You can register the brain.mgz (and so all conformed volumes) to MNI152 with the mni152reg script. This will create $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat. If you have a registration for the CT to freesurfer space, then you can combine them like: Rfinal = inv(Rct)*R152 with mri_matrix_multiply -iim Rct -im reg.mni152.2mm.dat -om Rfinal.dat Make sure to check with tkregister2 --mov ct.nii --reg Rfinal.dat --targ $FSLDIR/current/data/standard/MNI152_T1_2mm.nii.gz You can then used mri_vol2vol to put the CT directly into the 152 space.
doug On 10/08/2012 06:29 PM, octavian lie wrote: > Dear all, > I need to coregister a set of volumes/patient (brain.mgz, > ?dpial.ribbon.mgz, and rCT head (CT head already coregistered with the > T1.mgz in SPM and imported in FS) to MNI152 2mm space. > After I coregister the brain.mgz to MNI152, how do I apply the > generated register.dat matix to the ?dpial.ribbon.mgz and rCT > head volumes for normalization? > Also, that all patient volumes are 1mm and MNI template is 2 mm (I > need this specific one) is an issue during normalization? > Thank you, > Octavian Lie. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
