what is the nature of the customization? Ie, do you want to customize cortical, subcortical, or WM? For cortical, you will have to specify a different annotation with --ctx-annot when running gtmseg (and specify --o to call it a different name). You may have to update the lookup table generated by gtmseg to indicate the tissue type of any new parcellations. Then just run mri_gtmpvc specifying the new gtmseg
On 09/12/2017 12:30 PM, Elijah Mak wrote: > Hi Doug, > > Thanks for the clarification. According to the PetSurfer guide, it is > stated that there are “ways to customise this segmentation to use ROI > definitions”. How may I go about doing that? Appreciate 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 > > > On 12 September 2017 at 17:27:10, Douglas N Greve > (gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>) wrote: > >> what do you mean? You can only get gtm stats from the parcellations that >> you have used during the process. You can't get new values at the end. >> If you want to use different ROIs, then you need to run gtmseg again >> with a different parcellation, then run mri_gtmpvc with the new gtmseg >> >> >> On 09/12/2017 10:42 AM, Elijah Mak wrote: >> > Hi Doug, >> > >> > Would it be possible to use the gtmstats2table command to extract GTM >> > values from other parellations? >> > >> > Thanks! >> > >> > 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 >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
