What does ls give you?
It should (at least) return data.nii.gz nodif_brain_mask.nii.gz bvecs bvals.
Otherwise bedpostx_datcheck will not find them.
Mi Jung Kim wrote:
> Hi,
>
> Yes, it is right. I am in the right folder.
>
> What I did was following.
> 1. Merge files as 4D
> 2. do eddy current correction; I actually do not need it because I know
> my data do not have much eddy current distortion, but I did it anyway.
> 3. run bedpostx_datacheck because I cannot do 'dtifit'.
>
> I have 7 volumes such as b0 to b5 so that my vectors and values are 7.
>
> Any suggestion?
>
> Sincerely,
>
> Mi Jung
>
> On Tue, Mar 10, 2009 at 8:21 AM, Mareike Menz <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Mi Jung,
>
> the 4D file is needed anyway - that was missing before.
> For bedpostx_datacheck you should name it data.
> Funnily you have a file called data.ecclog - this is output of
> eddy_current correction (for whatever Input - b-all?). You should
> merge the volumes first, then correct for eddy currents and motion
> (eddy_correct) and finally run bedostx_datacheck.
> Your number of volumes needs to be exactly the same as entries in
> bvals and entries/line in bvecs.
> Without renaming you can also check the number of volumes with
> fslnvols <4D> (e.g. b-all).
>
> Greetings,
> Mareike
>
> Mi Jung Kim wrote:
>
> Hi Saad and Matt,
>
> Picture 1 is from when i ran 'dtifit'.
>
> I attached my bvecs and bvals. Could you take a look at them
> because bedpostx_datacheck shows that I do not have that files.
> I have ascii file and link them.
> I have 6 gradient directions with 16 NEX along with b=0 images.
> I used 'fslmerge -t b-all b0 b1 b2 b3 b4 b5 b6' to make a 4D file.
>
> Sincerely,
>
> Mi Jung
>
> On Tue, Mar 10, 2009 at 7:50 AM, Saad Jbabdi
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>
> Hi Mi Jung
> Can you please tell us what command you are running and what
> error
> messages you get?
>
> Cheers,
> Saad.
>
> On 10 Mar 2009, at 14:40, Mi Jung Kim wrote:
>
> Hi Matt,
>
> I think that I am supposed to some sort of data
> information after
> bedpostx_datacheck, am I right? But I do not see anything.
> The folder has following data sets;
> b-all.nii.gz b4.nii.gz bvecs
> b0.nii.gz b5.nii.gz bvecs.txt
> b1.nii.gz b6.nii.gz nodif.nii.gz
> b2.nii.gz bvals
> nodif_brain.nii.gz
> b3.nii.gz bvals.txt
> nodif_brain_mask.nii.gz
>
> Do I miss something?
>
> Sincerely,
>
> Mi Jung
>
> On Tue, Mar 10, 2009 at 7:05 AM, Matt Glasser
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>
> 1) Open a commandline terminal
>
> 2) Navigate to the folder that your data is
> stored in
>
> 3) Type bedpostx_datacheck
>
>
> Peace,
>
>
> Matt.
>
>
> ------------------------------------------------------------------------
>
> *From:* FSL - FMRIB's Software Library
> [mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>] *On
>
> Behalf Of *Mi Jung Kim
> *Sent:* Monday, March 09, 2009 11:31 PM
>
> *To:* [log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> *Subject:* Re: [FSL] capillary phantom for muscle dti
>
>
>
> Hi Matt,
>
> I am actually sort of beginner with dti analysis.
> Could you
> tell me how to run bedpostx_datacheck please?
>
> Sincerely,
>
> Mi Jung
>
> On Mon, Mar 9, 2009 at 7:54 PM, Matt Glasser
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>
> Please run bedpostx_datacheck in your data folder,
> and post
> the result here.
>
>
> Peace,
>
>
> Matt.
>
>
> ------------------------------------------------------------------------
>
> *From:* FSL - FMRIB's Software Library
> [mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>] *On
>
> Behalf Of *Mi Jung Kim
> *Sent:* Monday, March 09, 2009 9:45 PM
>
>
> *To:* [log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
>
> *Subject:* Re: [FSL] capillary phantom for muscle dti
>
>
>
> Hi Mark,
>
> Thanks a lot. I also tested with b0 images, but it
> still gives
> same error.
>
> Thanks,
>
> Mi Jung
>
> On Mon, Mar 9, 2009 at 6:04 PM, Matt Glasser
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>
> It looks like you are missing the b0 image. Amend
> your bvecs
> to be:
>
> {0.0 1.0 0.446 0.447 0.448 0.447 -0.449
> 0.0 0.0 0.895 0.275 -0.723 -0.724 -0.277
> 0.0 0.0 0.0 0.851 -0.525 0.526 0.850}-bvecs
>
> And your bvals to be:
>
> {0 500 500 500 500 500 500}-bvals
>
> Peace,
>
> Matt.
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library
> [mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>] On Behalf
> Of Mi Jung Kim
> Sent: Monday, March 09, 2009 6:43 PM
> To: [log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> Subject: [FSL] capillary phantom for muscle dti
>
> Hi All,
>
> I am trying to use probabilistic tractograph with my
> phantom
> data. I have
> problem with running 'dtifit'. Below are my bvecs and
> bvals.
> {1.0 0.446 0.447 0.448 0.447 -0.449
> 0.0 0.895 0.275 -0.723 -0.724 -0.277
> 0.0 0.0 0.851 -0.525 0.526 0.850}-bvecs
> {500 500 500 500 500 500]-bvals
>
> But I see some error message so that I suspect that
> my vectors
> and values
> are not matched with my dwi images. My images
> actually scaled
> images from
> dicom.Would it be a problem?
>
> Is there anybody who can help me?
>
> Thanks,
>
> Mi Jung
>
>
>
>
> Saad Jbabdi
> Oxford University FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222545 (fax 717)
> www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad>
> <http://www.fmrib.ox.ac.uk/%7Esaad>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
>
> --
> Mareike Menz
> NeuroImage Nord Lübeck
> University Medical Center Hamburg-Eppendorf, Bldg. S10
> Martinistr. 52
> 20246 Hamburg
> Germany
> +49 40 7410 53683
> [log in to unmask] <mailto:[log in to unmask]>
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> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
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>
--
Mareike Menz
NeuroImage Nord Lübeck
University Medical Center Hamburg-Eppendorf, Bldg. S10
Martinistr. 52
20246 Hamburg
Germany
+49 40 7410 53683
[log in to unmask]
-------------------------
() ascii ribbon campaign
/\ - against html mail
--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg
Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Ricarda Klein
Prof. Dr. Dr. Uwe Koch-Gromus
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