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.
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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Douglas N Greve -
octavian lie