Check if command "ITK-SNAP" for windows exists in manual_correction.py

sct-pipeline / ukbiobank-spinalcord-csa

Measure of the averaged cross-sectional area (cord CSA) between C2 and C3 of the spinal cord with UK Biobank Brain MRI dataset.

MIT License

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Check if command "ITK-SNAP" for windows exists in manual_correction.py #38

Closed sandrinebedard closed 3 years ago

sandrinebedard commented 3 years ago

Description

In the script manual_correction.py, to call ITK-SNAP, the command line is different for macOS and on windows. Right now, the script checks only if itksnap command exists and runs the command for windows ITK-SNAP if not.

The purpose of this issue is to:

Check if the command ITK-SNAP exists before running it.
Raise an exception if none of the commands work. (Say to user to check if itk-snap is installed and if it was added to PATH variable)