I’m new to Slicer and am working on a project trying to automate a few Slicer steps for many files by creating a python script and then running it without opening the Slicer GUI. I’ve been reading through sections in the slicer docs in particular the “Run a Python script file in the Slicer environm…

That process sounds very feasible. You’ll need to put together snippets of functionality from the script repository. I saw there weren’t specific batch processing examples so I put in a few examples in this PR .

Tips for getting started loading and batch segmenting files with Slicer in python?

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muratmaga (Murat Maga) September 6, 2022, 5:17am 4

Check this script example for running island tool and exporitng the segmentation and writing to the disk:

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Tips for getting started loading and batch segmenting files with Slicer in python?

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