Skip to content

Latest commit

 

History

History
61 lines (51 loc) · 1.53 KB

README.md

File metadata and controls

61 lines (51 loc) · 1.53 KB
Raw

Disconets_flow

Disconets_flow allows you to analyze the impact of a cavity on structural connectivity matrices.

Yeo atlas used in the paper link.

Please cite:

Mrah S, Descoteaux M, Wager M, Boré A, Rheault F, Thirion B, Mandonnet E. Network-level prediction of set-shifting deterioration after lower-grade glioma resection. J Neurosurg. 2022 Mar 4:1-9. doi: 10.3171/2022.1.JNS212257. Epub ahead of print. PMID: 35245898.

Build singularity or docker image

# Singularity
singularity build scilus_2.0.2.sif docker://scilus/scilus:2.0.2

# Docker
docker pull scilus/scilus:2.0.2

Run Disconets_flow

# With singularity image
nextflow run main.nf \
        --input [FullPathToLesions]/ \
        --atlas [FullPathToAtlas]/ \
        --tractograms [FullPathToTractograms]/ \
        -with-singularity scilus_2.0.2.sif \
        resume

# With docker image
nextflow run main.nf \
        --input [FullPathToLesions]/ \
        --atlas [FullPathToAtlas]/ \
        --tractograms [FullPathToTractograms]/ \
        -with-docker scilus/scilus:latest \
        resume

Disconets input structure

Root
├── S01
│   ├── *t1.nii.gz (optional)
│   └── *cavity.nii.gz
└── S02
    ├── *t1.nii.gz (optional)
    └── *cavity.nii.gz

Tractograms input structure

Root
├── T01
│   ├── *t1.nii.gz (optional)
│   └── *.trk
└── T02
    ├── *t1.nii.gz (optional)
    └── *.trk