functional_preprocessing: nipype-based scripts for resting-state preprocessing (see README in folder for more details)

quality_reports: nipype-based scripts for quality control

• quality_reports/julia_qa/ -> quality reports based on Julia Huntenburgs scripts (generate_report_part2.py)
• quality_reports/poldrack_qa -> quality reports based on Russ Poldrack (QA_and_header_fix_wf.py)
• compare_meanFD/ -> comparison of mean FD estimated by two pipelines (detection of error related to angle/radians in calculation of FD)
• hippocampal_subfields/ -> quality control of hippocampus connectivity (generate_report.py)

seedbased_connectivity: nipype-based scripts to generate hippocampus connectivity

• after_scrubbing_FS_derived_hc_ant_post (seed based connectivity based on Freesurfer ROIs & scrubbed data)
• SCA (seed based connectivity absed on MNI coordinates)
• FS_derived_hc_ant_post (seed based connectivity based on Freesurfer ROIs)
• transform_HC_to_MNI (transform HC maps to MNI space for quality control)

import_from_afs.sh (get data from AFS repository)