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 (greve@nmr.mgh.harvard.edu mailto:greve@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 greve@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