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USAGE
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USAGE
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ExtractorFlow pipeline
======================
Run ExtractorFlow pipeline.
Either your tractograms are already in the JHU template space or if you provide a t1 (diff space) it will register everything into the JHU space.
T1s have to be BET. if not, please use the option run_bet.
USAGE
nextflow run main.nf [OPTIONAL_ARGUMENTS] (--input)
DESCRIPTION
--input=/path/to/[root] Root folder containing multiple subjects
[root]
├── S1
│ └── *.trk
│ └── *_t1.nii.gz (diff space, optional)
└── S2
└── *.trk
└── *_t1.nii.gz (diff space, optional)
OPTIONAL ARGUMENTS (current value)
--output_dir Directory where to write the final results.
By default, will be in "./results_extractorflow"
--run_bet Run bet if your t1s are not brain extracted ($run_bet).
--orig Extract all trk in diffusion space (if t1 has been provided) ($orig).
--extended Extract bundles ($extended).
--keep_intermediate_steps Keep intermediate steps ($keep_intermediate_steps). MUST be used if you need to debug.
--quick_registration If set, will choose antsRegistrationSyNQuick.sh instead of antsRegistrationSyN.sh ($quick_registration).
--processes_bet_register_t1 Number of processes for T1 brain extraction task ($processes_bet_register_t1).
--processes_apply_registration Number of processes for registration application ($processes_apply_registration).
--processes The number of parallel processes to launch ($cpu_count).
Only affects the local scheduler.
AVAILABLE PROFILES (using -profile option (e.g. -profile macos))
macos When this profile is used, ExtractorFlow will modify a parameter (scratch) for MacOS users.
fully_reproducible When this profile is used, all the parameters will be set to have 100% reproducible results.