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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/1LenU0lNm3dfOywG0njDPZc5l9fJtDrLhnstVxKLgojhf4INu-xOt3zyWLiUb9GTtL6q6PFrGkH6PxIhILW2O0UiWG34x-erJOAdoNmNpDll7fxzgzn5Eq8TM-mur3NpVNYTf5yEJ-BG9LQNvrnjOazX4phGyZldVSNye1gh9F-owjFZxPgmz1igJu032-tuKJMIxLU8CYpfFg2ZfqwgL_oxlmJLr3r9tlMda-FkpUgRG91KiIPeW8JgvvNMufLJ6ROedKEPDUDXlY6fjK3XvjvPGRCoVOCeTiYC8jPqcScm84fjGl_2fTo6ED68j7ZOm/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/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