anat-processing

Pipeline to process anatomical data, including microstructure metrics from DWI and MT data

How to run the pipeline

Get s3_access_key and s3_secret_key 👉 contact Basile.

Then, set them:

export AWS_ACCESS_KEY_ID=<s3_access_key>
export AWS_SECRET_ACCESS_KEY=<s3_secret_key>

Get the data:

datalad install -r [email protected]:courtois-neuromod/anat.git
cd anat
datalad get .

Install Nextflow

1. Make sure that java 8 or later is installed

java -version

Note: version numbers 1.8.y_z and 8 identify the Java release.

2. Enter this command in your terminal to install Nextflow:

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

After the installation an executable named nextflow will be created in the directory where you called the command. You can simply copy this to a directory in your system $PATH to be able to call nextflow from any directory.

3. Run a simple demo

nextflow run hello

Pull Docker images

These Docker images will be orchestrated by the workflow to deal with dependencies:

docker pull qmrlab/minimal:v2.3.1
docker pull qmrlab/antsfsl:latest

If you are an OSX user and manually configured Docker to run in a virtual machine, please make sure that your /Users folder is mounted into the Docker VM. If you installed Docker using the Desktop Installer, this is automatically configured.

Run pipeline

nextflow run neuromod-process-anat.nf --bids /path/to/courtois-neuromod/directory