that includes GM regions. not sure what you want
On 10/13/17 8:58 PM, Elijah Mak wrote:
Hi Doug,
That subcort mask is only GM (sorry, should have indicated that when
I named it).
I just looked at the subcort mask in the cvs 2mm folder and it looks
like it is only subcortical? I am looking for a similar mask that also
includes the GM regions. Any idea?
Best Wishes,
Elijah
On 13 Oct 2017, at 17:06, Douglas Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@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 <gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu>
Reply: list Freesurfer support <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: 13 October 2017 at 16:14:34
To: Elijah Mak <fk...@medschl.cam.ac.uk>
<mailto:fk...@medschl.cam.ac.uk>, list Freesurfer support
<freesurfer@nmr.mgh.harvard.edu> <mailto: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 <gr...@nmr.mgh.harvard.edu
<mailto:gr...@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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