FC matrices row and column names

[ashapsoncoe]

Hi, thanks for the resource.

My understanding is that the micapipeline is supposed to be run on my own machine on the downloadable MICA-MICs dataset from the CONP portal, and that this will generate the output matrices for the structural connectome, and that this output will then be usable as demonstrated with the MICA pipeline as demonstrated here: https://micapipe.readthedocs.io/en/latest/pages/04.matrices/index.html#structural-connectome

But having downloaded the MICA-MICs dataset from the CONP portal, it seems it already contains the structural connectivity data (e.g. ...\derivatives\micapipe\sub-HC001\ses-01\dwi\sub-HC001_ses-01_space-dwinative_atlas-aparc_desc-sc.txt'), just lacking the row and column names (i.e. the regions of that parcellation.

According to the associated paper, "Rows and columns of GD and MPC matrices follow the order defined by annotation labels associated with their parcellation (see parcellations in https://github.com/MICA-LAB/micapipe)"

But when I look https://github.com/MICA-LAB/micapipe, the only place I can find parcellation labels is within subfolder 'lut' - would this be the right place to find the correct ordering for a given parcellation to correspond to the strauctural connectivity files such as '...\derivatives\micapipe\sub-HC001\ses-01\dwi\sub-HC001_ses-01_space-dwinative_atlas-aparc_desc-sc.txt' ?

If so, my understanding from the paper is that 14 subcortical structures are appeneded to the front of these files; "FC and SC matrices follow the same ordering, although entries for subcortical structures are appended before cortical parcels.". Could you confirm the ordering of these subcortical structures, or where they can be found?

Thanks very much!