Villeneuve Laboratory PET Pipeline (VLPP)

VLPP is an open-source software for analyzing PET images combined with freesurfer.

VLPP is builded with the Nextflow framework which enables scalable and reproducible scientific workflows.

Usage

vlpp.nf --pet <> --freesurfer <> --participant <> [-c <>]

Mandatories arguments:

• --pet: PET file (mnc, nii or nii.gz)
• --freesurfer: Freesurfer directory of the participant
• --participant: Participant ID

Optional arguments:

• --help: Print vlpp usage
• -c, -config: Add the specified file to configuration set
• -resume: Execute the script using the cached results, useful to continue executions that was stopped by an error
• -h or -help: Print the nextflow usage

Configurations

Default Parameters and explanation: see config/default.config

Using the pipeline on guillimin

Please follow this link.

Install

Software dependencies

• matlab
• spm
• fsl
• freesurfer
• ANTs
• minctools
• Nextflow
• graphviz

Python dependencies with conda

If you use conda. Python dependencies, nextflow and graphviz will be installed automatically.

conda config --add channels conda-forge
conda config --add channels bioconda

git clone https://github.com/villeneuvelab/vlpp.git
cd vlpp

conda env create -f environment.yml -n vlpp
source activate vlpp

#Install vlpp in edit mode
pip install -e .

After that, you should add the pipelines and scripts directories to your PATH.