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?

Support

Mike_Flanigan (Mike Flanigan) September 5, 2022, 10:52pm 3

Thank you!
That script got me well ahead and working.
I do have two follow up questions now, but they’re rather distinct so I’ve made them new questions:

Remove largest island functionality?
Export volume (or segment?) to stl file with python

Topic		Replies	Views
Export volume (or segment?) to stl file with python Development python	3	1535	September 21, 2022
Extract systematic volumes, quantify their and export their stl models Support	12	401	August 25, 2021
Islands segmentation via python script Support	6	791	December 13, 2021
How can I write a python CLI code using slicer internal module Support segmentation , python	7	645	June 9, 2021
Using Python Module to Render an Image in 3D Support	20	2400	July 1, 2020

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

Related Topics