Hi! Thanks for the fast answer. <div>If I do: diff id1.bvec id2.bvec</div><div>I can see some clear differences. </div><div><br></div><div>I was told that in FSL I should use the bvecs and bvals created in dcm2nii per subject, so I understand I should do the same now?</div>
<div>Do you think an option would be to script the creation of a dmrirc file per each subject and then launch as many trac-alls as subjects?</div><div><br></div><div>Thanks again,</div><div>Gari<br><br>On Thursday, September 26, 2013, Anastasia Yendiki  wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Hi Gari - Sorry, right now the assumption is that the gradient vectors are the same for all subjects. How different are they?<br>
<br>
a.y<br>
<br>
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using<br>
Siemens Dicoms, so I did not specify any setting for bval and bvec, but when<br>
trac-all -prep starts running it gives the following error: mv: cannot stat<br>
&#39;paths.../SubjectID/dmri/dwi_<u></u>orig_flip.mghdti.bvecs&#39;: No such file or<br>
directory<br>
<br>
Ok, so I understand that our problem is that we don&#39;t have MGH Siemens<br>
Dicom. <br>
<br>
So I used dcm2nii to convert it to .nii files and each conversion gives me a<br>
SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every<br>
.bvec file is a different one. <br>
<br>
I can edit &quot;set dcm_list = &quot; to include all the newly created .nii files,<br>
but<br>
<br>
My question is: <br>
- How can I specify every .bvec value for every subject? In the dmrirc file<br>
everything I see is a &quot;set bvecfile = &quot; option.<br>
<br>
Thank you very much,<br>
Gari<br>
<br>
<br>
</blockquote>
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