scilus/sf-tractomics is a medical imaging pipeline that processes diffusion MRI images of human brains and reconstructs white matter pathways using tractography.
- Read Inputs
- Preprocess DWI
- Preprocess T1
- Segment T1
- Reconstruct diffusion profiles
- Run tractography
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.
You can run the pipeline using:
nextflow run scilus/sf-tractomics \
-profile <docker/singularity/.../institute> \
--input <samplesheet.csv|/path/to/bids> \
--outdir <OUTDIR>Refer to the usage to see how to format your samplesheet or for extended informations.
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.
scilus/sf-tractomics is a port by @AlexVCaron of tractoflow, originally written by @GuillaumeTh.
We thank the following people for their extensive assistance in the development of this pipeline:
- @jchoude
- @frheault
- @arnaudbore
- @mdesco
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.
