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.
If you are on Linux, we recommend using the Singularity to run tractometry_flow pipeline.
If you have Apptainer (Singularity), launch your Nextflow command with:
-with-singularity ABSOLUTE_PATH/scilus-2.1.0.sif
Image is available here
If you are on MacOS or Windows, we recommend using the Docker container to run tractometry_flow pipeline.
Launch your Nextflow command with:
-with-docker scilus/scilus:2.1.0
The official release 2.1.0 is NOT available now.
Please, either build the singularity container using this command:
singularity build scilus_latest.sif docker://scilus/scilus:latest
and then launch your Nextflow command with:
-with-singularity ABSOLUTE_PATH/scilus_latest.sif
Or launch your Nextflow command with docker:
-with-docker scilus/scilus:latest
See USAGE or run nextflow run main.nf --help