask an= d mean FA
skeletonising mean FA
now view mean_FA_skeleton to check wh= ether the default threshold of 2000 needs changing, when running:
tbss_4_prestats [threshold]
[Data/dti_erp/TBSS_ERP] dpat% cd stats
[d= ti_erp/TBSS_ERP/stats] dpat% fv
[dti_erp/TBSS_ERP/stats] dpat% fslstats = all_FA.nii.gz -V
0 0.000000
[dti_erp/TBSS_ERP/stats] dpat% fslstats = all_FA.nii.gz -M
0.000000

On Jan 29, 2008 3:00 AM, Gwena=EBlle DOUAUD <[log in to unmask] r> wrote:
Hi Dianne,

it seems that at least a part of tbss_3_postreg has
ru= n properly. It should be quick indeed as it only
applies the non-linear = transformations (that you can
see in the 4D images *_to_target_nonlinear= .nii.gz)
calculated at the tbss_2 stage to the corresponding
images (*_to_target_= nonlinear_hr.nii
.gz). Then, it
concatenates all the *_hr.nii.gz images in the big 4D
= file called all_FA.nii.gz. If this one is really
empty, this is where th= e process failed. Have you got
any error message running tbss_3? Maybe try running it
again to see if t= he problem remains, and if this is
the case, I'll give you the few c= ommand lines that
will allow you to finish the tbss_3 stage and continue=
to the tbss_4 one.

Hope this helps,
Gwenaelle

--
Dianne Patterson, Ph.D.
[log in to unmask]
ERP Lab
University of Arizona 621-3256 (Office) ------=_Part_16067_25294634.1201637727208-- ========================================================================= Date: Tue, 29 Jan 2008 20:57:55 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Saad Jbabdi <[log in to unmask]> Subject: Re: Philips Scaling In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-53--5223340 --Apple-Mail-53--5223340 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed This either means that no tract reached your targets (easy to check by loading fdt_paths and your targets), or that you haven't set min- max correctly in fslview (you can check if the seeds_to_target contain non-zero voxels using fslstats -R) Cheers, Saad On 29 Jan 2008, at 19:09, Anastasia Ford wrote: > Saad, > > You are right, the seeds_to_target files are generated, but they do > not > contain any data, as seen from fslview. > > Sincerely, > > Anastasia > ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ --- --Apple-Mail-53--5223340 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
This either means that no tract reached your targets (easy to check = by loading fdt_paths and your targets), or that you haven't set min-max = correctly in fslview (you can check if the seeds_to_target contain = non-zero voxels using fslstats -R)

Cheers,
Saad
=


On 29 = Jan 2008, at 19:09, Anastasia Ford wrote:

Saad,

You are right, the = seeds_to_target files are generated, but they do not
contain any data, as seen from fslview.


Anastasia


Saad Jbabdi,=A0
Postdoctoral Research Assistant,=A0=A0
Oxford University FMRIB Centre

FMRIB, = JR Hospital, Headington, Oxford=A0=A0OX3 9DU, UK
+44 (0) 1865 222545=A0=A0(fax 222717)


=

= --Apple-Mail-53--5223340-- ========================================================================= Date: Tue, 29 Jan 2008 16:41:24 -0500 Reply-To: FSL - FMRIB's Software Library <
[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Wen-Ching Liu <[log in to unmask]> Subject: display zstats in standard space MIME-version: 1.0 Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed Dear All: When running a single subject session, the thres_stats is in data space, not registered to the standard space. Is there any way to obtain a thres_stats in standard space even running a single subject? Thanks, Wen Wen-Ching Liu, Ph.D. Assistant Professor Functional Imaging Laboratory Department of Radiology University of Medicine and Dentistry of New Jersey-New Jersey Medical School 973-972-2281/fax: 973-972-0836 http://njms.umdnj.edu/departments/radiology/fmri/index.cfm ========================================================================= Date: Tue, 29 Jan 2008 14:13:49 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephane Jacobs <[log in to unmask]> Subject: Re: display zstats in standard space In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Wen, Yes, you can use the renderhighres tool - see http://www.fmrib.ox.ac.uk/fsl/feat5/programs.html Best Stephane Wen-Ching Liu wrote: > Dear All: > > When running a single subject session, the thres_stats is in > data space, not registered to the standard space. Is there any > way to obtain a thres_stats in standard space even running a single > subject? > > Thanks, > > > > Wen > > > Wen-Ching Liu, Ph.D. > > Assistant Professor > Functional Imaging Laboratory > Department of Radiology > University of Medicine and Dentistry > of New Jersey-New Jersey Medical School > > 973-972-2281/fax: 973-972-0836 > http://njms.umdnj.edu/departments/radiology/fmri/index.cfm > > -- ::::::::::::::::::::::::::::::::::::::::::::::::::: Stephane Jacobs Postdoctoral Research Associate Human Neuroimaging and Transcranial Stimulation Lab Department of Psychology 1227 University of Oregon Eugene, OR 97403 - USA Email: [log in to unmask] Tel: (1) 541-346-4184 ::::::::::::::::::::::::::::::::::::::::::::::::::: ========================================================================= Date: Tue, 29 Jan 2008 15:29:06 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Jeanette Mumford <[log in to unmask]> Subject: Re: Mixed Anova 2x2 In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_17272_30868818.1201649346231" ------=_Part_17272_30868818.1201649346231 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Jonathan, A matrix is rank deficient if one column is a linear combination of other columns and since -sj1-sj2+sj3+sj4=gender, that's where the rank deficiency comes from. In other words, since you're already modeling a separate mean for each subject, you can't also model a mean effect for each gender. One solution I see is to remove your gender EV, but keep the rest of your model the same. If you're interested in the difference males-females you'd use the contrast -sj1-sj2+sj3+sj4, likewise the female mean would be sj1+sj2 and the male mean would be sj3+sj4. The interaction is still modeled as you have it. Jeanette On Jan 29, 2008 10:01 AM, Jonathan Hakun <[log in to unmask]> wrote: > I see this is a popular question -- and have tried to apply the help given > to other folks, but I keep hitting a wall... > > I've used the 2x2 ANOVA design in the FEAT manual with success. (my model > = > Gender x Stimulus type (2 types, A and B); 4 subjects for sake of > argument). > > If I assume independent measures for both factors and use the example > model > (below, a 4 sj example of the model I used) I encounter no errors: > > EV1 EV2 EV3 EV4 > input COPE Group Stim Gender Interaction Mn > Female_sj1_stimA 1 -1 -1 1 1 > Female_sj2_stimA 1 -1 -1 1 1 > Male_sj3_stimA 1 -1 1 -1 1 > Male_sj4_stimA 1 -1 1 -1 1 > Female_sj1_stimB 1 1 -1 -1 1 > Female_sj2_stimB 1 1 -1 -1 1 > Male_sj3_stimB 1 1 1 1 1 > Male_sj4_stimB 1 1 1 1 1 > > The issue is, as you may have noticed -- my group is not 8 independent > subjects, rather 4 subjects with a repeated measure (stimulus) and an > independent factor (gender). I'd like to model out within subject > variability: i.e. like the paired t-test. > > I see this was recommended to several people asking a similar question. > > This model looks like: > > EV1 EV2 EV3 EV4 EV5 EV6 EV7 > inputCOPE Group Stim Gender Interaction sj1 sj2 sj3 sj4 > Fem_sj1_stimA 1 -1 -1 1 1 0 0 0 > > Fem_sj2_stimA 1 -1 -1 1 0 1 0 0 > > Male_sj3_stimA 1 -1 1 -1 0 0 1 0 > > Male_sj4_stimA 1 -1 1 -1 0 0 0 1 > > Fem_sj1_stimB 1 1 -1 -1 1 0 0 0 > > Fem_sj2_stimB 1 1 -1 -1 0 1 0 0 > > Male_sj3_stimB 1 1 1 1 0 0 1 0 > > Male_sj4_stimB 1 1 1 1 0 0 0 1 > > > I assume that this accounts for the dependence of inputs 1 and 5, 2 and 6, > and so on. > > Problem I run into is everytime I try and use this model it reports a rank > deficient error. > > Any ideas on what might I be missing? > Thank you, > ~Jonathan > ------=_Part_17272_30868818.1201649346231 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Jonathan,

A matrix is rank deficient if one column is a linear combination of other columns and since -sj1-sj2+sj3+sj4=gender, that's where the rank deficiency comes from.  In other words, since you're already modeling a separate mean for each subject, you can't also model a mean effect for each gender. 

One solution I see is to remove your gender EV, but keep the rest of your model the same.  If you're interested in the difference males-females you'd use the contrast -sj1-sj2+sj3+sj4, likewise the female mean would be sj1+sj2 and the male mean would be sj3+sj4.  The interaction is still modeled as you have it.

Jeanette


On Jan 29, 2008 10:01 AM, Jonathan Hakun <[log in to unmask]> wrote:
I see this is a popular question -- and have tried to apply the help given
to other folks, but I keep hitting a wall...

I've used the 2x2 ANOVA design in the FEAT manual with success. (my model =
Gender x Stimulus type (2 types, A and B); 4 subjects for sake of argument).

If I assume independent measures for both factors and use the example model
(below, a 4 sj example of the model I used) I encounter no errors:

                         EV1    EV2       EV3      EV4
input COPE        Group  Stim  Gender  Interaction  Mn
Female_sj1_stimA   1     -1      -1         1        1
Female_sj2_stimA   1     -1      -1         1        1
Male_sj3_stimA     1     -1       1        -1        1
Male_sj4_stimA     1     -1       1        -1        1
Female_sj1_stimB   1      1      -1        -1        1
Female_sj2_stimB   1      1      -1        -1        1
Male_sj3_stimB     1      1       1         1        1
Male_sj4_stimB     1      1       1         1        1

The issue is, as you may have noticed -- my group is not 8 independent
subjects, rather 4 subjects with a repeated measure (stimulus) and an
independent factor (gender).  I'd like to model out within subject
variability: i.e. like the paired t-test.

I see this was recommended to several people asking a similar question.

This model looks like:

                      EV1    EV2       EV3      EV4  EV5  EV6  EV7
inputCOPE      Group  Stim  Gender  Interaction  sj1  sj2  sj3  sj4
Fem_sj1_stimA   1      -1     -1         1        1    0    0    0

Fem_sj2_stimA   1      -1     -1         1        0    1    0    0

Male_sj3_stimA  1      -1      1        -1        0    0    1    0

Male_sj4_stimA  1      -1      1        -1        0    0    0    1

Fem_sj1_stimB   1       1     -1        -1        1    0    0    0

Fem_sj2_stimB   1       1     -1        -1        0    1    0    0

Male_sj3_stimB  1       1      1         1        0    0    1    0

Male_sj4_stimB  1       1      1         1        0    0    0    1


I assume that this accounts for the dependence of inputs 1 and 5, 2 and 6,
and so on.

Problem I run into is everytime I try and use this model it reports a rank
deficient error.

