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.
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