Skip to content

Commit

Permalink
1565 Adding VoxelMorph tutorial on OASIS dataset (Project-MONAI#1566)
Browse files Browse the repository at this point in the history
Fixes Project-MONAI#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 <ktang@unc.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
  • Loading branch information
3 people authored Nov 17, 2023
1 parent 10da274 commit e4bcfec
Show file tree
Hide file tree
Showing 2 changed files with 1,006 additions and 0 deletions.
1,003 changes: 1,003 additions & 0 deletions 3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb

Large diffs are not rendered by default.

3 changes: 3 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,9 @@ This notebook shows a quick demo for learning based affine registration of `64 x
##### [3D registration using paired lung CT](./3d_registration/paired_lung_ct.ipynb)
This tutorial shows how to use MONAI to register lung CT volumes acquired at different time points for a single patient.

##### [3D registration using unpaired brain MR](./3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb)
This tutorial shows how to get started on using the general-purpose registration framework `VoxelMorph` offered in MONAI to register unpaired brain MR volumes.

##### [DeepAtlas](./deep_atlas/deep_atlas_tutorial.ipynb)
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.

Expand Down

0 comments on commit e4bcfec

Please sign in to comment.