FreeWater and FW corrected DTI metrics pipeline

Run the FreeWater pipeline, including FW-corrected DTI metrics estimation

If you use this pipeline, please cite:

Kurtzer GM, Sochat V, Bauer MW (2017)
Singularity: Scientific containers for mobility of compute.
PLoS ONE 12(5): e0177459. 

P. Di Tommaso, et al. (2017) Nextflow enables reproducible computational workflows.
Nature Biotechnology 35, 316–319 

O. Pasternak, et al. (2009) Free water elimination and mapping from diffusion MRI.
Magnetic Resonance in Medicine, 62(3), 717–730.

A. Daducci, et al. (2015). Accelerated Microstructure Imaging via Convex Optimization (AMICO)
from diffusion MRI data. NeuroImage, 105, 32–44. 

Requirements

• Nextflow
• Scilpy (https://github.com/scilus/scilpy)
• AMICO (https://github.com/daducci/AMICO)

Usage

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