elyz081 / rbx_flow

RecobundlesX pipeline

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Run the RecobundlesX pipeline. To access the example atlases: https://zenodo.org/record/7950602

If you use this pipeline, please cite:

Etienne St-Onge, Kurt Schilling, Francois Rheault, "BundleSeg: A versatile,
reliable and reproducible approach to white matter bundle segmentation.",
arXiv, 2308.10958 (2023)

Rheault, Francois. Analyse et reconstruction de faisceaux de la matière blanche.
page 137-170, (2020), https://savoirs.usherbrooke.ca/handle/11143/17255

Kurtzer GM, Sochat V, Bauer MW Singularity: Scientific containers for
mobility of compute. PLoS ONE 12(5): e0177459 (2017)
https://doi.org/10.1371/journal.pone.0177459

P. Di Tommaso, et al. Nextflow enables reproducible computational workflows.
Nature Biotechnology 35, 316–319 (2017) https://doi.org/10.1038/nbt.3820

Requirements

• Nextflow
• scilpy
• ants

Singularity/Docker

If you are on Linux, we recommend using the Singularity to run rbx_flow pipeline. If you have Apptainer (Singularity) launch your Nextflow command with: -with-singularity ABSOLUTE_PATH/scilus_1.6.0.sif

Image is available here

If you are on MacOS or Windows, we recommend using the Docker container to run rbx_flow pipeline. Launch your Nextflow command with: -with-docker scilus/scilus:1.6.0

Usage

See USAGE or run nextflow run main.nf --help