Hi Danielle

I believe that the template volume has the geometry/direction cosines to use for the output.

Note that this is an *old* binary and not really used any longer so I’m not sure it works ☹.

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Danielle Carrol
Sent: Wednesday, July 27, 2022 10:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_jacobian questions

        External Email - Use Caution        

Hello Freesurfer experts!

I have been trying to send this question a few times, but it has never shown up on the archive, so I'm not sure if it has been received. I apologize if everyone has been receiving the same question multiple times!

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, which is created during recon-all, 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:

${SUBJECTS_DIR}/<subject name>/mri/brain.mgz)? 

Is it the fsaverage MNI template:

$FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz? 

I also thought it could be this file: 

freesurfer-latest/average/RB_all_2016-05-10.vc700.gca    

since I saw on the wiki page for recon-all that in the creation of the .m3z morph file, the nonlinear transform is computed to align with the GCA atlas, so that could be the "template" (recon-all - Free Surfer Wiki (harvard.edu)).

I am using version 6.0.0.

Thank you for you advice and time,

Danielle

PhD Student

University of Wisconsin-Madison