Project-MONAI / Project-MONAI/tutorials

MAISI Inference

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Jupyter Notebook
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Description

I am trying to use MAISI inference and I have a couple of questions.

my pipeline now to generate a segmentation mask to give as input for MAISI inference is:

  1. generate segmentation mask using TotalSegmentatorV2
  2. generate segmentation mask using Visat3D
  3. unify labels (convert TS labels to same values of Vista3D)
  4. generate unified mask to take best segmentation
  5. use MAISI inference

my questions are:

  1. is that pipeline helps to get best results or it has some problems, as I could not neither find in the paper nor documentations how you prepare the segmentation masks.
  2. Important question: both segmentation networks do not provide segmentation masks for air or body regions. I investigated the training dataset and found that the value 200 is assigned to those parts, however I could not find anywhere what is HU threshold you are using, so please also if you can guide onto that part whether where to find it or what is the threshold being used. so if you can advise how you prepare the body segmentation mask with value 200 and integrate with the segmentation masks from the segmentation networks.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the MAISI inference workflow described in the issue, then compare the TotalSegmentatorV2 and Visat3D outputs with the training dataset. Document how labels are unified, how the value 200 is assigned to air or body regions, and which HU threshold is used; done means the mask-preparation procedure is clear enough to reproduce.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, pytorch
Domain
computer-vision, documentation, machine-learning
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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