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USAGE
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USAGE
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Pipeline for RecobundlesX
=========================
USAGE
nextflow run main.nf --input ... [OPTIONAL_ARGUMENTS]
To call with a container add:
-with-singularity scilus/scilus:1.6.0
-with-docker scilus/scilus:1.6.0
The recommanded atlas is available at https://zenodo.org/record/7950602
Warning
=======
Output images in mni space are named "*_mni.nii.gz", if not there are in native space.
If using this pipeline, please read and cite the following publications:
[1] Etienne St-Onge, Kurt Schilling, Francois Rheault, "BundleSeg: A versatile,
reliable and reproducible approach to white matter bundle segmentation.",
arXiv, 2308.10958 (2023)
[2] Rheault, François. "Analyse et reconstruction de faisceaux de la matière
blanche." Computer Science. Université de Sherbrooke (2020).
(Only chapter #4, in French)
DESCRIPTION
--input=/path/to/[root] Root folder containing multiple subjects
[root]
├── S1
│ ├── *fa.nii.gz
│ └── *tracking.trk
└── S2
└── *
--atlas_directory Path of the folder containing atlas
├── atlas
│ └── pop_average
├── centroids
├── config_fss_1.json
├── config_fss_2.json
└── mni_masked.nii.gz
OPTIONAL ARGUMENTS (current value)
--run_average_bundles Run average bundles ($run_average_bundles)
--minimal_vote_ratio Percentage of the vote to obtain in order to be considered valid ($minimal_vote_ratio)
--seed List of random seeds values for the rng ($seed)
--outlier_alpha Remove spurious streamlines based on shape ($outlier_alpha)
--register_processes Number of processes for registration task ($register_processes).
--rbx_processes Number of processes for bundle recognition task ($rbx_processes).
--single_dataset_size_GB Limit the number of parallel RBx to avoid RAM problem ($single_dataset_size_GB)
Average tracking files size per subject (round up for safety)
--processes The number of parallel processes to launch ($cpu_count).
Only affects the local scheduler.
AVAILABLE PROFILES (using -profile option (e.g. -profile fully_reproducible, cbrain))
fully_reproducible When this profile is used, all the parameters will be set to have 100% reproducible results.
macos When this profile is used, rbx_flow will modify a parameter (scratch) for MacOS users.
cbrain When this profile is used, Nextflow will copy all the output files in publishDir and not use symlinks.
NOTES
The 'scilpy/scripts' folder should be in your PATH environment variable. Not necessary if the
Singularity container is used.
The intermediate working directory is, by default, set to './work'.
To change it, use the '-w WORK_DIR' argument.
The default config file is tractoflow/nextflow.config.
Use '-C config_file.config' to specify a non-default configuration file.
The '-C config_file.config' must be inserted after the nextflow call
like 'nextflow -C config_file.config run ...'.