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