BABS: BIDS App Bootstrap

Full documentation at https://pennlinc-babs.readthedocs.io

About

BIDS App Bootstrap (BABS) is a reproducible, generalizable, and scalable Python package for BIDS App analysis of large datasets. It uses DataLad and adopts the FAIRly big framework. Currently it is compatible with SGE and Slurm clusters.

BABS functions

Schematic of BABS workflow

Documentations

• Overview of BABS
  • See also
• Installation
  • Step 1. Prepare a conda environment for BABS
  • Step 2. Install dependent software
  • Step 3. Install BABS
  • Step 4. (Optional) Check BABS version
• Step I: Get prepared
  • Prepare input BIDS dataset(s) as DataLad dataset(s)
  • Prepare containerized BIDS App as a DataLad dataset
  • Prepare a configuration YAML file for the BIDS App
• Step II: Create a BABS project
  • Initialize a BABS project using babs-init
  • Sanity checks and diagnosis via babs-check-setup
• Step III: Job submission and job status
  • List of included subjects (and sessions) to process
  • Recommended workflow of job submission and status checking
  • Example job status summary from babs-status
  • Explanation on job_status.csv
  • FAQ for job submission and status checking
  • See also
• Step IV: After jobs have finished
  • Step 3.1. Merge the results and provenance
  • Step 3.2. Get the results
• Example walkthrough
  • Step 1. Get prepared
  • Step 2. Create a BABS project
  • Step 3. Submit jobs and check job status
  • Step 4. After jobs have finished
• Command line reference
  • Set up a BABS project
  • Submit jobs and check job status
  • After jobs have finished
• Contributing to BABS
  • For potential contributors
  • Implementation details

Indices and tables

• Index

• Module Index

• Search Page