Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz


On 10/11/17 3:15 PM, Elijah Mak wrote:
Hi Doug,

Thanks. 

Could I check my workflow to perform the constrained smoothing of PET MGX-GM volumes? My objective here is to normalise the PET volumes to the CVS-MNI152 space to produce group-level PET maps. As such, should I be deriving the GM + Subcortical PVFs from the cvs_avg35_inMNI152 subject for the mask in mri_fwhm?

1. mri_cvs_register to bring T1s to CVS MNI152
2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 space) to CVS MNI152
3. mri_fwhm to smooth the PET volumes, using a binarised mask of GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
4. What is the best way to get the mask from the cvs_avg35_inMNI152 subject? 
5. Obtain group level PET maps in CVS MNI152 space using mri_concat —mean.

Thanks very much.

Best Wishes,
Elijah

On 4 Oct 2017, at 14:51, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

You mean for volume-based analysis? Yes, use the pvf.


On 10/4/17 9:42 AM, Elijah Mak wrote:
Hi Doug,

I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I would like to constrain the smoothing to the GM. Is it advisable to use the PVF in the aux folder for this purpose? If not, what is the best approach do this?

Thanks!

Best Wishes,
Elijah



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