This repository stores all necessary scripts to identify to the sample of participants who have been seen at least twice across a variety of developmental projects at the Brain Behavior Laboratory, copy that data into a Flywheel project, and ultimately process and analyze said data.
The processing steps are as follows:
- Run all subjects through fMRIPrep's (v20.0.5) implementation of Freesurfer (v6.0.1) to obtain quality metrics ('freeqc').
- Inspect distributions of quality metrics, and use previously conducted hand-validation, to determine if scans should be included in the next processing step.
- Construct single subject templates for all subjects with more than one scan remaining (antssst).
- Run the ANTs Longitudinal Cortical Thickness pipeline (antslongcort).
- Warp the Mind Boggle brains to the single subject templates and segment the individual scans to obtain structural metrics in the DKT atlas (antslongdkt).