You can use -cifti-replace-structure with the -volume-all option and a volume file of zeroes. If you have a lot of maps (or you want to do something similar to a long dtseries), you can make a cifti file with 1's in the surfaces and 0's in voxels, and use -cifti-math to multiply them together. For a small dscalar file, I would do it like this:
wb_command -cifti-separate <your-file> COLUMN -volume-all volspacetemp.nii.gz -crop wb_command -volume-math '0' zerovol.nii.gz -var x volspacetemp.nii.gz cp <your-file> data_subcort_zeroed.dscalar.nii wb_command -cifti-replace-structure data_subcort_zeroed.dscalar.nii COLUMN -volume-all zerovol.nii.gz -from-cropped I am curious, why do you want the subcortical data to be zero? It won't make the file smaller, and processing commands will still think there is data there, it won't interact with the surface data regardless of whether it is zero, and you can choose not to display the subcortical stuff anyway... Tim On Wed, Oct 4, 2017 at 10:07 AM, Xavier Guell Paradis <xavie...@mit.edu> wrote: > Dear HCP experts, > I have a dscalar file with one map of cortical and subcortical data. I > would like to transform all subcortical values to 0, and leave the cortical > surface values intact. I have explored the -cifti-stats and -volume-stats > options as well as -cifti-create-dense-scalar but cannot figure out a way > to do this. > > Thank you very much, > Xavier. > > _______________________________________________ > 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
