I got an error using the mri_jacobina.
The function returns:

The input morph originated from a tm3d (mri_cvs_register file).
GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000

mri_jacobian: could not read input morph /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d

The command is provided below:
mri_jacobian -tm3d /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz

Regards,
Andre Santos Ribeiro
PhD Student, Imperial College London

On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro <afs13@imperial.ac.uk> wrote:

Thank you! Didn't realized that function existed.

Regards,
Andre Santos Ribeiro

On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei <lzollei@nmr.mgh.harvard.edu> wrote:

Hi Andre

You can run:

mri_jacobian -tm3d <3d morph> <template volume> <output volume>

--Lilla

On Thu, 10 Jul 2014, André Ribeiro wrote:

Dear Freesurfer Community,

How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis?

Regards,
Andre Santos Ribeiro

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