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 > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu(mailto: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. > > > > _______________________________________________ > Freesurfer mailing list > 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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