Pipeline used to take functional data from DICOMs through group-level analyses.

Following python setup.py install or python setup.py develop, use the following entry points to trigger help, cli.

• func_processing : print out entrypoints below.

• check : print help, run cli.checks, used to determine which participants have which preprocessed files.
• ashs : trigger help of cli.ashs, for running Automated Hippocampal Subfield Segmentation.
• reface : trigger help of cli.reface, for de/refacing participant T1w files.
• fmriprep : trigger help of cli.fmriprep, for moving data found in dset through FreeSurfer and fMRIPrep.
• task_subj : trigger help of cli.afni_task_subj, move task EPI output of fmriprep through extra preprocessing, deconvolution.
• rs_subj : trigger help of cli.afni_resting_subj, move resting EPI output of fmriprep through extra preprocessing, deconvolution.
• task_group : trigger help of cli.afni_task_group, conduct group-level task EPI analyses.
• rs_group : trigger help of cli.afni_resting_group, conduct group-level resting EPI analyses.

Top Level

• dockerfiles : Dockerfile, shell script backup
• docs : Project documentation, for ReadTheDocs, assuming sphinx is cooperative. Build instruction found in build_docs.txt.
• func_processing : Main package

func_processing

• cli : Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows.
• examples : Contains example scripts and files.
• logs : Mainly for completed_preprocessing.tsv, other output logs written here.
• resources : Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports.
• tests : Scripts for testing resources and workflows.
• tools : Location for auxiliary/shell scripts. Currently contains (outdated) cron scripts
• workflow : Manages resources, controlled by cli.

See Wiki for details and description, now a little outdated due to refactoring.