From 1c5f0ebec95ee540398e662db9b15d1223d61174 Mon Sep 17 00:00:00 2001 From: Agah Date: Thu, 23 Dec 2021 14:16:49 -0500 Subject: [PATCH] Update README.md --- README.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0f55217..a9e0cc6 100644 --- a/README.md +++ b/README.md @@ -24,4 +24,20 @@ nextflow run venus-process-phantom.nf --bids /set/to/bids/directory -with-report Process in-vivo data ``` nextflow run venus-process-invivo.nf --bids /set/to/bids/directory -with-report invivo-report.html -``` \ No newline at end of file +``` + +## 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.