Parcel naming
mharms opened this issue · 9 comments
Thanks for making this available. It's great to have a rigorous network partition, including the addition of subcortex, of the Glasser parcellation.
However, it's a bit cumbersome to work with the current parcel naming scheme. Specifically, there is one parcel in each network that does not have a numeric suffix as part of its name. e.g., Most parcels in the visual network are named "Visual_#", but "Visual" is the name of one specific parcel as well . So not only does the name of one parcel for each network not map to a standard naming format, but the name of that parcel is identical to the name of the network itself.
Also, it is bit non-intuitive that the cortical parcels are named with an underscore, and the subcortical ones with a dash. A more intuitive distinction in the naming between the cortical and subcortical parcels would be helpful.
In terms of sorting, it would be convenient if the numeric portion of the parcel names was padded to a consistent number of digits.
Last, I know all the necessary information is already contained as part of the *.txt and *.dlabel.nii files, but it is a bit hard to integrate. It would be convenient if a single summary csv was provided that linked the parcel names, the name of the parcel in the original Glasser version, their hemisphere, their numeric position in the dlabel file, the parcels 'key' values, their network assignment, the networks 'key' value, and the parcels position when they are resorted according to the *order.txt files. Without this, it is challenging to navigate between the different data representations, especially since hemisphere is not encoded into the parcel names, and the numeric position in the dlabel file and the 'key' value in the dlabel file are not necessarily the same. Having such a single summary csv would make it much easier to interpret the structure of FC matrices that have been sorted according to the provided *order.txt files.
Hi Mike, these are great suggestions, we have now implemented the following changes in response. Hopefully these make sense but if you have any additional feedback please let me know!
- Renumber all cortical parcels for a network beginning with 1.
- Appended "L-Ctx" and "R-Ctx" to cortical parcels as appropriate for consistency with subcortical naming (e.g. "L-Caudate").
- Standardized underscores/hyphens across cortex/subcortex.
- Padded numbering to 2 digits.
- Provided the CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_LabelKey.txt, a text file showing all mappings for the wSubcorGSR parcellation between: Index; KeyValue; Label; Red; Green; Blue; Alpha; Hemisphere; Network; NetworkKey; NetworkSortedOrder
It looks like the suggestions made by mharms have been added to the latest version of the network partition. So I'll go ahead and close this issue.
Thanks. That all sounds very helpful!
Perhaps I'm missing it, but I still don't see any "key" that conveniently links back to the names that Glasser originally gave all the parcels...
Yes, that would be helpful, esp. since it isn't immediately obvious that you preserved the parcel order of the Glasser dlabel. Even armed with that knowledge, it would still be really helpful to have the original parcel names included as a column in the LabelKey for convenient linkage of the two different nomenclatures. Thx.
Great. That will be a very helpful addition to the LabelKey. Thx!