NIDMification of kwyk output
This project uses kwyk (https://github.com/neuronets/kwyk). Paper, code, and model corresponding to preprint, which is now published.
We include a BASH script, 'kwykput.sh' that takes a resulting output from kwyk, and used the FSL fslstats utility to determine the volume for each of the regions. This script uses the kwyk_region_list.txt file for the region lables (derived from FreeSurfer. It generates a text file (example provided test_out.txt) of the form:
kwyk_index label number_voxels vol_inmm3 1 Cerebral-White-Matter 496396 496396.000000 2 Ventricular-System 11025 11025.000000 3 Cerebellum-White-Matter 32515 32515.000000 4 Cerebellum-Cortex 144992 144992.000000 5 Thalamus-Proper 18118 18118.000000 6 Caudate 10851 10851.000000 etc...
The steps for this include generating a kwykmap.json file that described the content of out reults file (kwykmap.json).
Install kwyk2nidm
and call kwyk2nidm -f kwyk_stats_file