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 <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. 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> >>> >>> >>> 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. 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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