Questions regarding the parcellated functional timeseries from the ABCD-BIDS Community Collection

Courses ABCD ReproNim
1

i tried to read a Gordon2014FreeSurferSubcortical_desc-filtered_timeseries.ptseries.nii file (see 4. Derivatives - Collection 3165 - ABCD-BIDS Community Collection (ABCC)) using the “cifti” package in R, and it turns out to be a 352 x 1532 matrix. I presume the former number is the number of parcels and the latter is the number of timepoints. According to the atlas files here Cerebral Cortex Parcels | Petersen Neuroimaging Lab | Washington University in St. Louis the Gordon atlas only contains 333 parcels, so there seem to be an ‘extra’ 19 parcels in the Gordon2014FreeSurferSubcortical_desc-filtered_timeseries.ptseries.nii

is there some documentation on the Gordon atlas parcels used in the ABCC somewhere that i’ve missed?

2

i realized the information i’m looking for is in the dlabel files

3

Hi @gerardyu, can you expand on which dlabel files you’re referring to. Maybe provide an example of a relative path within a subject’s directory? Thanks

4

the dlabel file is not located within the subjects’ folders but on the same level. For instance the contents of /path/to/derivatives/abcd-hcp-pipeline directory should looking something like this

Gordon2014FreeSurferSubcortical_dparc.dlabel.nii
sub-NDARINV######
sub-NDARINV######
sub-NDARINV######
.
.
.

anyway the 19 extra parcels correspond to the subcortical ROIs derived from the freesurfer segmentations

1 Like