FreeSurfer pipeline

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Run the FreeSurfer recon-all pipeline and create the customize freesurfer, brainnetome and glasser connectivity atlas in native space.

If you use this pipeline, please cite:

Fischl, Bruce. "FreeSurfer." Neuroimage 62.2 (2012)
https://dx.doi.org/10.1016%2Fj.neuroimage.2012.01.021

Kurtzer GM, Sochat V, Bauer MW Singularity: Scientific containers for
mobility of compute. PLoS ONE 12(5): e0177459 (2017)
https://doi.org/10.1371/journal.pone.0177459

P. Di Tommaso, et al. Nextflow enables reproducible computational workflows.
Nature Biotechnology 35, 316–319 (2017) https://doi.org/10.1038/nbt.3820

Requirements

• Nextflow
• FreeSurfer
• scilpy

Usage

See USAGE or run nextflow run main.nf --help