The command to do this is -cifti-separate with the -volume option and -roi suboption, and the CEREBELLUM_LEFT and CEREBELLUM_RIGHT structures (we don't use the CEREBELLUM label in the volume, instead we split the hemispheres), however, it always outputs the data from the requested structure also, so you don't want to run it on a dconn (especially not for volume structures). Instead, run it on any dscalar or small dtseries file you have lying around that uses the same dense mapping (or use -cifti-reduce to make one from the dconn). Alternatively, if you are using a standard grayordinate space, you can extract the cerebellum halves from the volume label file in the Pipelines repository that defines the grayordinate voxels, with -volume-label-to-roi, like this:
wb_command -volume-label-to-roi Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz cerebellum_left_roi.nii.gz -name CEREBELLUM_LEFT wb_command -volume-label-to-roi Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz cerebellum_right_roi.nii.gz -name CEREBELLUM_RIGHT Since either way of getting these ROIs has the halves separate, you then need to combine them with -volume-math: wb_command -volume-math 'x || y' cerebellum_all_roi.nii.gz -var x cerebellum_left_roi.nii.gz -var y cerebellum_right_roi.nii.gz Tim On Fri, May 5, 2017 at 3:42 PM, Xavier Guell Paradis <[email protected]> wrote: > Thank you for your reply. > Runing -cifti-restrict-dense-map again with ROW direction has worked; now > I see cerebellum data only. However, I think it would be "cleaner" to do as > you suggested and "get the ROI of where cerebellum data exists from the > cifti file". How could I do this? > Thank you very much, > Xavier. > ------------------------------ > *From:* Timothy Coalson [[email protected]] > *Sent:* Friday, May 05, 2017 4:32 PM > *To:* Xavier Guell Paradis > *Cc:* [email protected] > *Subject:* Re: [HCP-Users] modify dconn file so that it only includes > cerebellum values? > > On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis <[email protected]> > wrote: > >> Dear HCP experts, >> I am trying to modify the group average dconn file >> (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it >> only includes data from the cerebellum (even though, of course, these data >> will correspond to the connectivity of each cerebellum voxel to the rest of >> the brain). >> I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile >> -vol-roi cerebellumatlas.nii >> ("cerebellumatlas.nii" is a cerebellum volume atlas which contains values >> for the cerebellum only) >> This has not worked. >> > > That should work, but you need to run it again on the output of that, this > time with the ROW direction, so that both directions are cerebellum-only. > Please be more specific than "has not worked", did you get an error (and if > so, copy the error message), or did its output not match what you expected? > >> > >> I have also tried to use the -cerebellum-roi option of >> -cifti-restrict-dense-map, without writing any metric file after >> -cerebellum-roi. This also doesn't work. >> > > This should have caused an error, as the current grayordinates space > doesn't use surfaces for cerebellum. Additionally, if you don't provide a > required argument to an option, you will get a different kind of error. > > Is there any way to tell wb_command that I only want to keep the >> cerebellar data, without having to include any file which indicates where >> the cerebellum is? >> > > No, this isn't a use case we expected, normally we want to match existing > cifti mappings (for instance, 91k grayordinates), not make new ones. It is > possible to get the ROI of where cerebellum data exists from the cifti > file, but since you say you already have that ROI...on the other hand, if > the specific error you got was something like "volume space doesn't match", > then you actually should derive the ROI from the cifti file, rather than > using whatever you have. > > >> Thank you very much, >> Xavier. >> >> _______________________________________________ >> 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
