Project-MONAI / Project-MONAI/tutorials
Add introductory k-space basics tutorial for MRI reconstruction
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- 主要语言
- Jupyter Notebook
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- 6 天 22 小时
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描述
Summary
Adds a beginner-friendly introductory tutorial for MRI reconstruction using the fastMRI knee single-coil dataset and MONAI's reconstruction transforms.
Changes
- New notebook:
reconstruction/MRI_reconstruction/tutorials/01_kspace_basics_fastmri_knee.ipynb- Part 1: What is k-space (loading real data, inverse FFT)
- Part 2: Fourier transform connection (low vs. high frequencies)
- Part 3: Undersampling and aliasing artifacts (1x, 2x, 4x, 8x)
- Part 4: Random vs. equispaced masks using
RandomKspaceMaskd/EquispacedKspaceMaskd - Part 5: Full MONAI preprocessing pipeline (
FastMRIReader→CenterSpatialCropd→ReferenceBasedNormalizeIntensityd) - Part 6: Zero-filled reconstruction → deep learning connection
- New README:
reconstruction/MRI_reconstruction/tutorials/README.md - Updated
README.md: Added missing Reconstruction section listing this tutorial plus existingunet_demoandvarnet_demo - Updated
runner.sh: Added notebook todoesnt_contain_max_epochs(no training loop)
Dataset
- Uses fastMRI knee single-coil validation set (non-commercial license)
- Only one
.h5file (~300 MB) required — no need for the full ~1.5 TB brain multi-coil download - Added to
skip_run_papermillvia existing.*MRI_reconstruction.*pattern
Design decisions
- Bridges the gap between newcomers and production tutorials (
unet_demo,varnet_demo) - Uses
CenterSpatialCropdinstead ofReferenceBasedSpatialCropdto handle the k-space (640×368) vs ground truth (320×320) dimension mismatch - No training loop — purely educational, runs without GPU
Test plan
- Notebook runs end-to-end on Google Colab with real fastMRI knee data (
file1000000.h5) - All 5 matplotlib visualizations render correctly
- Pipeline output shapes:
kspace_masked_ifftandreconstruction_escboth(1, 320, 320) - PEP 8 passes via
./runner.sh -t reconstruction/MRI_reconstruction/tutorials/01_kspace_basics_fastmri_knee.ipynb --no-run - Copyright header present with correct formatting
贡献指南
从这里开始
- 先读完整个 Issue,再读项目的贡献指南。
- 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
- Fork 仓库,在一个分支上完成修改。
- 提交 Pull Request,并在描述里引用这个 Issue 编号。
调研方向
从 reconstruction/MRI_reconstruction/tutorials/01_kspace_basics_fastmri_knee.ipynb 开始,并将其与现有的 unet_demo 和 varnet_demo 教程进行比较。运行 ./runner.sh -t reconstruction/MRI_reconstruction/tutorials/01_kspace_basics_fastmri_knee.ipynb --no-run,然后在 Colab 中使用 fastMRI 文件 file1000000.h5 验证该 notebook。可视化内容能够正常渲染、所述输出形状相匹配,并且 README 和 runner.sh 中的条目已更新,即表示完成。
由索引模型根据 Issue 内容生成。
评估
- 技术栈
- jupyter-notebook, pytorch
- 领域
- documentation, machine-learning
- Issue 类型
- 文档
- 难度
- 3/5
- 预计耗时
- 1-2 天
- 活跃度
- 停滞
- 描述清晰度
- 描述清楚
- 新手友好度
- 68/100