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.ko...@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.
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