Any ideas on what might I be missing?
Thank you,
~Jonathan

------=_Part_17272_30868818.1201649346231-- ========================================================================= Date: Tue, 29 Jan 2008 19:19:47 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Matt Glasser <[log in to unmask]> Subject: Re: Philips Scaling In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit What do you mean by seeds target masks? The output of seed classification mode are probabilities in each seed voxel of projection to each target. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Anastasia Ford Sent: Tuesday, January 29, 2008 1:47 PM To: [log in to unmask] Subject: Re: [FSL] Philips Scaling Hello, I have checked the output of dtifit and the tensor fit looks correct. The tractography images generated using waypoint seed masks look anatomically correct. However, the output of the tract connectivity analysis (classification targets) does not contain the seeds_to_target volumes, only the seeds_to_target masks and the fdt_paths image. Any help will be greatly appreciated. Sincerely, Anastasia ========================================================================= Date: Wed, 30 Jan 2008 16:59:24 +0900 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: [log in to unmask] Subject: tbss - FA comparison between one patient and a control group Mime-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit Hi all, I have one patient (n=1) and would like to compare his FA with a group of controls (n=5). I have been through all tbss steps as described in http://www.fmrib.ox.ac.uk/fsl/tbss/index.html (using the template FMRIB58 for corregistration). I am now ready to run the statistics but I am not sure about which procedure is the correct one. My problem is that I am trying to compare 1 patient with a whole group. Does anyone know which test can give me a map of FA differences between the patient and controls? I thank you in advance, Peace, Joyce! -- joyce ========================================================================= Date: Wed, 30 Jan 2008 08:29:55 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: tbss - FA comparison between one patient and a control group In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi - you can just set up your model like you would for any group comparison. I.e. 1 0 1 0 1 0 1 0 1 0 0 1 contrast 1 -1 -1 1 The problem is that you cannot use randomise, as you don't have enough potential permutations (only 5!), so you will have to assume normality and just use the t-maps from a single iteration of randomise. Multiple comparison correction is obviously a bit of a problem if you can't use permutation testing though, so you will need pretty high t- values to convince a reviewer. T On 30 Jan 2008, at 07:59, [log in to unmask] wrote: > Hi all, > > I have one patient (n=1) and would like to compare his FA with > a group of controls (n=5). > I have been through all tbss steps as described in > http://www.fmrib.ox.ac.uk/fsl/tbss/index.html (using the > template FMRIB58 for corregistration). > I am now ready to run the statistics but I am not sure about > which procedure is the correct one. My problem is that I am > trying to compare 1 patient with a whole group. > Does anyone know which test can give me a map of FA differences > between the patient and controls? > > I thank you in advance, > > Peace, > Joyce! > > -- > joyce > ========================================================================= Date: Wed, 30 Jan 2008 08:41:34 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: FSLView timeseries, combined runs In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit This just shows the cope outputs for each run concatenated through time. Cheers T On 29 Jan 2008, at 18:02, Carlos Faraco wrote: > I was just wondering how to interpet the linear function presented > for the > timeseries of combined runs for one subject? In other words, higher- > level > stats for the runs using FE. > > Thanks. > ========================================================================= Date: Wed, 30 Jan 2008 08:42:54 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: Smoothing SPM vs FSL In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi - Command-line smoothing is now integrated into fslmaths. You can use any kernel you want with the -kernel option. Cheers T On 29 Jan 2008, at 18:22, Carlos Faraco wrote: > I am wondering is there is a way to specify the smoothing kernel as > is done > in SPM? For example, can I specify a 5 x 7.5 x 7.5 kernel, instead > of just 5? > > I know there is suppossed to be a command line smoothing option, > ip, but I > cannot find it in my install (4.0.3, CentOS4-32bit) and from what > I've read > here, it does not appear able to do the above. > > Thanks, > > Carlos > ========================================================================= Date: Wed, 30 Jan 2008 09:51:39 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Juergen Haenggi <[log in to unmask]> Subject: Re: tbss - FA comparison between one patient and a control group In-Reply-To: <[log in to unmask]> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi Joyce The most appropriate statistical method is a z-value transformation. I recommend to produce a mean and sd image from your control subjects and the compute voxel-wise z-values by z = ((FA map patient - mean FA map controls)/(sd FA map controls)). Then you can threshold this map. Best regards Juergen PS: I would not restrict the FA values only on the skeleton produced by TBSS. Instead leave the TBSS stream after tbss_3_postreg and analyze the whole brain, i.e. All FA values > 2000. Regards Juergen On 30.1.2008 8:59 Uhr, "[log in to unmask]" <[log in to unmask]> wrote: > Hi all, > > I have one patient (n=1) and would like to compare his FA with > a group of controls (n=5). > I have been through all tbss steps as described in > http://www.fmrib.ox.ac.uk/fsl/tbss/index.html (using the > template FMRIB58 for corregistration). > I am now ready to run the statistics but I am not sure about > which procedure is the correct one. My problem is that I am > trying to compare 1 patient with a whole group. > Does anyone know which test can give me a map of FA differences > between the patient and controls? > > I thank you in advance, > > Peace, > Joyce! ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [log in to unmask] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- ========================================================================= Date: Wed, 30 Jan 2008 09:18:53 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: EV Setup, just need verification In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi Carlos - You should not model the baseline. You should only model the active conditions. These will then be compared against the implicit baseline in the GLM analysis. So you need one EV for OSPAN and one EV for Arith. The contrasts are then 1 0 for OSPAN > Base 0 1 for Arith > Base 1 -1 for OSPAN > Arith -1 1 for Arith > Base. Cheers T On 28 Jan 2008, at 20:41, Carlos Faraco wrote: > I am setting EVs and just wanted to make sure I am doing this > correctly. > > The study consists of an OSPAN (working memory task) portion), an > arithmetic > portion, and a baseline. It goes as follows. > > -----------I------------I ---------I > --------------- > OSPAN 30s Response 15s Arith 30s Repeat > > ----------I ---------I > Base 30s Base 30s > > So, the task w/ the response and the arithmetic are done 3 times > total, and > baseline is done 6 times. I am not interested in including the > response > condition in the analysis (this is just to verify they are paying > attention, > at least for now). > > I have setup the EVs as follows: > > For the OSPAN: Skip = 0s, Off = 105s, On = 30s, Phase = 105s, Stop > = -1. > > For Baseline, I set up two EVs because the intervals vary, so the > Baseline > after the OSPAN is: Skip = 0, Off= 105, On = 30, Phase = 60, Stop = > -1. > > Baseline after Arithemtic is: Skip = 0, Off = 105, On = 30, Phase = > 0, Stop > = -1. > > Arithemtic = Skip = 0, Off = 105, On = 30, Phase = 30, Stop = -1. > > Is this correct? Also, when I set up my contrast for OSPAN vs. > Baseline, I > choose OSPAN = 1, Baseline 1 = -.5, and Baseline 2 = -.5. This > should make > it as if there was just one baseline, correct? Or are the statistics > affected differently somehow? > > Lastly, I am setting the highpass filter at 135; this is the total > time for > one cycle. Is this too high though? > > Thanks. > ========================================================================= Date: Wed, 30 Jan 2008 09:20:59 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: Fsl-vbm and First In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: multipart/alternative; boundary=Apple-Mail-116-39360414 --Apple-Mail-116-39360414 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed H Jeff - I think this is fine. Cheers T On 28 Jan 2008, at 20:36, Jeffrey Spielberg wrote: > Hi, great, thanks. I have another question about Fsl-vbm/Randomise > usage. Are there some designs that are appropriate for use in Feat > but not in Randomise (in Fsl-vbm in particular)? Specifically, we > want to use a one group design correlating two questionnaire scores > with grey-matter. We set this up similarly to the example on the > Feat webpage, for example, > > Group Mean Quest_1 Quest_2 > 1 1 2.6 9.4 > 1 1 7.3 5.7 > 1 1 4.9 4.3 > 1 1 4.6 3.6 > 1 1 9.2 8.6 > > with one cope for the mean, one for each questionnaire, and one for > the difference between the two questionnaires. Is this design > appropriate for Randomise/Fsl-vbm? Thanks, > Jeff > > On Jan 26, 2008 1:21 AM, Steve Smith <[log in to unmask]> wrote: > Hi, > > On 24 Jan 2008, at 21:57, Jeff Spielberg wrote: > > > Hi, I have a couple of questions regarding Fsl-vbm and First. The > > scans we > > have been using for both have some signal loss superiorly and > > inferiorly. > > Due to this we do not get a good extraction with Bet (brain is > > excluded top > > and bottom). We have been dealing with this issue by correcting for > > the > > bias field with Fast and have gotten good results. Since Fsl-vbm > > applies > > Bet we have entered bias-corrected scans into our Vbm analyses. > > However, > > will this cause problems when segmentation is done in > > fslvbm_2_template (or > > anywhere else in Fsl-vbm)? > > The bias correction is fine, but if you have already run BET that > might compromise the FSL-VBM when you feed the already-betted image > into FSL-VBM. The simple solution is to apply the bias field > correction to the original image and feed that into FSL-VBM. That > should be fine then. > > > Also, is it best to use the bias-corrected scans in First as well? > > It seems > > possible that not correcting scan intensities for the bias field > will > > interfere with the identification of structures (since First uses > > intensities in this process), thanks, > > If it looks like the bias field correction has improved the image then > it should be better to feed the corrected image into FIRST than the > original. > > Cheers, Steve. > > > > > > Jeff > > > > > ---------------------------------------------------------------------- > ----- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > ---------------------------------------------------------------------- > ----- > --Apple-Mail-116-39360414 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 H Jeff -=A0
I think this is fine.

Cheers

T
On 28 Jan = 2008, at 20:36, Jeffrey Spielberg wrote:

Hi, great, = thanks.=A0 I have another question about Fsl-vbm/Randomise usage.=A0 Are = there some designs that are appropriate for use in Feat but not in = Randomise (in Fsl-vbm in particular)?=A0 Specifically, we want to use a = one group design correlating two questionnaire scores with grey-matter.=A0= We set this up similarly to the example on the Feat webpage, for = example,

Group=A0=A0=A0 Mean=A0=A0=A0 Quest_1=A0=A0=A0 = Quest_2
1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 2.6=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 9.4
1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= 1=A0=A0=A0=A0=A0=A0=A0=A0=A0 7.3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 5.7
1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 4.9=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.3
1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= 1=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.6=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 3.6
1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 9.2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 8.6

with one cope for the = mean, one for each questionnaire, and one for the difference between the = two questionnaires.=A0 Is this design appropriate for = Randomise/Fsl-vbm?=A0 Thanks,
Jeff

On Jan 26, 2008 1:21 AM, Steve Smith <[log in to unmask]> = wrote:
Hi,

On 24 Jan 2008, at 21:57, Jeff = Spielberg wrote:

> Hi, I have a couple of questions regarding = Fsl-vbm and First. =A0The
> scans we
> have been using for = both have some signal loss superiorly and
> inferiorly.
> = Due to this we do not get a good extraction with Bet (brain is
> = excluded top
> and bottom). =A0We have been dealing with this = issue by correcting for
> the
> bias field with Fast and = have gotten good results. =A0Since Fsl-vbm
> applies
> Bet = we have entered bias-corrected scans into our Vbm analyses.
> = However,
> will this cause problems when segmentation is done = in
> fslvbm_2_template (or
> anywhere else in Fsl-vbm)?
=
The bias correction is fine, but if you have already run BET = that
might compromise the FSL-VBM when you feed the already-betted = image
into FSL-VBM. The simple solution is to apply the bias = field
correction to the original image and feed that into FSL-VBM. = That
should be fine then.

> Also, is = it best to use the bias-corrected scans in First as well?
> It = seems
> possible that not correcting scan intensities for the bias = field will
> interfere with the identification of structures = (since First uses
> intensities in this process), = thanks,

If it looks like the bias field correction has = improved the image then
it should be better to feed the corrected = image into FIRST than the
original.

Cheers, Steve.
=

>
> = Jeff
>


--------------------------------------------------= -------------------------
Stephen M. Smith, Professor of Biomedical = Engineering
Associate Director, =A0Oxford University FMRIB Centre
=
FMRIB, JR Hospital, Headington, Oxford =A0OX3 9DU, UK
+44 (0) = 1865 222726 =A0(fax 222717)
[log in to unmask] =A0 =A0http://www.fmrib.ox.ac.uk/~steve
= --------------------------------------------------------------------------= -


