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Angelou0516 commited on
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Add UCSF-PDGM BraTS-format structural subset (495 patients: T1/T1c/T2/FLAIR + tumor_segmentation) + clinical metadata

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  1. .gitattributes +1 -59
  2. README.md +100 -0
  3. UCSF-PDGM-0004/UCSF-PDGM-0004_FLAIR.nii.gz +3 -0
  4. UCSF-PDGM-0004/UCSF-PDGM-0004_T1.nii.gz +3 -0
  5. UCSF-PDGM-0004/UCSF-PDGM-0004_T1c.nii.gz +3 -0
  6. UCSF-PDGM-0004/UCSF-PDGM-0004_T2.nii.gz +3 -0
  7. UCSF-PDGM-0004/UCSF-PDGM-0004_tumor_segmentation.nii.gz +3 -0
  8. UCSF-PDGM-0005/UCSF-PDGM-0005_FLAIR.nii.gz +3 -0
  9. UCSF-PDGM-0005/UCSF-PDGM-0005_T1.nii.gz +3 -0
  10. UCSF-PDGM-0005/UCSF-PDGM-0005_T1c.nii.gz +3 -0
  11. UCSF-PDGM-0005/UCSF-PDGM-0005_T2.nii.gz +3 -0
  12. UCSF-PDGM-0005/UCSF-PDGM-0005_tumor_segmentation.nii.gz +3 -0
  13. UCSF-PDGM-0007/UCSF-PDGM-0007_FLAIR.nii.gz +3 -0
  14. UCSF-PDGM-0007/UCSF-PDGM-0007_T1.nii.gz +3 -0
  15. UCSF-PDGM-0007/UCSF-PDGM-0007_T1c.nii.gz +3 -0
  16. UCSF-PDGM-0007/UCSF-PDGM-0007_T2.nii.gz +3 -0
  17. UCSF-PDGM-0007/UCSF-PDGM-0007_tumor_segmentation.nii.gz +3 -0
  18. UCSF-PDGM-0008/UCSF-PDGM-0008_FLAIR.nii.gz +3 -0
  19. UCSF-PDGM-0008/UCSF-PDGM-0008_T1.nii.gz +3 -0
  20. UCSF-PDGM-0008/UCSF-PDGM-0008_T1c.nii.gz +3 -0
  21. UCSF-PDGM-0008/UCSF-PDGM-0008_T2.nii.gz +3 -0
  22. UCSF-PDGM-0008/UCSF-PDGM-0008_tumor_segmentation.nii.gz +3 -0
  23. UCSF-PDGM-0009/UCSF-PDGM-0009_FLAIR.nii.gz +3 -0
  24. UCSF-PDGM-0009/UCSF-PDGM-0009_T1.nii.gz +3 -0
  25. UCSF-PDGM-0009/UCSF-PDGM-0009_T1c.nii.gz +3 -0
  26. UCSF-PDGM-0009/UCSF-PDGM-0009_T2.nii.gz +3 -0
  27. UCSF-PDGM-0009/UCSF-PDGM-0009_tumor_segmentation.nii.gz +3 -0
  28. UCSF-PDGM-0010/UCSF-PDGM-0010_FLAIR.nii.gz +3 -0
  29. UCSF-PDGM-0010/UCSF-PDGM-0010_T1.nii.gz +3 -0
  30. UCSF-PDGM-0010/UCSF-PDGM-0010_T1c.nii.gz +3 -0
  31. UCSF-PDGM-0010/UCSF-PDGM-0010_T2.nii.gz +3 -0
  32. UCSF-PDGM-0010/UCSF-PDGM-0010_tumor_segmentation.nii.gz +3 -0
  33. UCSF-PDGM-0011/UCSF-PDGM-0011_FLAIR.nii.gz +3 -0
  34. UCSF-PDGM-0011/UCSF-PDGM-0011_T1.nii.gz +3 -0
  35. UCSF-PDGM-0011/UCSF-PDGM-0011_T1c.nii.gz +3 -0
  36. UCSF-PDGM-0011/UCSF-PDGM-0011_T2.nii.gz +3 -0
  37. UCSF-PDGM-0011/UCSF-PDGM-0011_tumor_segmentation.nii.gz +3 -0
  38. UCSF-PDGM-0012/UCSF-PDGM-0012_FLAIR.nii.gz +3 -0
  39. UCSF-PDGM-0012/UCSF-PDGM-0012_T1.nii.gz +3 -0
  40. UCSF-PDGM-0012/UCSF-PDGM-0012_T1c.nii.gz +3 -0
  41. UCSF-PDGM-0012/UCSF-PDGM-0012_T2.nii.gz +3 -0
  42. UCSF-PDGM-0012/UCSF-PDGM-0012_tumor_segmentation.nii.gz +3 -0
  43. UCSF-PDGM-0013/UCSF-PDGM-0013_FLAIR.nii.gz +3 -0
  44. UCSF-PDGM-0013/UCSF-PDGM-0013_T1.nii.gz +3 -0
  45. UCSF-PDGM-0013/UCSF-PDGM-0013_T1c.nii.gz +3 -0
  46. UCSF-PDGM-0013/UCSF-PDGM-0013_T2.nii.gz +3 -0
  47. UCSF-PDGM-0013/UCSF-PDGM-0013_tumor_segmentation.nii.gz +3 -0
  48. UCSF-PDGM-0014/UCSF-PDGM-0014_FLAIR.nii.gz +3 -0
  49. UCSF-PDGM-0014/UCSF-PDGM-0014_T1.nii.gz +3 -0
  50. UCSF-PDGM-0014/UCSF-PDGM-0014_T1c.nii.gz +3 -0
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README.md ADDED
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+ ---
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+ license: cc-by-4.0
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+ pretty_name: UCSF-PDGM (BraTS-format structural subset)
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+ task_categories:
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+ - image-segmentation
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+ tags:
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+ - medical-imaging
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+ - mri
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+ - brain
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+ - glioma
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+ - brain-tumor
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+ - brats
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+ - tumor-segmentation
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+ - neuro-oncology
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+ ---
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+
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+ # UCSF-PDGM — BraTS-format structural subset (T1/T1c/T2/FLAIR + tumor segmentation)
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+
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+ > **⚠️ This repository is the *BraTS-format structural subset* of UCSF-PDGM — NOT the full multi-sequence release.**
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+ > Per patient it provides the **4 structural MRI modalities** (T1, T1c, T2, FLAIR) co-registered to the
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+ > **240 × 240 × 155 BraTS grid** (1 mm isotropic, skull-stripped) plus the **expert-corrected tumor segmentation**.
