Defining Custom Cross-Sectional Planes in 3D Slicer Using Vectors

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Hi everyone,

I’m writing here to ask whether something I’ve been doing in Amira can be replicated in an open-source software like 3D Slicer.

Specifically, I need to define a cross-sectional plane with a specific orientation and position, in order to extract cross-sectional images from a defined region. In Amira, this can be done by specifying two 3D vectors (to set the plane’s orientation) and a point of origin (to set the location of the plane). This is really useful for standardizing the procedure.

Is there a way to do something similar in 3D Slicer? Even better, is there a way to automate this through the console or scripting interface? In Amira, there’s no way to set the cross-sectional plane using commands - you have to manually copy and paste the coordinates of the vectors and origin, which is quite tedious when working with many samples.

I would really appreciate any help or guidance.

Thanks so much in advance!
Alex

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That all sounds quite doable. Have a look at the example scripts and you’ll find code for making markups, working with planes, transforming images, etc.

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