Thanks Danielle

Let us know how it goes Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Danielle Carrol Sent: Wednesday, July 27, 2022 3:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_jacobian questions

External Email - Use Caution Hi All,

I didn’t realize I had removed this conversation from the fs list, so I’m attaching the last message:

The command mri_jacobian certainly does run and outputs a volume file! I'm sorry, but I don't think I understood your original response that the "template" file should have the geometry/direction cosines. The mri_jacobian command takes three arguments (<3d morph> <template volume> <output volume>), and I thought that the first argument ("3d morph") was the file that contains these direction cosines (the transform file "talairach.m3z")? The command mri_jacobian actually runs no matter which volume file I load into that second argument.

Bruce indicated that the second argument, template volume, can be any volume in the recon dir (like orig.mgz) and the output maps would then be in that voxel space. If anyone has any other answers/input, it would be so much appreciated!

Thank you all,

Danielle

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: Wednesday, July 27, 2022 9:54 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_jacobian questions

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Danielle Carrol Sent: Wednesday, July 27, 2022 10:48 AM To: freesurfer@nmr.mgh.harvard.edumailto: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