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 <gr...@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? >> >> <PastedGraphic-1.png> >> >> 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 >>>> <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 >>>>>>>> <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. 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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 <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. >> >> >> >> _______________________________________________ >> 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 > 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. 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