05-bids-derivatives.md

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BIDS Apps

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

All BIDS Apps use the same command line format to run them:

<app_name> /data /output participant [options]

Building a singularity container is as easy as:

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

To run the container:

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