BIDS derivatives

Last updated on 2024-02-28 | Edit this page

Estimated time: 45 minutes

Overview

Questions

  • What are BIDS Apps?
  • What are containers?

Objectives

  • Learn about neuroimaging applications using BIDS data structures
  • Use neuroimaging applications through containers

BIDS Apps are containerized applications that run on BIDS data structures.

Some examples include:

  • mriqc
  • fmriprep
  • freesurfer
  • ciftify
  • SPM
  • MRtrix3_connectome

They rely on 2 technologies for container computing:

  • Docker
    • for building, hosting, and running containers on local hardware (Windows, Mac OS, Linux) or in the cloud
  • Singularity
    • for running containers on high performance compute clusters

Building a singularity container is as easy as:

BASH 

singularity build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1`

To run the container:

BASH 

singularity run --cleanenv \
  -B bids_folder:/data \
  mriqc-0.16.1.simg \
  /data /data/derivatives participant

Key Points

  • BIDS Apps are containerized applications that run on BIDS-compatible datasets.