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 <greve@nmr.mgh.harvard.edu mailto: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 mailto:greve@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 fkm24@medschl.cam.ac.uk mailto:fkm24@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?
- mri_cvs_register to bring T1s to CVS MNI152
- 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 mailto: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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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