You can combine the ROIs into a single map (with a different integer for each) with -cifti-reduce using INDEXMAX. You should then also mask out the areas that aren't in any ROI by using -cifti-reduce MAX on your ROIs file, and then using -cifti-math with 'index * (mask > 0)'. Finally, you need to make that into a dlabel file with -cifti-label-import, and then -cifti-parcellate will do what you expect.
If you have only a few ROIs, you could also split them into separate files with -cifti-merge, and use them one at a time in -cifti-stats. The -*-stats commands weren't originally designed to use multiple ROI maps on the same data in one command. The next release may have this feature. Tim On Tue, Jun 27, 2017 at 12:38 PM, Elam, Jennifer <e...@wustl.edu> wrote: > Hi Serguei, > > Not sure this helps your question, but it looks like the rest of the > thread ended up here: https://www.mail-archive.com/ > hcp-users@humanconnectome.org/msg04426.html > > > <https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04426.html> > > CC'ing Tim Coalson so he can help you directly, however he is currently at > OHBM so may take a few days to respond. > > > Best, > > Jenn > > > Jennifer Elam, Ph.D. > Scientific Outreach, Human Connectome Project > Washington University School of Medicine > Department of Neuroscience, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > e...@wustl.edu > www.humanconnectome.org > > ------------------------------ > *From:* hcp-users-boun...@humanconnectome.org <hcp-users-bounces@ > humanconnectome.org> on behalf of Astafiev, Serguei <astaf...@wustl.edu> > *Sent:* Tuesday, June 27, 2017 2:18:17 PM > *To:* hcp-users@humanconnectome.org > *Subject:* [HCP-Users] values from ROIs > > > Hello, > > I am having the same problems as in this post: > > > > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04421.html > > > > I have ROI (created by -cifti-rois-from-extrema) file where each ROI is in > different map. I want to extract z-values/beta values from each ROI, but I > get only one value (from ROI in map1): My ROIs do not overlap, so I can > combine them into a single map (not sure how to do it). > > > > wb_command -cifti-stats ${inputfile}.dscalar.nii -reduce MEAN -roi > ${ROIfile}.dscalar.nii -show-map-name > > 1: : 4.188334 > > > > > > -cifti-parcellate also is giving me the same value for 1 map only (after > converting ROIs to labels). > > wb_command -cifti-parcellate ${inputfile}.dscalar.nii > ${ROIfile}.dlabel.nii COLUMN ${outputfile}.pscalar.nii -method MEAN > > > > > > It has been almost 2 months since that post, so I wonder if somebody knows > the solution for this problem. > > > > Best regards, > > Serguei Astafiev > > > > > ------------------------------ > > 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 > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
