Update README.md

qMRLab · Dec 23, 2021 · 1c5f0eb · 1c5f0eb
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Showing 1 changed file with 17 additions and 1 deletion.
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@@ -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
-```
+```
+
+## 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.