= --Apple-Mail-116-39360414-- ========================================================================= Date: Wed, 30 Jan 2008 09:27:13 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: older version of fsl for cygwin In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit It would be very difficult to make this work because of compatibility problems between different versions of cygwin.. T On 28 Jan 2008, at 18:31, Pom Sailasuta wrote: > Hi, > > Can I still get an older fsl version compatible with cygwin? > > thanks > ========================================================================= Date: Wed, 30 Jan 2008 09:28:44 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Mark Jenkinson <[log in to unmask]> Subject: Re: about flirt In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi, If it is an average then the way you rethreshold your mask after transforming it can be very important. For small binary masks there can be a large difference between rethresholding at low levels (near zero) or high values (near one) as this will include/exclude contributions of voxels just outside the original ROI. For large masks this should be less important. Try rethresholding near 1 (if you are not already) and see if the values are more consistent. All the best, Mark On 29 Jan 2008, at 08:04, Li Jiang wrote: > Hi, > > It is an average over an ROI. > > First I genarate a ROI mask on the subject image. Then apply the > subject to MNI transformation matrix (.mat) to the ROI-to-MNI > volume.Then measure the intensity of ROI on the subject image and that > of ROI-to-MNI on the subject-to-MNI image with Matlab. > > Thanks. > > Li > > 2008/1/28, Mark Jenkinson <[log in to unmask]>: >> Hi, >> >> This still doesn't answer the important question: >> >> *HOW* are you measuring these intensities? >> >> Is it an average over an ROI? >> Is it from a single voxel? >> >> If it is a single voxel, is it a peak value surrounded by >> much smaller (even negative) values? >> >> If it is an ROI, how are you generating the ROIs and >> creating the average? >> >> All the best, >> Mark >> >> >> On 27 Jan 2008, at 05:11, Li Jiang wrote: >> >>> Hi, >>> >>> For example, with the methods I mentioned above, for one subject,the >>> intensity of the subjects data is 52.4554, but that of the subjects >>> data in MNI-space is only 36.1254. For another subject, the >>> intensity >>> is 46.7794 and 43.8556, which is similar. I don't know how to >>> explain >>> the different.I know that interpolation will affect a little. >>> Compare >>> trilinear and nearest neighbour, which is better? >>> >>> Thank you! >>> >>> Li >>> >>> 2008/1/26, Mark Jenkinson <[log in to unmask]>: >>>> Hi, >>>> >>>> Those commands are fine for flirt. >>>> But how are you judging that the intensity is decreased? >>>> >>>> Could it be due to including slightly different voxels on the >>>> edge of your ROI mask? When you transform a binary >>>> mask you need to rethreshold it afterwards to decide >>>> whether to be inclusive of small partial volume overlap >>>> (of the mask and the new voxels) or exclusive. >>>> This could be the source of changes in average intensity >>>> over the ROI. In addition, trilinear interpolation will do >>>> some smoothing of the image a little - which affects sharp >>>> peaks particularly. >>>> >>>> All the best, >>>> Mark >>>> >>>> >>>> On 25 Jan 2008, at 17:24, Li Jiang wrote: >>>> >>>>> Hi, >>>>> >>>>> That's what I have done. >>>>> >>>>> * get the transformation matrix file (*.mat) that transforms >>>>> subject-space CBF >>>>> volume to MNI-space >>>>> * get ROI volume in subject-space >>>>> * transform ROI volume into MNI-space using the same *.mat file >>>>> * use flirt: >>>>> >>>>> flirt -in -ref -out -applyxfm >>>>> -init >>>>> >>>>> Thanks. >>>>> >>>>> Li >>>>> >>>>> 2008/1/25, Steve Smith <[log in to unmask]>: >>>>>> Hi, >>>>>> >>>>>> I'm still not sure you have a problem. How are you judging >>>>>> that the >>>>>> intensity is decreased? >>>>>> >>>>>> Cheers. >>>>>> >>>>>> >>>>>> On 22 Jan 2008, at 06:28, Li Jiang wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Thank you very much. I still have a question. The original >>>>>>> subject >>>>>>> image is epi sequence.After I transform this image to highres T1 >>>>>>> image >>>>>>> and then to MNI-space, the intensity of the transformed sub2mni >>>>>>> image >>>>>>> decreased compare to the original epi image. When transform, >>>>>>> I use >>>>>>> trilinear interpolation and cost function is correlation >>>>>>> ratio. >>>>>>> How >>>>>>> can I improve this problem? Which interpolation method and cost >>>>>>> function should I apply? >>>>>>> >>>>>>> Li >>>>>>> >>>>>>> 2008/1/21, Steve Smith <[log in to unmask]>: >>>>>>>> Hi, >>>>>>>> >>>>>>>> avscale gives you a whole set of different pieces of >>>>>>>> information >>>>>>>> about >>>>>>>> the spatial affine transform, including the average scaling >>>>>>>> (size) >>>>>>>> change. It does not tell you anything about intensities. On >>>>>>>> average, >>>>>>>> in general, intensities don't change upon resampling, though of >>>>>>>> course >>>>>>>> any given voxel will change! >>>>>>>> >>>>>>>> Cheers. >>>>>>>> >>>>>>>> >>>>>>>> On 19 Jan 2008, at 15:12, Li Jiang wrote: >>>>>>>> >>>>>>>>> Dear Steve Smith, >>>>>>>>> >>>>>>>>> I use fsl to process the functional MR data. It is a great >>>>>>>>> software. >>>>>>>>> To process the data, I first transform the EPI (subject image) >>>>>>>>> data >>>>>>>>> to T1 volume then to MNI_space with affine transformation. And >>>>>>>>> I'll >>>>>>>>> measure the absolute value from the images have been >>>>>>>>> coregistered to >>>>>>>>> MNI-space . I learned from the lectures and noticed the >>>>>>>>> avscale >>>>>>>>> for >>>>>>>>> Inter-subject Registration. I wonder what's the scale mean. >>>>>>>>> If the >>>>>>>>> signal intensity of the subject image will change after affine >>>>>>>>> transformation or global intra-subject transformation. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Best regards. >>>>>>>>> >>>>>>>>> Li Jiang >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> --------------------------------------------------------------- >>>>>>>> -- >>>>>>>> -- >>>>>>>> -------- >>>>>>>> Stephen M. Smith, Professor of Biomedical Engineering >>>>>>>> Associate Director, Oxford University FMRIB Centre >>>>>>>> >>>>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>>>>>> +44 (0) 1865 222726 (fax 222717) >>>>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>>>>>>> --------------------------------------------------------------- >>>>>>>> -- >>>>>>>> -- >>>>>>>> -------- >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> -- >>>>>> -- >>>>>> ------ >>>>>> Stephen M. Smith, Professor of Biomedical Engineering >>>>>> Associate Director, Oxford University FMRIB Centre >>>>>> >>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>>>> +44 (0) 1865 222726 (fax 222717) >>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >>>>>> ----------------------------------------------------------------- >>>>>> -- >>>>>> -- >>>>>> ------ >>>>>> >>>>> >>>> >>> >> > ========================================================================= Date: Wed, 30 Jan 2008 12:30:42 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?iso-8859-1?q?Gwena=EBlle=20DOUAUD?= <[log in to unmask]> Subject: RE : Re: [FSL] tbss - FA comparison between one patient and a control group In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Juergen, could you please specify why you would recommend not to "restrict the FA values on the skeleton"?=20 The only downside I can think of about TBSS is the fact that it's only looking at the white matter, and not at the subcortical grey matter in which anyway the FA values can be lower than 2000, so would not be included in your recommended analysis...=20 For the study of white matter, using the FA values on the skeleton can only improve the interpretability of your results, without mentioning the fact that you increase the sensitivity of your results as well.=20 Cheers, Gwenaelle --- Juergen Haenggi <[log in to unmask]> a =E9crit : > Hi Joyce >=20 > The most appropriate statistical method is a z-value > transformation. I > recommend to produce a mean and sd image from your > control subjects and the > compute voxel-wise z-values by z =3D ((FA map patient > - mean FA map > controls)/(sd FA map controls)). Then you can > threshold this map. >=20 > Best regards > Juergen >=20 > PS: I would not restrict the FA values only on the > skeleton produced by > TBSS. Instead leave the TBSS stream after > tbss_3_postreg and analyze the > whole brain, i.e. All FA values > 2000. >=20 > Regards > Juergen >=20 >=20 > On 30.1.2008 8:59 Uhr, "[log in to unmask]" > <[log in to unmask]> wrote: >=20 > > Hi all, > >=20 > > I have one patient (n=3D1) and would like to compare > his FA with > > a group of controls (n=3D5). > > I have been through all tbss steps as described in > > http://www.fmrib.ox.ac.uk/fsl/tbss/index.html > (using the > > template FMRIB58 for corregistration). > > I am now ready to run the statistics but I am not > sure about > > which procedure is the correct one. My problem is > that I am > > trying to compare 1 patient with a whole group. > > Does anyone know which test can give me a map of > FA differences > > between the patient and controls? > >=20 > > I thank you in advance, > >=20 > > Peace, > > Joyce! >=20 >=20 > ----------------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > Division of Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > [log in to unmask] (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > ----------------------------------------------------------- >=20 ___________________________________________________________________= __________=20 Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! M= ail http://mail.yahoo.fr ========================================================================= Date: Wed, 30 Jan 2008 11:53:44 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Matthew Webster <[log in to unmask]> Subject: Re: FEAT gui error: balloonhelp? In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi, This is an occasional bug that we have had great difficulty replicating on our local systems - can you let me know what version of FSL you're using and on what platform? Also does the error occur on pressing a particular button or tool? Regards Matthew > Dear FSLers, > > I seem to keep having an error as I finish setting up the stats fr > a first level analysis, and I keep on getting the following error, > which seems to relate to the balloon-help > > bad window path name ".dialog1.f.viewport.f.btn" > bad window path name ".dialog1.f.viewport.f.btn" > while executing > "winfo rootx $win" > (procedure "balloonhelp_show" line 7) > invoked from within > "balloonhelp_show .dialog1.f.viewport.f.btn" > ("after" script) > > it seems to me to be a completely benign error -- that has to do > with the GUI, not with the contents of the analysis. > > Is this the case? Is there an obvious way to avoid it (errors > always give me chills.. :)) other than turning off the balloon help > I presume? > > cheers > > martin > ========================================================================= Date: Wed, 30 Jan 2008 12:01:59 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Giovanni Giulietti <[log in to unmask]> Subject: PICA operation Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1252" Hi, =20 I used MELODIC ICA on several fmri data sets. I was wondering the relevance of performing basic mathematical operations= =20 such as adding and meaning on these raw-z transformed IC maps=20 (melodic_IC.nii.gz). In other words, is it correct to consider them as z-= maps with the knowledge that they better fit the GGM (Gamma Gaussian=20 Mixture) model?=20 Thanks for your precision. Giovanni. ========================================================================= Date: Wed, 30 Jan 2008 12:16:18 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Martin M Monti <[log in to unmask]> Subject: Re: FEAT gui error: balloonhelp? In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Matthew, I'm running FSL 4.0.1 (and the associated FEAT 5.91), on a linux machine using Red Hat Enterprise 4 (and same problem happened when using RH Enterprise 3). I get the error after clicking on the Model image that appears when you click on DONE (or VIEW DESIGN) from the Full Model Setup window, in the Stats tab of FEAT. However, turning off the balloon helper is sufficient not to get the error anymore. let me know if there is any other info that may be of use, cheers martin Matthew Webster wrote: > Hi, > This is an occasional bug that we have had great difficulty > replicating on our local systems - can you let me know what version of > FSL you're using and on what platform? Also does the error occur on > pressing a particular button or tool? > > Regards > > Matthew > >> Dear FSLers, >> >> I seem to keep having an error as I finish setting up the stats fr a >> first level analysis, and I keep on getting the following error, >> which seems to relate to the balloon-help >> >> bad window path name ".dialog1.f.viewport.f.btn" >> bad window path name ".dialog1.f.viewport.f.btn" >> while executing >> "winfo rootx $win" >> (procedure "balloonhelp_show" line 7) >> invoked from within >> "balloonhelp_show .dialog1.f.viewport.f.btn" >> ("after" script) >> >> it seems to me to be a completely benign error -- that has to do with >> the GUI, not with the contents of the analysis. >> >> Is this the case? Is there an obvious way to avoid it (errors always >> give me chills.. :)) other than turning off the balloon help I presume? >> >> cheers >> >> martin >> ========================================================================= Date: Wed, 30 Jan 2008 14:05:25 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Serge Rombouts <[log in to unmask]> Subject: Higher level FEAT: Multi-Session & Multi-Subject Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, I think the example on the FSL website of how to do a ' Multi-Session & Multi-Subject (Repeated measures - three level)' analysis has recently changed. The current example shows how to first combine sessions separately for each subject using a fixed effects analysis. If I remember correctly, the old example showed how to do this using a mixed effects analysis, with all subjects and all sessions as inputs. I am not sure whether I understand why the example has changed. Is it not better to properly model between-session variance, as presented in the old example? Cheers, Serge. Serge A. Rombouts, PhD Leiden Institute for Brain and Cognition (LIBC) Leiden University - Institute for Psychological Research (LU-IPR) Department of Radiology, Leiden University Medical Center Postzone C2-S P.O. Box 9600 2300 RC Leiden The Netherlands www.libc-leiden.nl ========================================================================= Date: Wed, 30 Jan 2008 13:52:45 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Mark Woolrich <[log in to unmask]> Subject: Re: Higher level FEAT: Multi-Session & Multi-Subject In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-101-55666728 --Apple-Mail-101-55666728 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi Serge, You are correct - this has changed. Here is some text lifted from the FSL course explaining this: If you are carrying out a mid-level analysis (e.g., cross-sessions) that will be fed into an even higher-level analysis (e.g., cross- subjects), then it could be argued that a mixed-effects analysis should be done at the mid-level. A mixed-effects analysis would assume that the sessions are randomly sampled from a "population" of sessions that that subject could produce. This includes estimation of each subject's session-to-session variance. However, it is common for only a small number of sessions to be collected for each subject, making estimation of each subject's session-to-session variance impractical. One solution to this is to assume a common session-to- session variance for all subjects, thereby providing enough data for the session-to-session variance to be estimated. However, this has a downside in that you lose information about which subjects are good (i.e. low variance) and which subjects are bad (i.e. high variance). Hence, when only a small number of sessions has been collected for each subject (say, less than 10), it is recommended that you use a fixed effects analysis at the mid-level. This in effect treats the multiple first-level sessions (for each subject) as if they were one long session. Although this does ignore the session-session variability, it is arguable that this is not of interest anyway (this is a somewhat philosophical debate). In short, fixed effect is favoured as it avoids practical problems associated with esimating the session-to-session variance (when there are not many session per subject), at the same time as maintaining information about which subjects are good and bad. Cheers, Mark. ---- Dr Mark Woolrich EPSRC Advanced Research Fellow University Research Lecturer Oxford University Centre for Functional MRI of the Brain (FMRIB), John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich On 30 Jan 2008, at 13:05, Serge Rombouts wrote: > Hi, > > I think the example on the FSL website of how to do a ' Multi- > Session & > Multi-Subject (Repeated measures - three level)' analysis has recently > changed. > > The current example shows how to first combine sessions separately > for each > subject using a fixed effects analysis. If I remember correctly, > the old > example showed how to do this using a mixed effects analysis, with all > subjects and all sessions as inputs. > > I am not sure whether I understand why the example has changed. Is > it not > better to properly model between-session variance, as presented in > the old > example? > > Cheers, > > Serge. > > > Serge A. Rombouts, PhD > Leiden Institute for Brain and Cognition (LIBC) > Leiden University - Institute for Psychological Research (LU-IPR) > Department of Radiology, Leiden University Medical Center > Postzone C2-S > P.O. Box 9600 > 2300 RC Leiden > The Netherlands > www.libc-leiden.nl > --Apple-Mail-101-55666728 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi Serge,

