register_flow/USAGE at main · scilus/register_flow · GitHub

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register_flow pipeline
=====================

Register t1, metrics and tractograms to template space.
If a metric name includes *mask*, it will be registered with the nearest-neighbour option.
We suggest to use https://github.com/scilus/combine_flows to create input.

USAGE

nextflow run main.nf [OPTIONAL_ARGUMENTS] --input --template

DESCRIPTION

    --input=/path/to/[root]     Root folder containing multiple subjects
                                                [root]
                                                ├── S1
                                                │   │── *t1.nii.gz (orig space)
                                                |   └── metrics (optional)
                                                |   │   └── *.nii.gz
                                                |   └── tractograms (optional)
                                                |       └── *.trks
                                                └── S2
                                                    └── *

    --template=/path/to/template_t1.nii.gz      Path to a nifti T1 template used for registration.
                                                It has to be named template_t1.nii.gz

OPTIONAL ARGUMENTS (current value)
    --run_bet                                   Run bet(antsBrainExtraction) if your t1s are not brain extracted ($run_bet).
    --linear_registration                       If set, it will use linear registration instead of non linear registration ($linear_registration).

    --quick_registration                        If set, it will use antsRegistrationSyNQuick.sh instead of antsRegistrationSyN.sh for registration ($quick_registration).

TRK OPTIONS (current value)
    --trk_keep_invalid                          If set, it will keep invalid streamlines after registration ($trk_keep_invalid).
    --trk_cut_invalid                           If set, it will cut invalid points and may create sub-streamlines after registration ($trk_cut_invalid).
    --trk_remove_invalid                        If set, it will remove invalid streamlines after registration ($trk_remove_invalid).

AVAILABLE PROFILES (using -profile option (e.g. -profile fully_reproducible))

macos                                       When this profile is used, TractoFlow 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.


NOTES

To set the number of parallel processes to launch, please use:
'nextflow run -qs {nb_processes}'.

The intermediate working directory is, by default, set to './work'.
To change it, use the '-w WORK_DIR' argument.

The default config file is connectoflow/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 ...'.