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 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 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 supportfreesurfer@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
- mri_fwhm to smooth the PET volumes, using a binarised mask of GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
- What is the best way to get the mask from the cvs_avg35_inMNI152 subject?
- 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 mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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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