You are = correct - this has changed. Here is some text lifted from the FSL course = explaining this:

If you = are carrying out a mid-level analysis (e.g., cross-sessions) that will = be fed into an even higher-level analysis (e.g., cross-subjects), then = it could be argued that a mixed-effects analysis should be done at the = mid-level. A mixed-effects analysis would assume that the sessions are = randomly sampled from a "population" of sessions that that subject could = produce. This includes estimation of each subject's session-to-session = variance. However, it is common for only a small number of sessions to = be collected for each subject, making estimation of each subject's = session-to-session variance impractical. One solution to this is to = assume a common session-to-session variance for all subjects, thereby = providing enough data for the session-to-session variance to be = estimated. However, this has a downside in that you lose information = about which subjects are good (i.e. low variance) and which subjects are = bad (i.e. high variance). Hence, when only a small number of sessions = has been collected for each subject (say, less than 10), it is = recommended that you use a fixed effects analysis at the mid-level. This = in effect treats the multiple first-level sessions (for each subject) as = if they were one long session. Although this does ignore the = session-session variability, it is arguable that this is not of interest = anyway (this is a somewhat philosophical debate). In short, fixed effect = is favoured as it avoids practical problems associated with esimating = the session-to-session variance (when there are not many session per = subject), at the same time as maintaining information about which = subjects are good and bad.

Cheers, = Mark.

----
Dr Mark = Woolrich
EPSRC Advanced = Research Fellow=A0University Research Lecturer

Oxford = University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, = UK.

Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~wo= olrich



=

On 30 Jan 2008, at 13:05, Serge Rombouts = wrote:

Hi,

I think the = example on the FSL website of how to do a ' Multi-Session = &
Multi-Subject (Repeated measures = - three level)' analysis has recently

The current example shows how to first combine = sessions separately for each
subject using = a fixed effects analysis. If I remember correctly, the old
example showed how to do this using a mixed effects = analysis, with all
subjects and all sessions = as inputs.

I am not sure whether I understand why the example = has changed. Is it not
better to properly model = between-session variance, as presented in the old
example?

Cheers,

Serge. = =A0


Serge A. = Rombouts, PhD
Leiden Institute for Brain and = Cognition (LIBC)
Leiden University - Institute = for Psychological Research=A0 = (LU-IPR)
Department of Radiology, Leiden = University Medical Center
Postzone = C2-S
P.O. Box 9600
2300 RC Leiden
The = Netherlands
www.libc-leiden.nl

=

= --Apple-Mail-101-55666728-- ========================================================================= Date: Wed, 30 Jan 2008 10:21:17 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Wen-Ching Liu <[log in to unmask]> Subject: Re: display zstats in standard space In-Reply-To: <[log in to unmask]> MIME-version: 1.0 Content-type: multipart/alternative; boundary="Boundary_(ID_LH1Y7bfRzXfLPv7xFvoFeQ)" This is a multi-part message in MIME format. --Boundary_(ID_LH1Y7bfRzXfLPv7xFvoFeQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: quoted-printable Content-disposition: inline Hi Stephane=3AThank you for your reply=2E=A0 Do you think =22Renderhighr= es=22 also work for the outputof Melodic =27s =2Eica=A0dir=3FBecause whe= n I tried it=2C the program just generated a backgroundfile with no zsta= ts=A0information at all=2E=A0 Wen----- Original Message -----From=3A Ste= phane=A0Jacobs =3Csjacobs=40UOREGON=2EEDU=3EDate=3A Tuesday=2C January 2= 9=2C 2008 5=3A14 pmSubject=3A Re=3A =5BFSL=5D display zstats=A0in standa= rd spaceTo=3A FSL=40JISCMAIL=2EAC=2EUK=3E Hi Wen=2C=3E =3E Yes=2C you ca= n use the renderhighres=A0tool - see=3E http=3A//www=2Efmrib=2Eox=2Eac=2E= uk/fsl/feat5/programs=2Ehtml=3E =3E Best=3E =3E Stephane=3E =3E Wen-Chin= g Liu=A0wrote=3A=3E =3E Dear All=3A=3E =3E=3E =3E When running a single = subject session=2C the thres=5Fstats=A0is in=3E =3E data space=2C not re= gistered to the standard space=2E=A0 Is =3E there any=3E =3E way to obta= in a thres=5Fstats=A0in standard space even running a single=3E =3E subj= ect=3F=3E =3E=3E =3E Thanks=2C=3E =3E=3E =3E=3E =3E=3E =3E Wen=3E =3E=3E= =3E=3E =3E Wen-Ching Liu=2C Ph=2ED=2E=3E =3E=3E =3E Assistant Professor= =3E =3E Functional Imaging Laboratory=3E =3E Department of Radiology=3E = =3E University of Medicine and Dentistry=3E =3E of New Jersey-New Jersey= Medical School=3E =3E=3E =3E 973-972-2281/fax=3A 973-972-0836=3E =3E ht= tp=3A//njms=2Eumdnj=2Eedu/departments/radiology/fmri/index=2Ecfm=3E =3E=3E= =3E=3E =3E -- =3E =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A=3A=3A=3A=3A=3E Stephane Jacobs=3E =3E Postdoctoral Resea= rch Associate=3E Human Neuroimaging and Transcranial Stimulation Lab=3E = Department of Psychology=3E 1227 University of Oregon=3E Eugene=2C OR 97= 403 - USA=3E =3E Email=3A sjacobs=40uoregon=2Eedu=3E Tel=3A (1) 541-346-= 4184=3E =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A --Boundary_(ID_LH1Y7bfRzXfLPv7xFvoFeQ) Content-type: text/html; charset=us-ascii Content-transfer-encoding: quoted-printable Content-disposition: inline Hi Stephane=3A=3Cbr=3E=3Cbr=3EThank you for your reply=2E=26nbsp=3B =3Cb= r=3EDo you think =22Renderhighres=22 also work for the output=3Cbr=3Eof = Melodic =27s =2Eica=26nbsp=3Bdir=3F=3Cbr=3E=3Cbr=3EBecause when I tried = it=2C the program just generated a background=3Cbr=3Efile with no zstats= =26nbsp=3Binformation at all=2E=26nbsp=3B =3Cbr=3E=3Cbr=3EWen=3Cbr=3E=3C= br=3E----- Original Message -----=3Cbr=3EFrom=3A Stephane=26nbsp=3BJacob= s =26lt=3Bsjacobs=40UOREGON=2EEDU=26gt=3B=3Cbr=3EDate=3A Tuesday=2C Janu= ary 29=2C 2008 5=3A14 pm=3Cbr=3ESubject=3A Re=3A =5BFSL=5D display zstat= s=26nbsp=3Bin standard space=3Cbr=3ETo=3A FSL=40JISCMAIL=2EAC=2EUK=3Cbr=3E= =3Cbr=3E=26gt=3B Hi Wen=2C=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B Yes=2C you c= an use the renderhighres=26nbsp=3Btool - see=3Cbr=3E=26gt=3B http=3A//ww= w=2Efmrib=2Eox=2Eac=2Euk/fsl/feat5/programs=2Ehtml=3Cbr=3E=26gt=3B =3Cbr= =3E=26gt=3B Best=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B Stephane=3Cbr=3E=26gt=3B= =3Cbr=3E=26gt=3B Wen-Ching Liu=26nbsp=3Bwrote=3A=3Cbr=3E=26gt=3B =26gt=3B= Dear All=3A=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =26gt=3B When runn= ing a single subject session=2C the thres=5Fstats=26nbsp=3Bis in=3Cbr=3E= =26gt=3B =26gt=3B data space=2C not registered to the standard space=2E=26= nbsp=3B Is =3Cbr=3E=26gt=3B there any=3Cbr=3E=26gt=3B =26gt=3B way to ob= tain a thres=5Fstats=26nbsp=3Bin standard space even running a single=3C= br=3E=26gt=3B =26gt=3B subject=3F=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B= =26gt=3B Thanks=2C=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =26gt=3B=3C= br=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =26gt=3B Wen=3Cbr=3E=26gt=3B =26g= t=3B=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =26gt=3B Wen-Ching Liu=2C = Ph=2ED=2E=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =26gt=3B Assistant Pr= ofessor=3Cbr=3E=26gt=3B =26gt=3B Functional Imaging Laboratory=3Cbr=3E=26= gt=3B =26gt=3B Department of Radiology=3Cbr=3E=26gt=3B =26gt=3B Universi= ty of Medicine and Dentistry=3Cbr=3E=26gt=3B =26gt=3B of New Jersey-New = Jersey Medical School=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =26gt=3B = 973-972-2281/fax=3A 973-972-0836=3Cbr=3E=26gt=3B =26gt=3B http=3A//njms=2E= umdnj=2Eedu/departments/radiology/fmri/index=2Ecfm=3Cbr=3E=26gt=3B =26gt= =3B=3Cbr=3E=26gt=3B =26gt=3B=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B -- =3Cbr=3E= =26gt=3B =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A=3A=3Cbr=3E=26gt=3B Stephane Jacobs=3Cbr=3E=26gt=3B =3Cbr= =3E=26gt=3B Postdoctoral Research Associate=3Cbr=3E=26gt=3B Human Neuroi= maging and Transcranial Stimulation Lab=3Cbr=3E=26gt=3B Department of Ps= ychology=3Cbr=3E=26gt=3B 1227 University of Oregon=3Cbr=3E=26gt=3B Eugen= e=2C OR 97403 - USA=3Cbr=3E=26gt=3B =3Cbr=3E=26gt=3B Email=3A sjacobs=40= uoregon=2Eedu=3Cbr=3E=26gt=3B Tel=3A (1) 541-346-4184=3Cbr=3E=26gt=3B =3A= =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A=3A= =3A=3A --Boundary_(ID_LH1Y7bfRzXfLPv7xFvoFeQ)-- ========================================================================= Date: Wed, 30 Jan 2008 15:24:43 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: Re: EV Setup, just need verification Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Ahhhh, that's right. I knew something didn't seem right.=20 Is the highpass filter of 135s correct? Thank you. ========================================================================= Date: Wed, 30 Jan 2008 15:33:30 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: Re: FSLView timeseries, combined runs Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" So basically it is showing in which run the voxel was most active? In oth= er words, is the half-way point of that time series represents the end/beginning of the runs? Is there any way to see what the avg activity of the runs is across each volume, such as is shown for the individual runs? Thank you for all your replies today. ========================================================================= Date: Wed, 30 Jan 2008 16:25:52 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Donna Lloyd <[log in to unmask]> Organization: University of Manchester Subject: error report on pre-stats MIME-Version: 1.0 Content-Type: multipart/mixed; boundary=-------652b4325652b4325 This is a multi-part message in MIME format ---------652b4325652b4325 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Hi, I get an error message when running pre-stats in Feat but don't know what t= he problem is. Would you be able to take a look at the attached report and = give me a diagnosis? 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========================================================================= Date: Wed, 30 Jan 2008 16:30:40 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: EV Setup, just need verification In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit I think you'll get away with this, although the period of your design is 135 secs, so you might be pushing it a bit tight we usually recommend 1.5* the period. Cheers T On 30 Jan 2008, at 15:24, Carlos Faraco wrote: > Ahhhh, that's right. I knew something didn't seem right. > > Is the highpass filter of 135s correct? > > Thank you. > ========================================================================= Date: Wed, 30 Jan 2008 16:32:35 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: FSLView timeseries, combined runs In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Not sure I understand - If you do a higher level analysis, for example across 10 people, the filtered_func_data for that analysis will have 10 time-points. Each is a cope for a single person, representing the mean activity in the period in which that regressor was on. If you do a timeseries of this data, therefore, you see the cope-level at that voxel for each subject. Cheers T On 30 Jan 2008, at 15:33, Carlos Faraco wrote: > So basically it is showing in which run the voxel was most active? > In other > words, is the half-way point of that time series represents the > end/beginning of the runs? > > Is there any way to see what the avg activity of the runs is across > each > volume, such as is shown for the individual runs? > > Thank you for all your replies today. > ========================================================================= Date: Wed, 30 Jan 2008 16:36:35 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Matthew Webster <[log in to unmask]> Subject: Re: error report on pre-stats In-Reply-To: <20080130162552718.00000003776@MS-0014222BD695> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Hi, Is your system low on RAM - it looks like an fslmaths call is failing due to a bad_alloc? Regards Matthew > Hi, > > I get an error message when running pre-stats in Feat but don't > know what the problem is. Would you be able to take a look at the > attached report and give me a diagnosis? > > Thanks, Donna > > Dr. Donna Lloyd > Lecturer in Psychology > School of Psychological Sciences > The University of Manchester > Oxford Road > Manchester M13 9PL > U.K. > Tel: +44 (0) 161 275 2573 > Fax: +44 (0) 161 275 2685/2588 > > ========================================================================= Date: Wed, 30 Jan 2008 08:57:33 -0800 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Stephane Jacobs <[log in to unmask]> Subject: Re: display zstats in standard space In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Wen, I have no experience with Melodic, but I would guess it should work since it is just applying registration... Somebody with actual experience of this should be of more help, though! Best Stephane Wen-Ching Liu wrote: > Hi Stephane: > > Thank you for your reply. > Do you think "Renderhighres" also work for the output > of Melodic 's .ica dir? > > Because when I tried it, the program just generated a background > file with no zstats information at all. > > Wen > > ----- Original Message ----- > From: Stephane Jacobs <[log in to unmask]> > Date: Tuesday, January 29, 2008 5:14 pm > Subject: Re: [FSL] display zstats in standard space > To: [log in to unmask] > > > Hi Wen, > > > > Yes, you can use the renderhighres tool - see > > http://www.fmrib.ox.ac.uk/fsl/feat5/programs.html > > > > Best > > > > Stephane > > > > Wen-Ching Liu wrote: > > > Dear All: > > > > > > When running a single subject session, the thres_stats is in > > > data space, not registered to the standard space. Is > > there any > > > way to obtain a thres_stats in standard space even running a single > > > subject? > > > > > > Thanks, > > > > > > > > > > > > Wen > > > > > > > > > Wen-Ching Liu, Ph.D. > > > > > > Assistant Professor > > > Functional Imaging Laboratory > > > Department of Radiology > > > University of Medicine and Dentistry > > > of New Jersey-New Jersey Medical School > > > > > > 973-972-2281/fax: 973-972-0836 > > > http://njms.umdnj.edu/departments/radiology/fmri/index.cfm > > > > > > > > > > -- > > ::::::::::::::::::::::::::::::::::::::::::::::::::: > > Stephane Jacobs > > > > Postdoctoral Research Associate > > Human Neuroimaging and Transcranial Stimulation Lab > > Department of Psychology > > 1227 University of Oregon > > Eugene, OR 97403 - USA > > > > Email: [log in to unmask] > > Tel: (1) 541-346-4184 > > ::::::::::::::::::::::::::::::::::::::::::::::::::: -- ::::::::::::::::::::::::::::::::::::::::::::::::::: Stephane Jacobs Postdoctoral Research Associate Human Neuroimaging and Transcranial Stimulation Lab Department of Psychology 1227 University of Oregon Eugene, OR 97403 - USA Email: [log in to unmask] Tel: (1) 541-346-4184 ::::::::::::::::::::::::::::::::::::::::::::::::::: ========================================================================= Date: Wed, 30 Jan 2008 17:12:23 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?IBM850?Q?Christopher_Bell?= <[log in to unmask]> Subject: grand mean scaling Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="IBM850" FSLers, I am still slightly confused on what "grand mean scaling" does. My understanding was that each volume of an fmri 4D file would be scaled by = a constant factor of 10000, so that each individual volume's mean of non-ze= ro voxels would be 10000. This does not appear to be the case. Also, the mea= n of the entire 4D file is not 10,000. The values are always close though. = Is an individual "grand mean" for each 4D file calculated? Thanks! Chris Bell ========================================================================= Date: Wed, 30 Jan 2008 11:09:46 -0600 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Kimberly Chiew <[log in to unmask]> Subject: Re: Smoothing SPM vs FSL In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_3287_18912725.1201712986127" ------=_Part_3287_18912725.1201712986127 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Tim, On this topic, I'd like to use fslmaths in command line to smooth my data (8mm Gaussian filter) but am not sure which of the details to use. I'm pretty sure it's one of the following: fslmaths -s 8 ("spatial filtering") fslmaths -kernel gauss 8 ("kernel operations") If you could clarify, that would be great! Kim On Jan 30, 2008 2:42 AM, Tim Behrens <[log in to unmask]> wrote: > Hi - Command-line smoothing is now integrated into fslmaths. > > You can use any kernel you want with the -kernel option. > > Cheers > > T > On 29 Jan 2008, at 18:22, Carlos Faraco wrote: > > > I am wondering is there is a way to specify the smoothing kernel as > > is done > > in SPM? For example, can I specify a 5 x 7.5 x 7.5 kernel, instead > > of just 5? > > > > I know there is suppossed to be a command line smoothing option, > > ip, but I > > cannot find it in my install (4.0.3, CentOS4-32bit) and from what > > I've read > > here, it does not appear able to do the above. > > > > Thanks, > > > > Carlos > > > ------=_Part_3287_18912725.1201712986127 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Tim,
On this topic, I'd like to use fslmaths in command line to smooth my data (8mm Gaussian filter) but am not sure which of the details to use. I'm pretty sure it's one of the following:

