On 13 Oct 2017, at 17:06, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
That subcort mask is only GM (sorry, should have indicated that when I named it).

On 10/13/17 11:15 AM, Elijah Mak wrote:
Hi Doug,

Yes, but I am using the GM rather than the subcortical volume. How can we get a similar GM mask on CVS 2mm space?

Thanks for your help.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group

University of Cambridge,
Trinity College, CB21TQ, UK

http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Reply: list Freesurfer support <freesurfer@nmr.mgh.harvard.edu>
Date: 13 October 2017 at 16:14:34
To: Elijah Mak <fkm24@medschl.cam.ac.uk>, list Freesurfer support <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Constrain smoothing to GM for PET data
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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