This directory contains the 'harmonized' scripts for the ADRC and FTDC to submit T1 (and eventually hopefully other modalities) data for processing
We use the containers in /project/ftdc_pipeline/ftdc-picsl
For this version, we use
-pmacsT1wPreprocessing-0.6.2 for brain masking with the neck trim (https://github.com/ftdc-picsl/pmacsT1wPreprocessing )
-pmacsAntsnetct-0.4.4 with antsnetct container version 0.6.0 for the segmentation and cortical thickness estimate (https://github.com/ftdc-picsl/pmacsAntsnetct )
Make a config in configs/ for your dataset. The config requires a
bids_in="/path/to/bids"
t1pre_dir="/path/to/output/of/T1wPreprocessing_062"
antsnetct_dir="path/to/output/of/antsnetct_060"
Once you make a config, don't delete it unless you delete your whole output directory for provenance or something probably.
Updated: 12/2/2025