fslmaths -s 8 ("spatial filtering")
fslmaths -kernel gauss 8 ("kernel operations")

If you could clarify, that would be great!

Kim

On Jan 30, 2008 2:42 AM, Tim Behrens <[log in to unmask]> wrote:
Hi - Command-line smoothing is now integrated into fslmaths.

You can use any kernel you want with the -kernel option.

Cheers

T
On 29 Jan 2008, at 18:22, Carlos Faraco wrote:

> I am wondering is there is a way to specify the smoothing kernel as
> is done
> in SPM? For example, can I specify a 5 x 7.5 x 7.5 kernel, instead
> of just 5?
>
> I know there is suppossed to be a command line smoothing option,
> ip, but I
> cannot find it in my install (4.0.3, CentOS4-32bit) and from what
> I've read
> here, it does not appear able to do the above.
>
> Thanks,
>
> Carlos
>

------=_Part_3287_18912725.1201712986127-- ========================================================================= Date: Wed, 30 Jan 2008 12:21:12 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: David Kideckel <[log in to unmask]> Subject: Comparing 3 Groups with TBSS MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_15976_4233763.1201713672428" ------=_Part_15976_4233763.1201713672428 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear FSLers, Can one compare 3 groups in TBSS all at once, or is it a requirement of TBSS to make three separate comparisons, essentially running three separate TBSS analyses to obtain all possible comparisons, i.e., CON vs EXP1, CON vs EXP2, and EXP1 vs EXP2. Thank you. David Kideckel ------=_Part_15976_4233763.1201713672428 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear FSLers,

Can one compare 3 groups in TBSS all at once, or is it a requirement of TBSS to make three separate comparisons, essentially running three separate TBSS analyses to obtain all possible comparisons, i.e., CON vs EXP1, CON vs EXP2, and EXP1 vs EXP2.

Thank you.

David Kideckel
------=_Part_15976_4233763.1201713672428-- ========================================================================= Date: Wed, 30 Jan 2008 17:24:48 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: Smoothing SPM vs FSL In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: multipart/alternative; boundary=Apple-Mail-134-68389132 --Apple-Mail-134-68389132 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Matt will correct me if I am wrong, but I think -kernel sets up the kernel and then the spatial operations use this kernel. -s is the only exception. This ignores the kernel completely and does gaussian smoothing. Note that -kernel does not actually do any smoothing, it just defines the kernel for other operations. T On 30 Jan 2008, at 17:09, Kimberly Chiew wrote: > Hi Tim, > On this topic, I'd like to use fslmaths in command line to smooth > my data (8mm Gaussian filter) but am not sure which of the details > to use. I'm pretty sure it's one of the following: > > fslmaths -s 8 ("spatial filtering") > fslmaths -kernel gauss 8 ("kernel operations") > > If you could clarify, that would be great! > > Kim > > On Jan 30, 2008 2:42 AM, Tim Behrens <[log in to unmask]> wrote: > Hi - Command-line smoothing is now integrated into fslmaths. > > You can use any kernel you want with the -kernel option. > > Cheers > > T > On 29 Jan 2008, at 18:22, Carlos Faraco wrote: > > > I am wondering is there is a way to specify the smoothing kernel as > > is done > > in SPM? For example, can I specify a 5 x 7.5 x 7.5 kernel, instead > > of just 5? > > > > I know there is suppossed to be a command line smoothing option, > > ip, but I > > cannot find it in my install (4.0.3, CentOS4-32bit) and from what > > I've read > > here, it does not appear able to do the above. > > > > Thanks, > > > > Carlos > > > --Apple-Mail-134-68389132 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Matt will correct me if I am = wrong, but I think -kernel sets up the kernel and then the spatial = operations use this kernel.=A0

-s is the only exception. = This ignores the kernel completely and does gaussian = smoothing.=A0
Note that -kernel does not actually do any = smoothing, it just defines the kernel for other = operations.

T

On= 30 Jan 2008, at 17:09, Kimberly Chiew wrote:

Hi = Tim,
On this topic, I'd like to use fslmaths in command line to = smooth my data (8mm Gaussian filter) but am not sure which of the = details to use. I'm pretty sure it's one of the = following:

fslmaths -s 8 ("spatial filtering")
fslmaths = -kernel gauss 8 ("kernel operations")

If you could clarify, that = would be great!

Kim

On Jan 30, = 2008 2:42 AM, Tim Behrens <[log in to unmask]> = wrote:
Hi - Command-line smoothing is now integrated into = fslmaths.

You can use any kernel you want with the -kernel = option.

Cheers

T
On 29 Jan 2008, at 18:22, Carlos = Faraco wrote:

> I am wondering is there is a way to specify = the smoothing kernel as
> is done
> in SPM? For example, can = I specify a 5 x 7.5 x 7.5 kernel, instead
> of just = 5?
>
> I know there is suppossed to be a command line = smoothing option,
> ip, but I
> cannot find it in my install = (4.0.3, CentOS4-32bit) and from what
> I've read
> here, it = does not appear able to do the above.
>
> = Thanks,
>
> = Carlos
>


= --Apple-Mail-134-68389132-- ========================================================================= Date: Wed, 30 Jan 2008 17:26:28 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: Comparing 3 Groups with TBSS In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit You can set up a GLM with an EV for each group, and test any comparison you like with the contrast matrix - all in one TBSS run. T On 30 Jan 2008, at 17:21, David Kideckel wrote: > Dear FSLers, > > Can one compare 3 groups in TBSS all at once, or is it a > requirement of TBSS to make three separate comparisons, essentially > running three separate TBSS analyses to obtain all possible > comparisons, i.e., CON vs EXP1, CON vs EXP2, and EXP1 vs EXP2. > > Thank you. > > David Kideckel ========================================================================= Date: Wed, 30 Jan 2008 17:27:49 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: EV Setup, just need verification In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit Guru wooly says 1x the period is fine - as there is a very slow roll- off on the filter... Cheers T On 30 Jan 2008, at 16:30, Tim Behrens wrote: > I think you'll get away with this, although the period of your > design is 135 secs, so you might be pushing it a bit tight we > usually recommend 1.5* the period. > > Cheers > > T > On 30 Jan 2008, at 15:24, Carlos Faraco wrote: > >> Ahhhh, that's right. I knew something didn't seem right. >> >> Is the highpass filter of 135s correct? >> >> Thank you. >> > ========================================================================= Date: Wed, 30 Jan 2008 12:32:55 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: David Kideckel <[log in to unmask]> Subject: Re: Comparing 3 Groups with TBSS In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_16041_9940432.1201714375673" ------=_Part_16041_9940432.1201714375673 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thank you for the response. How exactly do I do this. Do I have to run all TBSS preprocessing steps before this though, and place all subjects' FA maps into the original file folder? Once I get to the design matrix, can I set up a script that will allow me to do this 3 group comparison with a cluster threshold of 3? Cheers. David On Jan 30, 2008 12:26 PM, Tim Behrens <[log in to unmask]> wrote: > You can set up a GLM with an EV for each group, and test any > comparison you like with the contrast matrix - all in one TBSS run. > > > T > On 30 Jan 2008, at 17:21, David Kideckel wrote: > > > Dear FSLers, > > > > Can one compare 3 groups in TBSS all at once, or is it a > > requirement of TBSS to make three separate comparisons, essentially > > running three separate TBSS analyses to obtain all possible > > comparisons, i.e., CON vs EXP1, CON vs EXP2, and EXP1 vs EXP2. > > > > Thank you. > > > > David Kideckel > ------=_Part_16041_9940432.1201714375673 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thank you for the response. How exactly do I do this. Do I have to run all TBSS preprocessing steps before this though, and place all subjects' FA maps into the original file folder?
Once I get to the design matrix, can I set up a script that will allow me to do this 3 group comparison with a cluster threshold of 3?
Cheers.
David

On Jan 30, 2008 12:26 PM, Tim Behrens <[log in to unmask]> wrote:
You can set up a GLM with an EV for each group, and test any
comparison you like with the contrast matrix - all in one TBSS run.


