Hi,

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?

No, there is nothing wrong. In the above command you are just not composing the right files. I assume that you have run the default mri_cvs_register command. In that case there are two non-linear registration steps one aided by aseg info and one by intensities. In the above you are skipping the morph created by the former so that is why you are not getting the same combined output. Instead of "morph el_reg_toTEMPLATE.tm3d" you would need to use "morph combined*aseg.tm3d"

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.

It is correct. The jacobians of fullCVSmorph.tm3d and nlalign-afteraseg-norm.m3z will not match. I am a bit confused about whey you think they should.

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?

Yes. In the most current FS version though we use the m3z files as we are trying to phase out the tm3d format.

Lilla

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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