Thank you for the explanation but in that case there are two things that seems odd.

First, in the mri_cvs_register I kept all the files and therefore the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" file was not removed. If I try to replicate this file through the
"createMorph --out fullCVSmorph.tm3d --template template.mgz --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z morph el_reg_toTEMPLATE.tm3d" the file produced is different from the one previously created by the program (and gives far worse registration results when used with the "applyMorph"). Is something wrong here?

Second, even if the two files gave the same results wouldn’t this fullCVSmorph.tm3d (otherwise called combined_toIBSR_02_elreg_afteraseg-norm.tm3d) have both information from  *afteraseg-norm.m3z and el_reg_toTEMPLATE.tm3d, and therefore the Jacobian applied solely to the nlalign-afteraseg-norm.m3z would not match.

Lastly, am I right assuming the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" is the last registration (and most accurate) performed by mri_cvs_register?


Regards,
Andre Santos Ribeiro



On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei <lzollei@nmr.mgh.harvard.edu> wrote:

Hi, You should use the final m3z file. The -tm3d flag just indicates that the file was created by mri_cvs_register.
Lilla


On Fri, 11 Jul 2014, André Ribeiro wrote:

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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