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Hello,

I am trying to compute the Jacobian for use in VBM. I found the following command on this email archive (Re: [Freesurfer] Jacobian mri_cvs_register (mail-archive.com)https://secure-web.cisco.com/1qsFwf44rr-eT9vRJ1SxsVMe3116pQYdJVNi9THejnTrxkF-e3jpyn5GMmseW8E7QLHMszrt8ETgoweSnkXBEinzGdSmEV8jTlze_GfOb5ksY4jPLXItwQC7ERdX9kCGrBNtB8REckhpvVyRM-0CMUsijzngXvCqA_73mw9nKANklsiTLy4WKhDsIObZyXxQxu77gN_CoJ8KI8mPUZEernkdvEEXvzhCplJmFkf0pbk3LnImhWXjxgyZe0SjEuFrnCPVtuI271WnhbsE0oGRKzBV_y1_esnNup697Qdbc67KTIeGcWRFAHTgqk6km5S8k2Ecgmmn4lgQj7U-5ouebdw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg37388.html:

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/orig.mgz)? Or is it the fsaverage template $FREESURFER_HOME/subjects/fsaverage ?

Thank you,

DC PhD Student University of Wisconsin-Madison