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)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