T
On 30 Jan 2008, at 17:21, David Kideckel wrote:

> Dear FSLers,
>
> Can one compare 3 groups in TBSS all at once, or is it a
> requirement of TBSS to make three separate comparisons, essentially
> running three separate TBSS analyses to obtain all possible
> comparisons, i.e., CON vs EXP1, CON vs EXP2, and EXP1 vs EXP2.
>
> Thank you.
>
> David Kideckel

------=_Part_16041_9940432.1201714375673-- ========================================================================= Date: Wed, 30 Jan 2008 17:39:56 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Tim Behrens <[log in to unmask]> Subject: Re: Comparing 3 Groups with TBSS In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v752.3) Content-Type: multipart/alternative; boundary=Apple-Mail-135-69296765 --Apple-Mail-135-69296765 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi On 30 Jan 2008, at 17:32, David Kideckel wrote: > Thank you for the response. How exactly do I do this. Do I have to > run all TBSS preprocessing steps before this though, and place all > subjects' FA maps into the original file folder? Yes > > Once I get to the design matrix, can I set up a script that will > allow me to do this 3 group comparison with a cluster threshold of 3? > Cheers. What question do you want to ask of your three groups? The simplest one you can ask is where are there any differences between any of the groups. For this, you design matrix looks like 1 0 0 1 0 0 ... 0 1 0 0 1 0 ... 0 0 1 0 0 1 your contrast looks like 1 -1 0 1 0 -1 0 1 -1 and then you compute an F-statistic across all three contrasts. You can then use randomise with whatever F-threshold you want using -F Cheers T > > David > > On Jan 30, 2008 12:26 PM, Tim Behrens <[log in to unmask]> wrote: > You can set up a GLM with an EV for each group, and test any > comparison you like with the contrast matrix - all in one TBSS run. > > > T > On 30 Jan 2008, at 17:21, David Kideckel wrote: > > > Dear FSLers, > > > > Can one compare 3 groups in TBSS all at once, or is it a > > requirement of TBSS to make three separate comparisons, essentially > > running three separate TBSS analyses to obtain all possible > > comparisons, i.e., CON vs EXP1, CON vs EXP2, and EXP1 vs EXP2. > > > > Thank you. > > > > David Kideckel > --Apple-Mail-135-69296765 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hi
On 30 Jan 2008, at 17:32, David Kideckel wrote:

Thank you = for the response. How exactly do I do this. Do I have to run all TBSS = preprocessing steps before this though, and place all subjects' FA maps = into the original file folder?

Yes


Once I get to the design matrix, can I set up a script = that will allow me to do this 3 group comparison with a cluster = threshold of 3?
Cheers.

What question do you want = to ask of your three groups?
The simplest one you can ask is = where are there any differences between any of the = groups.=A0
For this, you design matrix looks like
1 = 0 0=A0
1 0 0
...
0 1 0=A0
0 1 = 0
...
0 0 1
0 0 1

your contrast looks = like

1 -1 = 0=A0
1 0 -1
0 1 -1

and then you compute an = F-statistic across all three contrasts.=A0

You can then use randomise = with whatever F-threshold you want using -F

Cheers

T



David

On Jan 30, = 2008 12:26 PM, Tim Behrens <[log in to unmask]> = wrote:
You can set up a GLM with an EV for each group, and test = any
comparison you like with the contrast matrix - all in one TBSS = run.


T
On 30 Jan 2008, at 17:21, David Kideckel wrote:
=
> Dear FSLers,
>
> Can one compare 3 groups in TBSS = all at once, or is it a
> requirement of TBSS to make three = separate comparisons, essentially
> running three separate TBSS = analyses to obtain all possible
> comparisons, i.e., CON vs EXP1, = CON vs EXP2, and EXP1 vs EXP2.
>
> Thank = you.
>
> David = Kideckel


= --Apple-Mail-135-69296765-- ========================================================================= Date: Wed, 30 Jan 2008 17:59:55 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Nicholas P Holmes <[log in to unmask]> Subject: Re: ntdir stdtr error at 3rd level ME, but not FE analysis Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1252" Hi All, I am also getting these problems (see the other thread I started=20 yesterday), but: 1) When running FE, not ME 2) On the latest version of FSL (4.0.3-1) 3) for Ubuntu, not Debian 4) On IDENTICAL analyses which worked fine just a few days ago, before=20= updating to the latest version (so, it can't be due to outliers in my=20 data, else I should have had these errors last week, and i haven't made=20= any changes to or noticed anything funny in my computer) 5) On FE analyses which seem to invoke FLAME 1+2 processes (I get errors=20= telling me that the results of FLAME 1 and FLAME 1+2 are very different=20= but I chose the FE option, which usually takes 10 minutes, but now takes=20= hours) this is very much a shot-in-the dark, but, since there are quite a few=20= posts in the archives on these sorts of topics, i wondered: Since the number-labelling of the four possible higher-level analyses in=20= the design.fsf file in feat is: 1st option FE - 3 2nd OLS - 0 3rd ME(FLAME 1) - 2 4th ME(FLAME 1+2)- 1 is it possible that, somewhere along the way, and differently in differen= t=20 versions, this non-intuitive number/ordering (3-0-2-1) is causing some=20= confusions or human error in the programs? I can't otherwise think why when I select the first option FE (#3), I get= =20 error messages related to the fourth option (#1) on identical analyses=20= which worked fine before the latest update... i hope we can find the problem(s) soon - i can no longer work... cheers, nick ========================================================================= Date: Wed, 30 Jan 2008 18:33:01 -0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Matthew Webster <[log in to unmask]> Subject: Re: ntdir stdtr error at 3rd level ME, but not FE analysis In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Can you upload the full report_log.html file(s) from the problem analy= ses? > > I am also getting these problems (see the other thread I started > yesterday), but: > > 1) When running FE, not ME > 2) On the latest version of FSL (4.0.3-1) > 3) for Ubuntu, not Debian > 4) On IDENTICAL analyses which worked fine just a few days ago, before > updating to the latest version (so, it can't be due to outliers in my > data, else I should have had these errors last week, and i haven't made > any changes to or noticed anything funny in my computer) > 5) On FE analyses which seem to invoke FLAME 1+2 processes (I get error= s > telling me that the results of FLAME 1 and FLAME 1+2 are very different > but I chose the FE option, which usually takes 10 minutes, but now take= s > hours) > > > this is very much a shot-in-the dark, but, since there are quite a few > posts in the archives on these sorts of topics, i wondered: > > Since the number-labelling of the four possible higher-level analyses i= n > the design.fsf file in feat is: > 1st option FE - 3 > 2nd OLS - 0 > 3rd ME(FLAME 1) - 2 > 4th ME(FLAME 1+2)- 1 > > is it possible that, somewhere along the way, and differently in differ= ent > versions, this non-intuitive number/ordering (3-0-2-1) is causing some > confusions or human error in the programs? > > I can't otherwise think why when I select the first option FE (#3), I g= et > error messages related to the fourth option (#1) on identical analyses > which worked fine before the latest update... > > i hope we can find the problem(s) soon - i can no longer work... > > cheers, > nick > > ========================================================================= Date: Wed, 30 Jan 2008 19:17:19 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: =?iso-8859-1?q?Gwena=EBlle=20DOUAUD?= <[log in to unmask]> Subject: RE : Re: [FSL] Smoothing SPM vs FSL In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Kimberley, the -s option is actually doing what you want BUT with sigma values instead of FWHM. So if you want precisely 8mm for the FWHM, sigma should be 8/(sqrt(ln2x8))=3D roughly 3.4mm Cheers, Gwenaelle --- Kimberly Chiew <[log in to unmask]> a =E9crit : > Hi Tim, > On this topic, I'd like to use fslmaths in command > line to smooth my data > (8mm Gaussian filter) but am not sure which of the > details to use. I'm > pretty sure it's one of the following: >=20 > fslmaths -s 8 ("spatial filtering") > fslmaths -kernel gauss 8 ("kernel operations") >=20 > If you could clarify, that would be great! >=20 > Kim >=20 > On Jan 30, 2008 2:42 AM, Tim Behrens > <[log in to unmask]> wrote: >=20 > > Hi - Command-line smoothing is now integrated into > fslmaths. > > > > You can use any kernel you want with the -kernel > option. > > > > Cheers > > > > T > > On 29 Jan 2008, at 18:22, Carlos Faraco wrote: > > > > > I am wondering is there is a way to specify the > smoothing kernel as > > > is done > > > in SPM? For example, can I specify a 5 x 7.5 x > 7.5 kernel, instead > > > of just 5? > > > > > > I know there is suppossed to be a command line > smoothing option, > > > ip, but I > > > cannot find it in my install (4.0.3, > CentOS4-32bit) and from what > > > I've read > > > here, it does not appear able to do the above. > > > > > > Thanks, > > > > > > Carlos > > > > > >=20 ___________________________________________________________________= __________=20 Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! M= ail http://mail.yahoo.fr ========================================================================= Date: Wed, 30 Jan 2008 19:54:43 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Nicholas P Holmes <[log in to unmask]> Subject: Re: ntdir stdtr error at 3rd level ME, but not FE analysis Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1252" sure, they are with no: 834857 cheers, n ========================================================================= Date: Wed, 30 Jan 2008 20:41:59 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: Re: FSLView timeseries, combined runs Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Tim, I do not know if we are talking about different things or if this is my l= ack of experience with FSL shinning through. =3D] Let me describe the graph better. So again, this is 2 runs processed thro= ugh higher level FE and I am looking at the rendered_thresh_zstat . The x coordinate of the timeseries is time, and runs from 0 to 1 in intervals o= f .2. For each voxel (without choosing a model) I see only 1 red diagonal l= ine. My other question then is: how can I see an actual per volume timeseries,= as is presented for the individual runs, for the combined runs? ========================================================================= Date: Thu, 31 Jan 2008 14:30:27 +0900 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: [log in to unmask] Subject: how to convert .ima (GE) into .dcm Mime-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit Hi all, Does anyone know how to convert .ima raw files (fMRI/anat/DTI) coming from a GE scanner into .dcm (or other formats)? I have no problems with .ima from a Siemens scanner ... but GE seems to be different... thank you in advance! Joyce! -- joyce ========================================================================= Date: Thu, 31 Jan 2008 14:37:58 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Thomas Nichols <[log in to unmask]> Subject: Re: group and fstat design file Comments: To: [log in to unmask] In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_18591_29280877.1201790278450" ------=_Part_18591_29280877.1201790278450 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Kelly, To follow up on Steve's reply, if you've got paired (aka repeated measures) data, then you *must *use a group file to tell randomise about what is exchangeable. If you have 3 subjects in group A and 2 subjects in group B, then your design matrix might look like 1 0 1 0 0 0 0 # Sick, Pre -1 0 1 0 0 0 0 # Sick, Post 1 0 0 1 0 0 0 # Sick, Pre -1 0 0 1 0 0 0 # Sick, Post 1 0 0 0 1 0 0 # Sick, Pre -1 0 0 0 1 0 0 # Sick, Post 0 1 0 0 0 1 0 # Not Sick, Pre 0 -1 0 0 0 1 0 # Not Sick, Post 0 1 0 0 0 0 1 # Not Sick, Pre 0 -1 0 0 0 0 1 # Not Sick, Post and your contrast of interest [-1 1 ]. Randomise doesn't have to worry about different group variance, but it *does* need to know that it only make sense (under Ho) to swap pre and post data within subject. Hence you need to use a group file consisting of 1 1 2 2 3 3 4 4 5 5 which defines 5 'groups' (technically known as exchangeability blocks). Can you try this and let me know if works? -Tom ____________________________________________ Thomas Nichols, PhD Director, Modelling & Genetics GlaxoSmithKline Clinical Imaging Centre Senior Research Fellow Oxford University FMRIB Centre On Jan 24, 2008 10:10 PM, SUBSCRIBE FSL Kelly Brown <[log in to unmask]> wrote: > Hi FSLers, > > I have a question, if I am using randomise to analyze an ANOVA type > design, > do I need to include a design.grp file for my two groups? I want to look > at > differences in pre and post and differences in sick and not sick... And if > so, how should it look because I keep getting an error when I try to run > randomise with the design.grp file and the design.fts file...I have > checked > the number of rows etc and they match my datapoints... > > group.datis not a valid vest file > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Aborted > > I get the same message when I try to make a F test file... > > design.grp > > %! VEST > /NumWaves 1 > /NumPoints 10 > /Skip > /PPheights 1 1 > > /Matrix > 1 > 1 > 1 > 2 > 2 > 1 > 1 > 1 > 2 > 2 > > > Thanks! > Kelly Brown > UCHSC Research Fellow > > ------=_Part_18591_29280877.1201790278450 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Kelly,

To follow up on Steve's reply, if you've got paired (aka repeated measures) data, then you must use a group file to tell randomise about what is exchangeable. 

