OAI_analysis_2

OAI_analysis_2 copied to clipboard

WIP: extract itk sub mesh

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@HastingsGreer wip, todo: generate the new sub mesh based on the face identifiers and https://itk.org/Doxygen/html/classitk_1_1AutomaticTopologyMeshSource.html

thewtex

HastingsGreer

The original code validated against known good thickness measurements here: https://github.com/uncbiag/OAI_analysis/blob/master/validate_thickness_results.py We should do the same.

HastingsGreer

documentation for how to install and use the code

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Update the README.md section on how to use and install the code. Will likely also need to change once dask support is fully included (ie., running via script vs Jupyter...

marcniethammer

Target cuda 11.7/11.8

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Available on longleaf, along with: cuda: cuda/8.0, cuda/9.0, cuda/9.2, cuda/10.0, cuda/10.1, cuda/11.2, cuda/11.3, cuda/11.4, cuda/11.5, cuda/11.8, cuda/12.2

thewtex

There is a “T2_analysis” branch in “OAI_analysis_2" that Boqi wrote. As well as a “notebooks/T2Demo.py” for the demo and here’s the affine registration model: https://drive.google.com/file/d/156LnBZqv3lEQUdcmzYYPHqBKyjoTVrr3/view?usp=share_link

thewtex

The repository is currently 753 MB, and takes 17 minutes to clone from GitHub. There are some large files in Git history and large files in the current working directory...

thewtex

Create function to move a mesh using an ITK transform

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HastingsGreer

HastingsGreer

Old order: warp segmentation of cartilage extract mesh compute thickness New order: extract mesh compute thickness warp mesh, bringing metadata with it move mesh to atlas cartilage mesh move mesh...

HastingsGreer