Hi,
Ok so most of my problems are now fixed, but there is still one problem
regarding the Jacobian.
So first of all my images were normalized as follows:
createMorph --out fullCVSmorph.tm3d --template f2/mri/brain.mgz --subject
f1/mri/brain.mgz --in gcam combined_tof2_elreg_afteraseg-norm.m3z
Hi Andre,
What do you mean by they do not seem to match voxel-wise? Are they of
different size or are they not in a corresponding space?
Which version of FreeSurfer are you using?
Could you send the volumes over? I don't see anything wrong with the
commands so I would like ot take a look
Thank you! Didn't realized that function existed.
Regards,
Andre Santos Ribeiro
On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@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
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
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).
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
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
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?
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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