Dear fellow Surfers,

I am trying to overlay

FreeSurfer 5.1 MNI305 (=fsaverage) aparc+aseg.mgz 3D volumes (caudate, putamen, pallidum, etc)

onto

FSL MNI152 2mm resolution volume.

I first extract the nuclei from MNI305 aparc+aseg.mgz, for example:

mri_extract_label $FREESURFER_HOME/subjects/fsaverage/mri/aparc+aseg.mgz 11 MNI305_3D_masks/mask_lh_caudate.nii

I then try to resample the extracted volume into FSL MNI152 2mm space, using the registration that comes with FS 5.1 (.dat format):

mri_vol2vol --mov MNI305_3D_masks/mask_lh_caudate.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o MNI152_3D_masks/mask_lh_caudate.nii

Unfortunately, caudate appears in a clearly incorrect location, both when checking the result with tkmedit2, and when viewing the volumes with freeview. Adding --inv does not fix this either.

However, if I simply overlay the volume extracted from MNI305 aparc+aseg on the FSL MNI152 2 mm volume, the location looks just fine. It therefore appears that MNI305 and MNI152 are in the same space, and mri_vol2vol is not needed. Is this correct? Or am I just using an incorrect register.dat file?

Thanks!

Tommi

Details:

On machine ernie nmr-std-env (5.1.0 stable) $FSLDIR = /usr/pubsw/packages/fsl/current/ $FREESURFER_HOME = /usr/local/freesurfer/stable5_1_0/

--- Tommi Raij, MD, PhD TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.