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Run the RecobundlesX pipeline. To access the example atlases: https://zenodo.org/record/4104300#.YmMEk_PMJaQ
If you use this pipeline, please cite:
Rheault, Francois. Analyse et reconstruction de faisceaux de la matière blanche.
page 137-170, (2020), https://savoirs.usherbrooke.ca/handle/11143/17255
Garyfallidis, Eleftherios, et al. Recognition of white matter bundles using
local and global streamline-based registration and clustering.
NeuroImage 170 (2018) https://doi.org/10.1016/j.neuroimage.2017.07.015
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 Singularity == 3.*, launch your Nextflow command with:
-with-singularity scilus/scilus:1.2.0_rbxflow-1.1.0
If you have rebuild singularity Singularity == 2.* image is available here
Launch your Nextflow command with: -with-singularity ABSOLUTE_PATH/scilus-1.2.0_rbxflow-1.1.0.img
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:1.2.0_rbxflow-1.1.0
See USAGE or run nextflow run main.nf --help