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1565 Adding VoxelMorph tutorial on OASIS dataset (#1566)
Fixes #1565. ### Description Added VoxelMorph tutorial on Learn2Reg 2021 Task 3 (OASIS dataset). ### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Avoid including large-size files in the PR. - [x] Clean up long text outputs from code cells in the notebook. - [x] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [x] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`. Execution takes ~2 mins, output of `runner.sh` below: ``` Executing: 100%|████████████████████████████████████████████████████████████████████| 37/37 [02:19<00:00, 3.76s/cell] /home/kaibo/miniforge3/envs/tutorial/lib/python3.8/site-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : - warnings.warn( real 2m19.352s user 5m54.674s sys 5m3.732s Testing finished. All 1 executed tests passed! ``` --------- Signed-off-by: kaibo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <[email protected]>
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3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb

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README.md

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##### [3D registration using paired lung CT](./3d_registration/paired_lung_ct.ipynb)
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This tutorial shows how to use MONAI to register lung CT volumes acquired at different time points for a single patient.
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##### [3D registration using unpaired brain MR](./3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb)
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This tutorial shows how to get started on using the general-purpose registration framework `VoxelMorph` offered in MONAI to register unpaired brain MR volumes.
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##### [DeepAtlas](./deep_atlas/deep_atlas_tutorial.ipynb)
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This tutorial demonstrates the use of MONAI for training of registration and segmentation models _together_. The DeepAtlas approach, in which the two models serve as a source of weakly supervised learning for each other, is useful in situations where one has many unlabeled images and just a few images with segmentation labels. The notebook works with 3D images from the OASIS-1 brain MRI dataset.
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