Hello,

 

I am trying to compute the Jacobian for use in VBM. I found the following command on this email archive (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be Re: [Freesurfer] Jacobian mri_cvs_register (mail-archive.com):

              

        mri_jacobian <3d morph> <template volume> <output volume>

 

I am assuming the 3d morph is the file mri/transforms/talairach.m3z, since this file provides the nonlinear warp. However, I am confused about which file should be the “template volume”. Is this the final transformed/registered volume for each subject (i.e. ${SUBJECTS_DIR}/<subject name>/mri/brain.mgz)? Is it the fsaverage template $FREESURFER_HOME/subjects/fsaverage ? I am using version 6.0.0.

 

Thank you,

 

DC

PhD Student

University of Wisconsin-Madison