ds005256 - MRIQC derivatives

This dataset is a BIDS Derivatives dataset resulting from running MRIQC on ds005256.

Methods

MRIQC documentation can be found on https://mriqc.readthedocs.io/.

A containerized version of MRIQC is stored in code/containers/mriqc_24_0_2.sif. This container was built using

apptainer build code/containers/mriqc_24_0_2.sif docker://nipreps/mriqc:24.0.2

Products were generated with the Slurm script code/run. That script uses Slurm arrays to process participants in parallel (one participant per job). Slurm logs (combined stdout and stderr) are stored in logs/$SLURM_ARRAY_TASK_ID.log. Running all participants would entail setting the array argument during the call to sbatch.

sbatch --array=0-116 code/run

Derivatives were saved in the dataset with git/git-annex using code/save. For example, to save sub-0133, run the following.

# NOTE: the argument (116) is the SLURM_ARRAY_TASK_ID, not the participant_label
./code/save 116

Environment

$ apptainer --version
apptainer version 1.2.2-2.el8

Caveats

Some of the logs contain lines that reflect an outdated organization of this dataset. Initially, the outputs were stored in derivatives/mriqc, with the logs being written to derivatives/mriqc-logs.

Initially, the logs generated by MRIQC (logs/config*toml and logs/mriqc*log) were not captured in the automated addition of products. So, those logs are not included in the commits that added participants' outputs. The missing logs have been added in a bulk commit.

At the time of writing, most MRIQC products are not covered by BIDS, and so most of this dataset is covered by a .bidsignore.

Acknowledgements

These derivatives were generated on the Texas Advanced Computing Center Lonestar6 computing system.