NF-SurgeryFlow

NF-SurgeryFlow is a Nextflow pipeline for processing neuroimaging data. This pipeline includes various preprocessing, reconstruction, tracking, and segmentation steps.

Table of Contents

• NF-SurgeryFlow
  • Table of Contents
  • Introduction
  • Installation
  • Usage

Introduction

nf-SurgeryFlow is an end-to-end tractography pipeline dedicated to clinicians in a pre-surgical setting. It performs preprocessing, T1 segmentation, DTI and fODF metrics computations, tractography and virtual dissection.

![nf-surgeryflow-schema(/nf-surgeryflow-schema.png)]

Installation

To install NF-SurgeryFlow, you need to have Nextflow and Docker installed. Follow these steps:

1. Install Nextflow:

   curl -s https://get.nextflow.io | bash

2. Install Docker: Follow the instructions on the Docker website.

3. Clone the repository:

   git clone https://github.com/yourusername/nf-surgeryflow.git
   cd nf-surgeryflow

Usage

Note

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

Configurations profiles

1. -profile docker: Each process will be run using docker containers.
2. -profile apptainer or -profile singularity: Each process will be run using apptainer/singularity images.

Using either -profile docker or -profile apptainer is highly recommended, as it controls the version of the software used and avoids the installation of all the required softwares.

To run the pipeline, use the following command:

nextflow run main.nf --input /path/to/input --atlas /path/to/atlas --fs_license /path/to/license.txt