Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add the demo walkthrough, demo video, and the blog post to the 3D MRI example #31

Merged
merged 6 commits into from
May 2, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,4 @@
*.nii.gz
examples/3d-brain-mri/sample-data/3d-brain.json
examples/3d-brain-mri/sample-data/dataset-3d-brain.zip
.ipynb_checkpoints/
Binary file added deploy/images/platform_step01_data.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added deploy/images/platform_step02_training.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added deploy/images/platform_step03_deployment.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
4 changes: 2 additions & 2 deletions examples/3d-brain-mri/readme.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
This example is based on the **UCSF-PDGM: The University of California San Francisco Preoperative Diffuse Glioma MRI** research dataset, which can be found here:<br/>
https://www.cancerimagingarchive.net/collection/ucsf-pdgm/

The original dataset contains data from 495 unique subjects. The dataset is formed by taking several MRI scans for each patient, “skull stripping” the scan (leaving just the brain image), and de-identifying the patient. The result is 4 MRI volumes per subject, as well as a target segmentation mask. In the [sample-data](./sample-data/) folder, you will find a small subset of the data from 87 subjects ([dataset-3d-brain.zip](./sample-data/dataset-3d-brain.zip)), which will be used to train the model. Given the size of the subset data being 1.1 GiB, the data is stored in a separate location. The data is stored in a Hugging Face dataset (https://huggingface.co/datasets/determined-ai/3d-brain-mri). To download the data, navigate to the [`sample-data`](sample-data) directory and run the following commands:
The original dataset contains data from 495 unique subjects. The dataset is formed by taking several MRI scans for each patient, “skull stripping” the scan (leaving just the brain image), and de-identifying the patient. The result is 4 MRI volumes per subject, as well as a target segmentation mask. In the [sample-data](./sample-data/) folder, you will download a small subset of the data from 87 subjects ([dataset-3d-brain.zip](./sample-data/dataset-3d-brain.zip)), which will be used to train the model. Given the size of the subset data being 1.1 GiB, the data is stored in a Hugging Face dataset (https://huggingface.co/datasets/determined-ai/3d-brain-mri). To download the data, navigate to the [`sample-data`](sample-data) directory and run the following commands:

```bash
wget https://huggingface.co/datasets/determined-ai/3d-brain-mri/resolve/main/dataset-3d-brain.zip
Expand Down Expand Up @@ -109,4 +109,4 @@ The return response should be JSON block with a very long list of values.

&nbsp;

### In the [sample-data](./sample-data/) folder, you will also find a Jupyter Notebook example showing how to load images from a folder or from the sample .json file and generate predictions.
### In the [sample-data](./sample-data/) folder, you will also find a [Jupyter Notebook demo walkthrough](sample-data/3DBrainMRIDemoWalkthrough.ipynb) with a [corresponding video demo](https://youtu.be/YkchRpVqHIE?si=22ogT5rq-ZFkz7Cy) showing how to load the volumes, run a distributed hyperparameter search and run a prediction from Kserve. Make sure to deploy the PDK environment before running the code. You can also read the blog post written on this demo: https://www.determined.ai/blog/brain-mri-demo
504 changes: 0 additions & 504 deletions examples/3d-brain-mri/sample-data/3D-Brain-MRI_Prediction.ipynb

This file was deleted.

Loading
Loading