If you have 3 subjects in group A and 2 subjects in group B, then your design matrix might look like

   1     0     1     0     0     0     0     # Sick, Pre
  -1     0     1     0     0     0     0
     # Sick, Post
   1     0     0     1     0     0     0     # Sick, Pre
  -1     0     0     1     0     0     0     # Sick, Post
   1     0     0     0     1     0     0     # Sick, Pre
  -1     0     0     0     1     0     0     # Sick, Post
   0     1     0     0     0     1     0     # Not Sick, Pre
   0    -1     0     0     0     1     0     # Not Sick, Post
   0     1     0     0     0     0     1     # Not Sick, Pre
   0    -1     0     0     0     0     1     # Not Sick, Post

and your contrast of interest [-1 1 ].  Randomise doesn't have to worry about different group variance, but it *does* need to know that it only make sense (under Ho) to swap pre and post data within subject.  Hence you need to use a group file consisting of

1
1
2
2
3
3
4
4
5
5

which defines 5 'groups' (technically known as exchangeability blocks).  Can you try this and let me know if works?

-Tom

____________________________________________
Thomas Nichols, PhD
Director, Modelling & Genetics
GlaxoSmithKline Clinical Imaging Centre

Senior Research Fellow
Oxford University FMRIB Centre



On Jan 24, 2008 10:10 PM, SUBSCRIBE FSL Kelly Brown <[log in to unmask]> wrote:
Hi FSLers,

I have a question, if I am using randomise to analyze an ANOVA type design,
do I need to include a design.grp file for my two groups? I want to look at
differences in pre and post and differences in sick and not sick... And if
so, how should it look because I keep getting an error when I try to run
randomise with the design.grp file and the design.fts file...I have checked
the number of rows etc and they match my datapoints...

group.datis not a valid vest file
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted

I get the same message when I try to make a F test file...

design.grp

%! VEST
/NumWaves   1
/NumPoints  10
/Skip
/PPheights  1     1

/Matrix
1
1
1
2
2
1
1
1
2
2


Thanks!
Kelly Brown
UCHSC Research Fellow



------=_Part_18591_29280877.1201790278450-- ========================================================================= Date: Thu, 31 Jan 2008 15:47:49 +0100 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: "S. Groppa" <[log in to unmask]> Subject: TBSS in stroke In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear DTI & TBSS experts, I am wondering if somebody of you have gathered experience with the use of TBSS in stroke patients data (cortical vs subcortical lesions)... Limitations, strengths, robustness... grateful for your reflections sincerely Sergiu ========================================================================= Date: Thu, 31 Jan 2008 15:56:31 -0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: "Barker, Gareth" <[log in to unmask]> Subject: Post in rtfmri MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable > > Apologies for anyone receiving this multiple times. Please see = below > > for details of a post available looking at real time fMRI which > > may be of interest to people ... > >=20 > >=20 > > ________________ > > Gareth J. Barker,=09 > > King's College London, > > Institute of Psychiatry, > > Department of Clinical Neuroscience, > > Centre for Neuroimaging Sciences, (Box 089), > > De Crespigny Park, London SE5 8AF, UK. > >=20 > > email : [log in to unmask] > > phone : +44 20 3228 3059 > > fax : +44 20 3228 2116 > >=20 >=20 Research Worker in Real-Time fMRI Department of Psychiatry & Centre for Neuroimaging=20 We are inviting applications for a full-time (negotiable) Non-Clinical = Research Worker post (RA1B/1A Spine point 6 -8) which is funded for one = year. The successful candidate will be working in the Dept of = Psychiatry (Professor Anthony David, Dr Emma Lawrence) in collaboration = with the Centre for Neuroimaging Sciences (Professor Gareth Barker, Dr = Vincent Giampietro) on an interdisciplinary project to develop, = implement and pilot 'real-time' functional magnetic resonance imaging = techniques, at the Institute of Psychiatry, King's College London. =20 The main role of the post holder will be to develop MRI scanner-specific = software to enable the rapid transfer and analysis of fMRI data. The = appointee will have some programming and technical skills, and ideally, = knowledge of cognitive neuroscience research.=20 Starting salary in the range =A323,800 pa to =A328, 417 (inclusive of = =A32,323 pa London Allowance), depending on qualifications and = experience. =20 To obtain further particulars and information about the Institute, = please see our website at http://www.iop.kcl.ac.uk/vacancies or = alternatively email [log in to unmask] For infromation about this = post email [log in to unmask] Applications, in the form of a = CV (including details of two referees), covering letter and equal = opportunities statement, should be emailed to this address or posted to = the address given in the further particulars. =20 Please quote reference number 08/R11 in all correspondence. =20 Closing date for applications 29 February 2008. Only candidates shortlisted for interview will be contacted. Equality of opportunity is College policy ========================================================================= Date: Thu, 31 Jan 2008 16:21:34 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: David Lythgoe <[log in to unmask]> Subject: Re: Post in rtfmri In-Reply-To: <[log in to unmask]> Mime-version: 1.0 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable This prompted me to look at the IOP vacancies. I see Simone has a PhD project advertised. "<1> optimizing the data acquisition (on 3 Tesla scanners) of structural MRI, functional MRI, DTI, and resting state MRI " Bloody hell, not more optimisation of acquisition! On 31/1/08 15:56, "Barker, Gareth" <[log in to unmask]> wrote: >>> Apologies for anyone receiving this multiple times. Please see below >>> for details of a post available looking at real time fMRI which >>> may be of interest to people ... >>>=20 >>>=20 >>> ________________ >>> Gareth J. Barker,=20 >>> King's College London, >>> Institute of Psychiatry, >>> Department of Clinical Neuroscience, >>> Centre for Neuroimaging Sciences, (Box 089), >>> De Crespigny Park, London SE5 8AF, UK. >>>=20 >>> email : [log in to unmask] >>> phone : +44 20 3228 3059 >>> fax : +44 20 3228 2116 >>>=20 >>=20 >=20 >=20 >=20 > Research Worker in Real-Time fMRI > Department of Psychiatry & Centre for Neuroimaging >=20 > We are inviting applications for a full-time (negotiable) Non-Clinical > Research Worker post (RA1B/1A Spine point 6 -8) which is funded for one y= ear. > The successful candidate will be working in the Dept of Psychiatry (Profe= ssor > Anthony David, Dr Emma Lawrence) in collaboration with the Centre for > Neuroimaging Sciences (Professor Gareth Barker, Dr Vincent Giampietro) on= an > interdisciplinary project to develop, implement and pilot 'real-time' > functional magnetic resonance imaging techniques, at the Institute of > Psychiatry, King's College London. >=20 > The main role of the post holder will be to develop MRI scanner-specific > software to enable the rapid transfer and analysis of fMRI data. The appo= intee > will have some programming and technical skills, and ideally, knowledge o= f > cognitive neuroscience research. >=20 > Starting salary in the range =A323,800 pa to =A328, 417 (inclusive of =A32,323 = pa > London Allowance), depending on qualifications and experience. >=20 > To obtain further particulars and information about the Institute, please= see > our website at http://www.iop.kcl.ac.uk/vacancies or alternatively email > [log in to unmask] For infromation about this post email > [log in to unmask] Applications, in the form of a CV (including > details of two referees), covering letter and equal opportunities stateme= nt, > should be emailed to this address or posted to the address given in the > further particulars. > Please quote reference number 08/R11 in all correspondence. > Closing date for applications 29 February 2008. >=20 > Only candidates shortlisted for interview will be contacted. >=20 > Equality of opportunity is College policy ========================================================================= Date: Thu, 31 Jan 2008 16:44:48 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Anastasia Ford <[log in to unmask]> Subject: Re: Philips Scaling Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Saad, Thanks for your quick reply. I have checked the fdt_paths file and it does contain an anatomically correct tract. The fslstats seeds_to_target -R does show the range from 0= to 1 as expected. I reset the min/max to be 0/1 and only 3 voxels all with t= he value of 1 show up. No other voxels with values lower than 1 are containe= d in the seeds_to_target image. Is there any reason why so few voxels are contained in the seeds_totarget when the number of voxels in the fdt_path= image contains a lot of voxels with high intensities. Thanks for your help Anastasia ========================================================================= Date: Thu, 31 Jan 2008 12:08:15 -0500 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Matt Glasser <[log in to unmask]> Subject: Re: Philips Scaling In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit The seeds_to_targets mode only saves the probabilities in each seed voxel, not path distributions for the whole brain. It is useful for comparing the probability of projection of one region to several others, and segmenting the seed region according to probability of projection to the targets. If you want to dissect tracts, you should use the path distribution mode. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Anastasia Ford Sent: Thursday, January 31, 2008 11:45 AM To: [log in to unmask] Subject: Re: [FSL] Philips Scaling Saad, Thanks for your quick reply. I have checked the fdt_paths file and it does contain an anatomically correct tract. The fslstats seeds_to_target -R does show the range from 0 to 1 as expected. I reset the min/max to be 0/1 and only 3 voxels all with the value of 1 show up. No other voxels with values lower than 1 are contained in the seeds_to_target image. Is there any reason why so few voxels are contained in the seeds_totarget when the number of voxels in the fdt_path image contains a lot of voxels with high intensities. Thanks for your help Anastasia ========================================================================= Date: Thu, 31 Jan 2008 17:14:53 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Saad Jbabdi <[log in to unmask]> Subject: Re: Philips Scaling In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-68-154194028 --Apple-Mail-68-154194028 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed If you have only three voxels with a value of one in seed_to_target, that means only three out of your N sample tracts have reached the target. To check that, you can set your target as a waypoint, then your fdt_paths will contain much fewer voxels... Saad. On 31 Jan 2008, at 16:44, Anastasia Ford wrote: > Saad, > Thanks for your quick reply. > > I have checked the fdt_paths file and it does contain an anatomically > correct tract. The fslstats seeds_to_target -R does show the range > from 0 to > 1 as expected. I reset the min/max to be 0/1 and only 3 voxels all > with the > value of 1 show up. No other voxels with values lower than 1 are > contained > in the seeds_to_target image. Is there any reason why so few voxels > are > contained in the seeds_totarget when the number of voxels in the > fdt_path > image contains a lot of voxels with high intensities. > > Thanks for your help > > Anastasia > ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ --- --Apple-Mail-68-154194028 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
If you have only three voxels with a value of one in = seed_to_target, that means only three out of your N sample tracts have = reached the target. To check that, you can set your target as a = waypoint, then your fdt_paths will contain much fewer = voxels...

Saad.


On 31 Jan 2008, = at 16:44, Anastasia Ford wrote:

Saad,
Thanks for = your quick reply.

I have checked the fdt_paths file and it does = contain an anatomically
correct = tract. The fslstats seeds_to_target -R does show the range from 0 = to
1 as expected. I reset the min/max to be 0/1 = and only 3 voxels all with the
value of 1 = show up. No other voxels with values lower than 1 are = contained
in the seeds_to_target image. Is = there any reason why so few voxels are
image contains a=A0 lot of voxels with high = intensities.

