Also, a warning: using -cifti-merge-dense can put the structures in a different order than the standard grayordinate space, so -cifti-create-dense-from-template is recommended.
Tim On Fri, Sep 9, 2016 at 1:12 PM, Timothy Coalson <[email protected]> wrote: > Try -cifti-create-dense-from-template. I'll look into why > -cifti-merge-dense might be misbehaving (it is supposed to work for this). > > Tim > > > On Fri, Sep 9, 2016 at 5:47 AM, Maarten Vaessen <[email protected]> > wrote: > >> Hello experts, >> >> I'm trying to create a combined cortical and subcortical dlabel file to >> do parcellated connectivity analysis. In particular, I want to combine the >> newly released 180 regions cortical parcellation (Glasser 2016), with the >> subcortical ROI's from the freesurfer/HCP pipeline. >> >> I tried several commands including wb_command -cifti-create-label to >> create a .dlabel file from the Atlas_ROIs.2.nii.gz file and wb_command >> -cifti-merge-dense to merge left and right cortex dlabels and the >> subcortical ones. >> >> wb_command -cifti-create-label >> subj/MNINonLinear/ROIs/Atlas_ROIs.2.dlabel.nii >> -volume subj/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz >> subj/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz >> >> wb_command -cifti-merge-dense COLUMN all_labels.dlabel.nii -cifti >> Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii >> -cifti >> Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii >> -cifti subj/MNINonLinear/ROIs/Atlas_ROIs.2.dlabel.nii >> >> >> However, this seems to incorrectly merge the cortical and subcortical >> ROI's based on the 'key' value they have. When applying this dlabel to a >> .dtseries file with wb_command -cifti-parcellate, I see this output from >> wb_command file-information: >> >> CIFTI Dim[0]: 226 >> CIFTI Dim[1]: 360 >> ALONG_ROW map type: SERIES >> Start: 0.000 >> Step: 1.000 >> Units: Seconds >> ALONG_COLUMN map type: PARCELS >> Has Volume Data: true >> Volume Dims: 91,109,91 >> CortexLeft: 32492 vertices >> CortexRight: 32492 vertices >> Parcel 1: R_V1_ROI >> CortexRight: 783 vertices >> Parcel 2: R_MST_ROI >> CortexRight: 73 vertices >> Parcel 3: R_V6_ROI >> CortexRight: 123 vertices >> Parcel 4: R_V2_ROI >> CortexRight: 611 vertices >> Parcel 5: R_V3_ROI >> CortexRight: 400 vertices >> Parcel 6: R_V4_ROI >> CortexRight: 263 vertices >> Parcel 7: R_V8_ROI >> CortexRight: 67 vertices >> Parcel 8: R_4_ROI >> CortexRight: 772 vertices >> 8709 voxels >> Parcel 9: R_3b_ROI >> CortexRight: 540 vertices >> Parcel 10: R_FEF_ROI >> CortexRight: 179 vertices >> 1288 voxels >> Parcel 11: R_PEF_ROI >> CortexRight: 100 vertices >> 728 voxels >> Parcel 12: R_55b_ROI >> CortexRight: 101 vertices >> 1060 voxels >> >> >> What is the recommended way to combine cortical and subcortical label >> files? >> >> Thx, >> >> -Maarten >> >> _______________________________________________ >> 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
