VENUS

Analysis repository for VEndor NeUtral Sequence (VENUS) dataset

Above data is acquired for sub-phantom (ISMRM/NIST system phantom) and for 3 healthy subjects, yielding 24 for acquisitions.

To execute workflows

1. Install Nextflow
2. Pull Docker images:

   docker pull qmrlab/minimal:v2.5.0b
   docker pull qmrlab/antsfsl:latest
   

3. Download the dataset
4. Run

Process phantom data

nextflow run venus-process-phantom.nf --bids /set/to/bids/directory -with-report phantom-report.html

Process in-vivo data

nextflow run venus-process-invivo.nf --bids /set/to/bids/directory -with-report invivo-report.html

If Docker is not available

You need to make sure that following dependencies are installed on your local machine/environment and accessible via shell (i.e. added to the system PATH):

• ANTs
• FSL
• MATLAB or Octave

In the config file, set the following parameter to false, this will enforce workflow to look for local executables. https://github.com/qMRLab/VENUS/blob/90df3f94aa0c07ee2a116b9ad5785b2b0057fa60/nextflow.config#L131-L133

Next, set MATLAB or Octave executable path and qMRLab directory https://github.com/qMRLab/VENUS/blob/90df3f94aa0c07ee2a116b9ad5785b2b0057fa60/nextflow.config#L144-L148

Execute the workflows using the commands above.