Label commands take pains to avoid making collisions between labels with different names, or altering label key values when not necessary. They also generally don't remove labels simply for not being used in the output, because that could introduce problems when a small, hard to find area is missed - instead of shifting all the key values for that subject or making a label table with a missing key, it keeps the label around despite being unused. The label import commands do have options to make different choices in these situations, but will still not compact the key values into a minimal range. There is a command to modify the keys for gifti label files, but it appears I haven't yet made volume and cifti equivalents.
Having non-compact key values or unused label names is probably okay for most processing. If you want them reduced and compacted, you could take a parcellated cifti file, and use wb_command -cifti-parcel-mapping-to-label on it - the colors will be random, but the key values will be compact and in the order of the parcels in the file. Tim On Thu, Sep 13, 2018 at 3:31 PM, Leonardo Tozzi <lto...@stanford.edu> wrote: > To Whom it may concern, > > > > I followed the indications in this thread: > > > > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03976.html > > > > To merge the subcortical labels of > Gordon333_FreesurferSubcortical.32k_fs_LR.dlabel.nii > with the cortical ones from Q1-Q6_RelatedValidation210. > CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii. > > In particular I used -cifti-separate with the -volume-all option, followed > by -cifti-create-dense-from-template. With the same commands reported in: > > > > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03979.html > > > > When I look at my atlas in connectome workbench, everything “looks” fine: > the subcortical volumes are displayed in the volume tab, the surface colors > correspond with the Glasser parcellation. Clicking in the view window also > displays the correct labels in the information window. However, if I click > in “Edit map labels” in the workbench interface, I noticed that the keys of > the Gordon atlas are still present and the “new” labels seem to start at > key 334 (since the Gordon has 333 regions). Opening the dlabel file with > ciftiopen in Matlab also returns data that goes from 0 to 712: > > > > atlas=ciftiopen('mergedatlas.dlabel.nii', '/Applications/workbench/bin_ > macosx64/wb_command') > > atlas = > > > > struct with fields: > > > > cdata: [91282×1 single] > > > > max(atlas.cdata) > > > > ans = > > > > single > > > > 712 > > > > Interestingly, doing a task analysis using the HCP pipeline and entering > the merged dlabel file as atlas only returns a cifti with the number of > regions I would expect: > > > > img=ciftiopen(‘tfMRI_EMOTION_LR_Atlas_s2_mergedatlas.ptseries.nii’, > '/Applications/workbench/bin_macosx64/wb_command') > > img = > > > > struct with fields: > > > > cdata: [379×176 single] > > > > > > My question is: why are the labels of the Gordon atlas being displayed in > the workbench? Are they being “carried over” as labels that do not actually > correspond to any greyordinates? Should I be worried that these “Phantom > labels” might affect my analyses? > Thank you very much. > > Yours faithfully, > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > _______________________________________________ > 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
