Hi! Thanks for the fast answer. If I do: diff id1.bvec id2.bvec I can see some clear differences.
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? 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?
Thanks again, Gari
On Thursday, September 26, 2013, Anastasia Yendiki wrote:
Hi Gari - Sorry, right now the assumption is that the gradient vectors are the same for all subjects. How different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using
Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_**orig_flip.mghdti.bvecs': No such file or directory
Ok, so I understand that our problem is that we don't have MGH Siemens Dicom.
So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one.
I can edit "set dcm_list = " to include all the newly created .nii files, but
My question is:
- How can I specify every .bvec value for every subject? In the dmrirc
file everything I see is a "set bvecfile = " option.
Thank you very much, Gari
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