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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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)<https://secure-web.cisco.com/1PxtNE3QwqzX1SDyVeD_p5OwDGQgLiBBekceqUimQr0kRg9-qJTCQSMrRBRzLVfHg4Twnkbj_7DVf24lggbNBI5JrT68fMvlpmlfzP0DBmnR8oaSMi42BY3SQfLkH5__Oa91xsq9CFVRF5J8u8MNS_J0L__he7I1h2JoIe2eiGzbX_cGJxY2FdKIgCZ8hWejJ_0dJbj1xVnKYAf0NhJ6QJoDUmSjhbhHOeedt8ml6uVqmBaNjZfNvnBWhwhADhKw1FWt00fWkr_H875_fcbjqDBEwluq9H6bCO5QinX3yrZRWqP0j5rgP-O_Rg07w29iAQGWMbLZwfKw3vLQv5Ylnhw/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, 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)<https://secure-web.cisco.com/1dWy6gXJGfzUBSGAO9bR9NM58WNn9B3AwqHd2Y8dt6SwThZ2IMnLMMwozFkbNgOhP7XplH9RQHNuidHO-h1QQCKaP9Hryqdexnkhmi1Z_St4Y6wS-NyPpQjeTmfJhrbR3JiQoBJmZaxFD8FazjRIHUnir-we1vK8Qup8h9nE_-Id-0Ac2saAbl4v9fD44Ptz7QbZZyGRhN8g5kYTVIPu_mRic6QAyF6DYRXohmsKj3iNbAgxKW_kK8dPOAeSfGsfNNwuHY2ntcSs0xJBQRqeqDGu9I9VRy6QpswPHZPHFmpGdwtiFOcWix0bTUzfFDO-7BJAj2tf_Z8NnTVbEUUoS-w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23EM.28GCA.29Registration.28-.3Cno.3Egcareg.29>).
I am using version 6.0.0.
Thank you for you advice and time,
Danielle
PhD Student
University of Wisconsin-Madison
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