USAGE

Scilpy dMRI tractometry pipeline
================================

Compute tractometry on each bundles/metrics

USAGE

nextflow run main.nf [OPTIONAL_ARGUMENTS] (--input)

DESCRIPTION

--input=/path/to/[root]     Input folder containg multiple subjects

                            [root]
                            ├── S1
                            │   ├── *lesion_mask.nii.gz (optional)
                            │   ├── *fodf.nii.gz (optional to generate fixel AFD)
                            │   ├── metrics
                            │   │   └── *.nii.gz
                            │   └── bundles
                            │       └── *.trk
                            └── S2
                                ├── *lesion_mask.nii.gz (optional)
                                ├── *fodf.nii.gz (optional to generate fixel AFD)
                                ├── metrics
                                │   └── *.nii.gz
                                └── bundles
                                    └── *.trk

                            Bundle centroid will be computed on-the-fly if no
                            pre-computed centroids have been provided.

                            You can provide pre-computed centroids such as
                            (and use --use_provided_centroids true)

                            [root]
                            ├── S1
                            │   ├── metrics
                            │   │   └── *.nii.gz
                            │   ├── centroids
                            │   │   └── [Bundle_Name]_centroid.trk
                            │   └── bundles
                            │       └── [Bundle_Name].trk
                            └── S2
                                ├── metrics
                                │   └── *.nii.gz
                                ├── centroids
                                │   └── [Bundle_Name]_centroid.trk
                                └── bundles
                                    └── [Bundle_Name].trk

                            Bundle and centroid file names must match the
                            format described above.

                            All subjects in the [root] folder must contain
                            pre-computed centroids if pre-computed centroids
                            are provided. In other words, you can not mix
                            subjects with and without pre-computed centroids


Metrics should be compressed Nifti files (.nii.gz) and centroids and fiber bundles should be
in Trackvis format (.trk)

OPTIONAL ARGUMENTS (current value)

--nb_points                                 Split the fiber bundle in --nb_point sections ($nb_points)
--min_lesion_vol                            To be consider 'a lesion' for the pipeline, a lesion must be at least ($min_lesion_vol) mm3.
--use_provided_centroids                    Use the provided pre-computed centroids rather than using automatic computation ($use_provided_centroids)
--skip_tract_profiles                       Skip all the steps that include tract profiling ($skip_tract_profiles)

--bundle_suffix_to_remove                   Use to remove the suffix from RBx-Flow ($bundle_suffix_to_remove)

--mean_std_density_weighting                Weight the mean/std by the local tract density ($mean_std_density_weighting)
--mean_std_per_point_density_weighting      Weight the mean/std per point by the local tract density ($mean_std_per_point_density_weighting)
--endpoints_metric_stats_normalize_weights  Normalize the weights to the [0, 1] range ($endpoints_metric_stats_normalize_weights)
--skip_projection_endpoints_metrics         Skip the (slow) process that projects metrics onto the endpoints of streamlines  ($skip_projection_endpoints_metrics)

--processes                                 The number of parallel processes to launch ($cpu_count).
                                            Only affects the local scheduler.
--output_dir                                Directory where to write the final results.
                                            By default, will be in "./results_tractometry"


AVAILABLE PROFILES (using -profile option (e.g. -profile macos, cbrain))
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 ...'.