Hey Timothy, thanks for your response. Before continuing with the questions about the exact implementation I am not very sure as to why you refer to my ROIs in plural. As ROI, I used the dscalar file which I got as an output of PALM, i.e. it is a file showing where there was a significant difference between two groups. I threshholded it in the Workbench and saved the changes, so that the file now only shows the really significantly different areas. In my understanding this is only one ROI/one map. Do I understand it wrongly? I can attach the file if you want.
I just want to see what the mean myelination in these exact areas that turned out to be significant is in the groups I compared. Hope it makes sense. Thanks again! Lisa On 18 October 2017 at 01:12, Timothy Coalson <tsc...@mst.edu> wrote: > The -cifti-parcellate command is currently the easier way to do this, if > your ROIs don't overlap. The -roi option to -cifti-stats currently uses > only the first map, and only tests for whether the value is greater than 0, > so probably the first map in your roi input is actually all positive. Also > note that MEAN does not take a dash in front of it, which would cause an > error. > > Tim > > > On Tue, Oct 17, 2017 at 5:57 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > >> It might only be using the first ROI. Tim will know better what is the >> issue. You might try converting the ROIs to a parcellation and then >> parcellating the myelin map and converting the parcellated file to text or >> whatever you need. >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa >> Kramarenko <lisa.kramare...@gmail.com> >> Date: Tuesday, October 17, 2017 at 7:11 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Extraction of mean myelination values from a custom >> roi >> >> Dear experts, >> >> I have a question about extracting average myelination value from a >> custom roi. What I did was the following: >> >> wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce >> -MEAN -roi file_with_significant_differences_between_the_groups_ >> thresholded_at_1.3.dscalar.nii >> >> I get a series of numbers (for every of the merged maps), however they >> don't change if I omit the roi part which leads me to believe that the >> average is calculated across the whole cortex and not specifically in areas >> I want to specify. >> >> What would be the best way to find out the mean myelination values in a >> specific roi (which is defined by the file with significantly different >> areas)? >> >> I hope you understand what I mean. >> >> Thanks a lot for your help! >> >> Best, >> Lisa >> >> _______________________________________________ >> 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 >> > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
