Hi Jan,
Is the functional image already coregistered to the T1? If you have a registration file, you could try:
mri_vol2vol --mov fstcmc.nii.gz --reg registrationfile --tal --talres 2 --o fstcmc.mni305.2mm.nii.gz
.. to bring the functional image to MNI305. Are you planning to your restrict your analysis (assuming it is a voxelwise analysis?) to the subcortical regions? You could use the subcort.mask.mgz in fsaverage/mri.2mm as as mask in your mri_glmfit.
I will leave it to Doug to confirm if those steps are suitable for your objectives.
Best Wishes, Elijah
Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24
On 12 Oct 2017, at 16:14, Jan Willem Koten Jan.Koten@gmx.de wrote:
Normalize to mni
Dear Doug,
We have a very simple question. In a first step we segmented brains using the recon all command. Our functional pipeline created a „fstcmc.nii.gz“ file. We would like to do some subcortical analysis and need to perfrorm this in MNI 305 space. We also need the subcortical labels for the actual analysis itself. Does someone know the trick? In short how do we get from fstcmc.nii.gz“ to subcortical functional ROI's?
Greetings Jan Jan Willem Koten (van Grevenbicht)
Zollernstrasse 57, 52070 Aachen, Germany Telephone: (0049) (0)241 212 44
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.