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 >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
