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 <[email protected]> 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: <[email protected]> on behalf of Lisa > Kramarenko <[email protected]> > Date: Tuesday, October 17, 2017 at 7:11 AM > To: "[email protected]" <[email protected]> > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > 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
