Overview

Automated FSL-based processing pipeline for DTI (Diffusion Tensor Imaging) data. Specifically for non-brain images (e.g. images of DRG (Dorsal Root Ganglia))

What does this pipeline do?

• optionally ROIs are extracted from the images, using fslroi
• all images with b-value 0 are extracted (in both AP and PA direction) and recombined for topup
• the AP and PA file (nifti, bvec, and bval) are concatenated for eddy
• config files for topup and eddy are created
• then topup and eddy are applied
• dtifit is applied to the eddy corrected data
• bedpostX is applied to the eddy corrected data

The workflow can be run with slurm (--executor slurm). Start it in the root of a BIDS dataset and all subjects and sessions with dwi images in dir-AP and dir-PA are processed. Outputs are stored under derivatives/dti_smk.

Requirements

The listed versions are the ones this pipeline was developed with. It might work with other (particularly newer) versions.

• FSL (6.0.7.18)
• Snakemake (9.9.0)
• (optional) snakemake-executor-plugin-slurm (1.6.0)

How to run it?

Navigate into the root of your BIDS dataset and run (adjusting the path to the Snakefile and number of cpus):

snakemake --snakefile /path/to/workflow/Snakefile --cores 6

If you are on a SLURM cluster (and you have snakemake-executor-plugin-slurm installed), you can run (again adjusting parameters as appropriate):

snakemake --snakefile /path/to/workflow/Snakefile --executor slurm --default-resources mem_mb=1000 cpus_per_task=2 runtime=60 --jobs 10 --latency-wait 60 

Additional naming requirements

the full BIDS specification is not supported, yet.

There are currently still some limitations:

• the session level is not optional (_ses-<label>)
• the PhaseEncodingDirection has to be in _dir-<label> and only "AP" and "PA" are supported (in uppercase letters)
• no additional file name components are currently accepted (acq, rec, run, part, chunk)

For developers

Install dependencies with:

uv sync

Run tests with:

uv run pytest test

Contributing

Contributions are welcome, including but not limited to bug fixes, new features, documentation, and tests.