Segment Brain in its subparts

[unichronic]

This PR is part of GSoC 2025.

It adds the feature of a Segmentation tool to segment the various Subparts of the brain (for example: precuneus, superiorfrontal, hippocampus, etc.) using the Fastsurfer open-source CNN models and add support for PyTorch as well as Onnx models.

It also updates the data panel with categories for the subpart masks.

Tasks Done -

• Added the Subpart segmentation Dialog.
• Implemented all the pre-processing steps.
• Converted the models to Onnx.
• Added support for both Pytorch and Tinygrad (Onnx) inference.
• Added processing to label map the segmented output.
• Generated binary masks from the labelled output.
• Added Category feature to Data Panel.
• Added Hide/Unhide and Select All to category header in the Surfaces tab.
• Added a "Create all surfaces" feature to create multiple surfaces from the selected masks at once.
• Enhanced the look and controls of the Data Panel.

Pending -

• Notes Tab (will raise separate PR)

[tfmoraes]

Hi @unichronic. Some comments:

• Please, don't add weights in the repository. I added the weights here https://github.com/invesalius/weights/tree/main/fastsurf
• Please, for ONNX try to use Tinygrad
• I think it's better to add fastsurf folder inside deep_learning folder.

[unichronic]

Yeah sure I will add Tinygrad support.
I will move the fastsurfer directory and keep the other points in mind.

[rmatsuda]

Really nice! Thanks again @unichronic! I have just a few comments

[rmatsuda]

Also, could you please run Ruff to fix the pre-commit issues? https://github.com/invesalius/invesalius3/actions/runs/17199530210/job/48787491498?pr=1005

You can find setup instructions here: https://github.com/invesalius/invesalius3/wiki/Setting-Up-pre%E2%80%90commit

[unichronic]

Also, could you please run Ruff to fix the pre-commit issues? https://github.com/invesalius/invesalius3/actions/runs/17199530210/job/48787491498?pr=1005

I have pre-commit setup with my git, but turns out I was using an older Ruff version.
but even after updating to match the current version in Invesalius, the pre-commit check was still raising errors, although it did pass in my CLI. So I went ahead and just fixed it manually.

[rmatsuda]

Thanks @unichronic! Could you please add the extra dependencies (like torchvision and yacs) to both the requirements.txt and environment.yml files?

[unichronic]

Thanks @unichronic! Could you please add the extra dependencies (like torchvision and yacs) to both the requirements.txt and environment.yml files?

Sure!