You can
mri_binarize --gm --i aparc+aseg.mgz --o gm.mask.mgz
On 10/16/17 12:41 PM, Elijah Mak wrote:
Hi Doug,
I am looking for a total GM mask that includes cortical and subcortical regions.
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
On 16 Oct 2017, at 16:09, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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?
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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? > > 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 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person >> to whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >
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