Building Singularity containers for BrainGnomes

Running singularity

On most HPC systems, Singularity is not available on login nodes. Thus, to build containers, you must enter an interactive compute session and build there. For example, on SLURM, for an 8-hour session with 32 GB RAM, use:

srun -t 8:00:00 --mem=32gb -p interact -N 1 -n 4  --pty /bin/bash

Now that you’re in that session, you can proceed with building containers needed for BrainGnomes

Heudiconv

singularity pull docker://nipy/heudiconv:latest

More details here: https://heudiconv.readthedocs.io/en/latest/installation.html

fmriprep

Fill in a version, such as 25.1.3

singularity build /proj/hng/software/containers/fmriprep-<version>.simg docker://nipreps/fmriprep:<version>

MRIQC

singularity build /proj/mnhallqlab/mriqc-latest.simg docker://nipreps/mriqc:latest

fmripost-aroma (ICA-AROMA)

singularity build /proj/hng/software/containers/aroma-latest.simg docker://nipreps/fmripost-aroma:main

Details: https://github.com/nipreps/fmripost-aroma?tab=readme-ov-file#installation

FSL

Used in postprocessing. NeuroDesk has a number of pre-built containers that work well, whereas building FSL from a container file (e.g., https://www.repronim.org/neurodocker/user_guide/examples.html) was throwing tricky errors on the UNC HPC.

Image for FSL 6.0.7.16

curl -X GET https://neurocontainers.neurodesk.org/fsl_6.0.7.16_20250131.simg -O

AFNI

Not currently used, but if you want it!

singularity build /proj/hng/software/containers/afni-latest.simg  docker://afni/afni_make_build

BIDS-validator

Not quite as easy

module load node
npm install -g deno
deno compile -ERWN -o bids-validator jsr:@bids/validator

Michael Hallquist

29 Jul 2025