I think I misunderstood the problem, a single ROI should work fine. Are you talking about thresholding in the display settings (the wrench icon on the layer in wb_view)? That doesn't actually threshold the file into an ROI, that just changes the display of it to not color the outside-threshold values. To actually threshold it to make an ROI file, you need to do something like this:
wb_command -cifti-math 'x > 5.3' ROI.dscalar.nii -var x inputstatistic.dscalar.nii Tim On Thu, Oct 19, 2017 at 2:02 AM, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote: > 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_thresho >>> lded_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
