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VENUS

Analysis repository for VEndor NeUtral Sequence (VENUS) dataset

Binder

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.

VENUS/nextflow.config

Lines 131 to 133 in 90df3f9

docker {
enabled = true
}

Next, set MATLAB or Octave executable path and qMRLab directory

VENUS/nextflow.config

Lines 144 to 148 in 90df3f9

matlab_path = null
octave_path = null
qmrlab_path = null

Execute the workflows using the commands above.