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]>> 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]>> 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]>] *On
>> Behalf Of *Mi Jung Kim
>> *Sent:* Monday, March 09, 2009 11:31 PM
>>
>> *To:* [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]>> 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]>] *On
>> Behalf Of *Mi Jung Kim
>> *Sent:* Monday, March 09, 2009 9:45 PM
>>
>>
>> *To:* [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]>> 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]>] On Behalf
>> Of Mi Jung Kim
>> Sent: Monday, March 09, 2009 6:43 PM
>> To: [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>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
--
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
|