Thanks for your help


=

Saad Jbabdi,=A0
Postdoctoral Research Assistant,=A0=A0
Oxford University FMRIB Centre

FMRIB, = JR Hospital, Headington, Oxford=A0=A0OX3 9DU, UK
+44 (0) 1865 222545=A0=A0(fax 222717)


=

= --Apple-Mail-68-154194028-- ========================================================================= Date: Thu, 31 Jan 2008 17:27:40 +0000 Reply-To: FSL - FMRIB's Software Library <
[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: Error when re-runnning stats & post-stats ERROR:: Empty mask image Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I have encountered this error a couple of times when re-running stats and= post-stats. This occurs during the stats portion on the constrasts compar= ing the 2 EVs. usr/local/fsl40/bin/fslstats thresh_zstat2 -l 0.0001 -R ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image 0.000000 0.000000=20 /usr/local/fsl40/bin/fslstats thresh_zstat4 -l 0.0001 -R ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image ERROR:: Empty mask image 0.000000 0.000000=20 So, obviously the are no activation clusters in the resulting files. Thanks in advance. ========================================================================= Date: Thu, 31 Jan 2008 17:44:10 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Carlos Faraco <[log in to unmask]> Subject: Re: Error when re-runnning stats & post-stats ERROR:: Empty mask image Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" Correction, the above occurs during the post-stats. ========================================================================= Date: Thu, 31 Jan 2008 18:29:13 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Roman Loonis <[log in to unmask]> Subject: Thresholding output from probtrac? Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain I am using probtrac to track fibers from a seed mask to one particular ta= rget mask. The outcome of=20 the results is just messy and all over the place. I would like to know if= there is any way to threshold=20 the results of the probtrac (or maybe while I run probtrac) so that I onl= y see the stronger=20 connections. Anybody have any ideas? ========================================================================= Date: Thu, 31 Jan 2008 18:36:01 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Saad Jbabdi <[log in to unmask]> Subject: Re: Thresholding output from probtrac? In-Reply-To: <[log in to unmask]> Mime-Version: 1.0 (Apple Message framework v753) Content-Type: multipart/alternative; boundary=Apple-Mail-70-159061960 --Apple-Mail-70-159061960 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi From the FSL-FAQ: ------- How should I threshold the path distribution estimates from ProbTrack? There is no right or wrong way to threshold these values. They form a continuous distribution which has been discretised in an arbitrary fashion (for example, if you double the voxel size, the probability of passing through each voxel will roughly double!). Note that this is NOT true for the "connectivity-based seed-voxel classification" mode where the discretisation is generally anatomically meaningful (the target masks are prespecified anatomical regions). In practice, thresholding at very low values (e.g., 10 out of 5000 samples) often tidies up path distribution estimates considerably. You will have to choose where to threshold based on your own specific question. -------- Also, whenever you can, you may "threshold" based on targets/ waypoints, i.e. select tracts based on your prior knowledge about the anatomy. Cheers, Saad. On 31 Jan 2008, at 18:29, Roman Loonis wrote: > I am using probtrac to track fibers from a seed mask to one > particular target mask. The outcome of > the results is just messy and all over the place. I would like to > know if there is any way to threshold > the results of the probtrac (or maybe while I run probtrac) so that > I only see the stronger > connections. Anybody have any ideas? > ------------------------------------------------------------------------ --- Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222545 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~saad ------------------------------------------------------------------------ --- --Apple-Mail-70-159061960 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
Hi

=46rom= the FSL-FAQ:
-------
How = should I threshold the path distribution estimates from = ProbTrack?
There is no right or wrong = way to threshold these values. They form a continuous distribution which = has been discretised in an arbitrary fashion (for example, if you double = the voxel size, the probability of passing through each voxel will = roughly double!). Note that this is NOT true for the "connectivity-based = seed-voxel classification" mode where the discretisation is generally = anatomically meaningful (the target masks are prespecified anatomical = regions). In practice, thresholding at very low values (e.g., 10 out of = 5000 samples) often tidies up path distribution estimates considerably. = You will have to choose where to threshold based on your own specific = question.
--------

Also, whenever you can, = you may "threshold" based on targets/waypoints, i.e. select tracts based = on your prior knowledge about the anatomy.


Cheers,
Saad.



On 31 Jan 2008, = at 18:29, Roman Loonis wrote:

I am using probtrac to track fibers from a seed mask = to one particular target mask. The outcome of=A0
the = results is just messy and all over the place. I would like to know if = there is any way to threshold=A0
the = results of the probtrac (or maybe while I run probtrac) so that I only = see the stronger=A0
connections. Anybody have any ideas?

=

Saad Jbabdi,=A0
Postdoctoral Research Assistant,=A0=A0
Oxford University FMRIB Centre

FMRIB, = JR Hospital, Headington, Oxford=A0=A0OX3 9DU, UK
+44 (0) 1865 222545=A0=A0(fax 222717)


=

= --Apple-Mail-70-159061960-- ========================================================================= Date: Thu, 31 Jan 2008 19:51:30 +0000 Reply-To: FSL - FMRIB's Software Library <
[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Roman Loonis <[log in to unmask]> Subject: Re: thresholding output from probtrac? Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain The FSL-FAQ says the following: "In practice, thresholding at very low va= lues (e.g., 10 out of 5000=20 samples) often tidies up path distribution estimates considerably." How c= ould I do that? How can I=20 threshold my results? It may be really easy, I just do not know the proce= dure on how. ========================================================================= Date: Thu, 31 Jan 2008 13:09:29 -0700 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Dianne Patterson <[log in to unmask]> Subject: Re: thresholding output from probtrac? In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_27631_8066482.1201810169431" ------=_Part_27631_8066482.1201810169431 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You can use fslmaths with one of several threshold commands: -thr : use following number to threshold current image (zero anything below the number) -thrp : use following percentage (0-100) of ROBUST RANGE to threshold current image (zero anything below the number) -thrP : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold below -uthr : use following number to upper-threshold current image (zero anything above the number) -uthrp : use following percentage (0-100) of ROBUST RANGE to upper-threshold current image (zero anything above the number) -uthrP : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold above For example: >fslmaths directory/fdt_paths -thrp 5 directory/fdt5p I hope that helps, Dianne =================================== On Jan 31, 2008 12:51 PM, Roman Loonis <[log in to unmask]> wrote: > The FSL-FAQ says the following: "In practice, thresholding at very low > values (e.g., 10 out of 5000 > samples) often tidies up path distribution estimates considerably." How > could I do that? How can I > threshold my results? It may be really easy, I just do not know the > procedure on how. > > -- Dianne Patterson, Ph.D. [log in to unmask] ERP Lab University of Arizona 621-3256 (Office) ------=_Part_27631_8066482.1201810169431 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You can use fslmaths with one of several threshold commands:

 -thr   : use following number to threshold current image (zero anything below the number)
 -thrp  : use following percentage (0-100) of ROBUST RANGE to threshold current image (zero anything below the number)
 -thrP  : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold below
 -uthr  : use following number to upper-threshold current image (zero anything above the number)
 -uthrp : use following percentage (0-100) of ROBUST RANGE to upper-threshold current image (zero anything above the number)
 -uthrP : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold above

For example:
>fslmaths directory/fdt_paths -thrp 5 directory/fdt5p

I hope that helps,

Dianne

===================================
On Jan 31, 2008 12:51 PM, Roman Loonis <[log in to unmask]> wrote:
The FSL-FAQ says the following: "In practice, thresholding at very low values (e.g., 10 out of 5000
samples) often tidies up path distribution estimates considerably." How could I do that? How can I
threshold my results? It may be really easy, I just do not know the procedure on how.




--
Dianne Patterson, Ph.D.
[log in to unmask]
ERP Lab
University of Arizona
621-3256 (Office) ------=_Part_27631_8066482.1201810169431-- ========================================================================= Date: Thu, 31 Jan 2008 20:27:59 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Anastasia Ford <[log in to unmask]> Subject: Re: Philips Scaling Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" I have a few more questions about the seed_to_target segmentation analysi= s. My seed is the anterior limb of internal capsule and two targets are leve= l of CN3 and the corpus callosum. The seed_to_CN3 show up as only a few vox= els with max intensity value of 2, but the seed_to_CC produces a large array = of voxels with max intensity of 3335. Since there are a lot of white matter tracts (e.g. cortico-spinal) that run from internal capsule down to the brainstem shouldnt there be more voxels with values higher than 2 in the seeds_to_CN3 image? Thank you, Anastasia ========================================================================= Date: Thu, 31 Jan 2008 20:41:52 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Robert Kelly <[log in to unmask]> Subject: Re: MELODIC multi-session temporal concatenation Comments: To: "Christian F. Beckmann" <[log in to unmask]> Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="windows-1252" Dear Christian, Thank you for your quick reply to my questions and for reassuring me that= =20 the first Eigenvector timecourse plot produced for multi-session temporal= =20 concatenation is irrelevant for resting state analyses. Some follow-up questions: 1) Exactly what does the Sessions/Subject mode=20= plot at the bottom of the component report page represent? Specifically,= =20 for resting state data (or any case where a common time course is not=20 assumed to exist) does the plot represent the effect size of the fit for=20= each session/subject with the component displayed or is it based on the=20= rank-1 approximation? 2) Do you have any suggestions for how to test for= =20 group differences using some measure of how well each group fits with the= =20 given component? Thanks again, Robert ========================================================================= Date: Thu, 31 Jan 2008 23:03:59 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: Thomas Nichols <[log in to unmask]> Subject: Re: Cluster Thresholding Vs FDR Comments: To: Greg ----- <[log in to unmask]> In-Reply-To: <[log in to unmask]> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_20616_21212450.1201820639877" ------=_Part_20616_21212450.1201820639877 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Greg, On Jan 31, 2008 8:43 PM, Greg ----- <[log in to unmask]> wrote: > Is it feasible to use fsl's cluster thresholding alongside fdr to look for > regions of activation or is this considered "fishing for result" per se? > FDR aside, doing both cluster- and voxel-wise inference isn't "fishing" per se, but it will result in inflated false positive rates. Hence, once has to commit to a single inference strategy before seeing the data to be sure you can trust your P-values. To be clear, cluster inference in FSL always uses a familywise error (FWE) correction--a 0.05-corrected significant cluster controls the chance of 1 or more false positive clusters anywhere in the brain. Similarly, the standard FSL voxel-wise corrected significance controls for the chance of 1 or more false postive *voxels* anywhere in the brain. FDR is only available for voxel-wise inference (it has been proposed for cluster inference, but FDR works best with many many tests and sparse signals, and there just aren't that many clusters in a typical image). Hence your question suggested a combination of FWE cluster-wise inference and voxel-wise FDR inference, which isn't so much apples and oranges, as apples and turnips. Hope this helps! -Tom ____________________________________________ Thomas Nichols, PhD Director, Modelling & Genetics GlaxoSmithKline Clinical Imaging Centre Senior Research Fellow Oxford University FMRIB Centre ------=_Part_20616_21212450.1201820639877 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Greg,

On Jan 31, 2008 8:43 PM, Greg ----- <[log in to unmask]> wrote:
Is it feasible to use fsl's cluster thresholding alongside fdr to look for regions of activation or is this considered "fishing for result" per se?
 
FDR aside, doing both cluster- and voxel-wise inference isn't "fishing" per se, but it will result in inflated false positive rates.  Hence, once has to commit to a single inference strategy before seeing the data to be sure you can trust your P-values.

To be clear, cluster inference in FSL always uses a familywise error (FWE) correction--a 0.05-corrected significant cluster controls the chance of 1 or more false positive clusters anywhere in the brain.  Similarly, the standard FSL voxel-wise corrected significance controls for the chance of 1 or more false postive *voxels* anywhere in the brain.  FDR is only available for voxel-wise inference (it has been proposed for cluster inference, but FDR works best with many many tests and sparse signals, and there just aren't that many clusters in a typical image).

Hence your question suggested a combination of FWE cluster-wise inference and voxel-wise FDR inference, which isn't so much apples and oranges, as apples and turnips.

Hope this helps!

-Tom

____________________________________________
Thomas Nichols, PhD
Director, Modelling & Genetics
GlaxoSmithKline Clinical Imaging Centre

Senior Research Fellow
Oxford University FMRIB Centre ------=_Part_20616_21212450.1201820639877-- ========================================================================= Date: Thu, 31 Jan 2008 23:19:59 +0000 Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Sender: FSL - FMRIB's Software Library <[log in to unmask]> From: "Joseph T. Devlin" <[log in to unmask]> Subject: Tissue segmentation in macaques Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi FSLers, I've been trying to use FAST to get a good grey/white segmentation of some monkey brains and having been running into some difficulties. FAST does a nice job with the ventral half of the brain but more dorsally, it is classifying most voxels as white matter. Although by eye, there is a clear grey-white demarcation, in the more dorsal areas the grey matter values appear to be closer to WM values, especially WM values in the ventral part of the brain. I thought this might be a bias field issue, but the bias field outputted by FAST definitely does not show a ventral-dorsal gradient. To be honest, I'm not sure how this is generated, so I'm not certain what to make of that. Regardless, the information necessary to successfully segment GM from WM appears to be present in the image -- at least to my eye, the differences are clear and robust throughout the entire image. Nonetheless, I can't seem to find a way to robustly extract this with FAST and would welcome any suggestions. Thanks, in advance. Joe