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 applyMorph --template f2/mri/brain.mgz --transform fullCVSmorph.tm3d vol f1/mri/brain.mgz reg_f1_brain.nii.gz trilinear
then for the Jacobian: mri_jacobian -tm3d combined_tof2_elreg_afteraseg-norm.m3z f1_brain.nii.gz jacobian.nii.gz
Now if I visualize both the reg_f1_brain.nii.gz and jacobian.nii.gz they do not seem to match voxel-wise, and therefore cannot be applied for VBM. Both the jacobian and the registered t1 brain image use the same transform and therefore should be aligned. Am I making some mistake here?
Sorry for this question in advance.
Regards, Andre Santos Ribeiro PhD Student, Imperial College London
On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei lzollei@nmr.mgh.harvard.edu wrote:
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 justindicates 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_registerfile). 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> <outputvolume>
--Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformationfield estimated through mri_cvs_register for further use like VBM analysis?
Regards, Andre Santos Ribeiro _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for theperson to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.