nf-pediatric

Introduction

nf-pediatric is an end-to-end connectomics pipeline for pediatric (0-18y) dMRI and sMRI brain scans. It performs tractography, t1 reconstruction, cortical and subcortical segmentation, and connectomics. Final outputs are connectivity matrices for a variety of diffusion (or not) related metrics.

A detailed description of the minimal outputs can be found here.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

The pipeline required input is in the form of a samplesheet containing the path to all your input files for all your subjects. For the most basic usage (-profile tracking), your input samplesheet should look like this:

samplesheet.csv:

subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
sub-1000,/input/sub-1000/t1.nii.gz,/input/sub-1000/dwi.nii.gz,/input/sub-1000/dwi.bval,/input/sub-1000/dwi.bvec,/input/sub-1000/rev_b0.nii.gz

Each row represents a subject, and each column represent a specific file that can be passed as an input.

Now, you can run the pipeline using:

nextflow run scilus/nf-pediatric \
    -r main \
    -profile docker,tracking \
    --input samplesheet.csv \
    --outdir <your_outdir>

With this command, you will run the tracking profile for non-infant data. There is no need to git clone the pipeline prior to lauching it, nextflow will do it for you! Additional information on running multiple profiles and the infant profile can be found here.

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

nf-pediatric was originally written by Anthony Gagnon.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.