USAGE

FreeSurfer pipeline
===================

Run recon-all on all subjects and create the customize freesurfer,
brainnetome and glasser connectivity atlas in native space. This pipeline also
creates the 5 scales of the 2008 Lausanne Atlas. It is also possible to run
this nextflow if your FreeSurfer is already computed.

The input can be the input for freesurfer, in this case the pipeline will start
with recon-all. The input can also be the output folders from freesurfer, in
this case the pipeline will start with the creation of the customize atlas.

Both options can be used together, but running freesurfer on CBRAIN is recommanded
to reduce usage on ComputeCanada's clusters. Running Freesurfer on CBRAIN is
faster and better optimized for large number of subjects.

This pipeline must be used with a custom freesurfer singularity, several
hard-to-get files are needed as well as custom scripts. The singularity
container is available on braindata and the recipe is in the Git repository.

USAGE

nextflow run main.nf [OPTIONAL_ARGUMENTS] --root

DESCRIPTION

    --root_fs_input = false=/path/to/[root]     Root folder containing multiple subjects
                                                [root]
                                                ├── S1
                                                │   └── t1.nii.gz
                                                └── S2
                                                    └── t1.nii.gz

    --root_fs_output = false=/path/to/[root]    Root folder containing multiple subjects
                                                [root]
                                                ├── S1
                                                │   └── label, mri, [...], stats, surf, touch
                                                └── S2
                                                    └── label, mri, [...], stats, surf, touch

OPTIONAL ARGUMENTS (current value)
--atlas_utils_folder                    Folder needed for other atlas conversion ($atlas_utils_folder)
--nb_threads                            Number of threads used by recon-all and the atlases creation ($nb_threads)

--compute_FS_BN_GL_SF                   Compute the connectivity-friendly atlases Freesurfer (adapted), 
                                            brainnetome, glasser and Schaefer 100/200/400  ($compute_FS_BN_GL_SF)
--compute_lausanne_multiscale           Compute the connectivity multiscale atlases from lausanne ($compute_lausanne_multiscale)
--processes                             The number of parallel processes to launch ($cpu_count).
                                            Only affects the local scheduler.


NOTES

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

Need to have FreeSurfer v. 6.0

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

The default config file is freesurfer-nf/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 ...'.