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Hello,

I am trying to compute the Jacobian for use in VBM. I found the following command on the email archive:

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