Use -cifti-weighted-stats, it reports the measures separately per hemisphere (and can integrate over surface area instead of a naive mean), and use the -roi option to report within an ROI. If you want to use a lot of ROIs that don't overlap, look at -cifti-parcellate.
Tim On Wed, Nov 2, 2016 at 3:20 PM, Timothy Hendrickson <[email protected]> wrote: > Thanks Matt. > > Hmm I am still confused. So here is my command to extract myelin for the > entire cortex: wb_command -cifti-stats 43387.MyelinMap.32k_fs_LR.dscalar.nii > -reduce MEAN. > Since -cifti-stats requires the -reduce flag the data I receive is only > one number. What I am hoping to accomplish is to extract the average > surface myelin for the left and right hemisphere and all surface ROIs. > For example with freesurfer I can rather easily generate a stats file > which informs me a measurement (of my choosing) at each particular > location. For example see attached: lh.allSite.aparc.thickness.csv. > > I apologize for the continued questions. I am fairly new to HCP data and > am still learning the in and outs :) > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > > On Wed, Nov 2, 2016 at 1:20 PM, Glasser, Matthew <[email protected]> > wrote: > >> You should be able to do that with the commands Tim mentioned with the >> -roi sub option. >> >> Peace, >> >> Matt. >> >> From: <[email protected]> on behalf of Timothy >> Hendrickson <[email protected]> >> Date: Wednesday, November 2, 2016 at 11:42 AM >> To: Timothy Coalson <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] Myelin Map Summary Statistics >> >> Hmm, I have a follow up question. I can extract average myelin for the >> entire cortex rather easily however I am having more trouble extracting >> hemispheric and ROI information. >> Suggestions? >> >> Timothy Hendrickson >> Department of Psychiatry >> University of Minnesota >> Mobile: 507-259-3434 (texts okay) >> >> On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson <[email protected]> wrote: >> >>> Take a look at http://www.humanconnectome.org/software/workbench-command >>> .php?function=-cifti-weighted-stats and/or http://www.humanconnect >>> ome.org/software/workbench-command.php?function=-cifti-stats . >>> >>> Tim >>> >>> >>> On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson <[email protected]> >>> wrote: >>> >>>> HCP experts, >>>> >>>> Is there a way to extract myelin values from individual dscalar CIFTI >>>> files? >>>> What I am looking for is an average myelin value at the hemispheric and >>>> ROI level. >>>> >>>> -Tim >>>> >>>> Timothy Hendrickson >>>> Department of Psychiatry >>>> University of Minnesota >>>> Mobile: 507-259-3434 (texts okay) >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> [email protected] >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>> >>> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