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+ > The full UCSF-PDGM release additionally contains DWI, ADC, ASL, SWI, HARDI/DTI and derived diffusion maps, N4
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+ > bias-corrected (`_bias`) images, and whole-brain / parenchyma masks — **all intentionally excluded here** to keep
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+ > a compact, BraTS-compatible glioma-segmentation dataset.
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+
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+ The University of California San Francisco Preoperative Diffuse Glioma MRI (UCSF-PDGM) dataset is a cohort of
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+ preoperative 3 T brain MRI from patients with histopathologically confirmed diffuse gliomas.
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+
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+ ## Contents
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+
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+ - **495 patients** — one folder each, `UCSF-PDGM-XXXX/`, with **5 NIfTI volumes**.
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+ - `UCSF-PDGM-metadata_v5.csv` — official clinical metadata (sex, age, WHO CNS grade, final WHO-2021 diagnosis,
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+ MGMT status/index, 1p/19q, IDH, overall survival, extent of resection, and the **BraTS21 ID / cohort columns**).
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+ - `UCSF-PDGM-metadata_glossary.csv` — glossary for the metadata columns.
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+
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+ > Note: the metadata table has **501 rows** (imaging studies) while there are **495 image folders** (unique patients);
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+ > 6 follow-up/duplicate studies are not included as images.
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+
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+ ## Per-patient series layout (do not infer — this is the authoritative mapping)
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+
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+ Every `UCSF-PDGM-XXXX/` folder contains exactly these five files:
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+
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+ | File | Series | Description | Role |
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+ |----------------------------------------|--------|--------------------------------------|-------------|
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+ | `UCSF-PDGM-XXXX_T1.nii.gz` | T1 | Pre-contrast T1-weighted | image |
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+ | `UCSF-PDGM-XXXX_T1c.nii.gz` | T1c | Post-contrast (gadolinium) T1-w | image |
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+ | `UCSF-PDGM-XXXX_T2.nii.gz` | T2 | T2-weighted | image |
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+ | `UCSF-PDGM-XXXX_FLAIR.nii.gz` | FLAIR | T2-FLAIR | image |
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+ | `UCSF-PDGM-XXXX_tumor_segmentation.nii.gz` | seg | Tumor segmentation | **ground truth mask** |
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+
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+ All five volumes share identical geometry — shape `(240, 240, 155)`, 1 mm isotropic — and are voxel-aligned.
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+
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+ ## Tumor segmentation labels (BraTS convention)
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+
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+ | Label | Region |
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+ |-------|---------------------------------------------------|
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+ | 0 | Background |
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+ | 1 | Non-enhancing tumor core / necrosis (NCR) |
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+ | 2 | Peritumoral edema (ED) |
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+ | 4 | Enhancing tumor (ET) |
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+
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+ Masks were produced for the **BraTS 2021** challenge: an automated ensemble of prior BraTS-winning algorithms,
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+ then **manually corrected and approved by neuroradiologists**.
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+
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+ ## ⚠️ Benchmark-overlap warning (BraTS 2021 / 2023)
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+
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+ Roughly **298 of the 495 cases (~60 %) overlap with BraTS 2021**, and therefore with **BraTS 2023** (which inherits
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+ the BraTS 2021 glioma data). The `BraTS21 ID`, `BraTS21 Segmentation Cohort`, and `BraTS21 MGMT Cohort` columns in
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+ `UCSF-PDGM-metadata_v5.csv` identify exactly which cases. **Do not treat UCSF-PDGM as an independent benchmark
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+ alongside BraTS2023 without first excluding the intersection** — otherwise evaluation is contaminated by
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+ train/test leakage.
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+
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+ ## Joining metadata to images (ID padding differs)
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+
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+ Metadata IDs are **3-digit zero-padded** (`UCSF-PDGM-004`); image folders/filenames are **4-digit**
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+ (`UCSF-PDGM-0004`). Normalize by stripping the `UCSF-PDGM-` prefix and parsing the integer to join the two.
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+
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+ ## Preprocessing
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+
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+ - Co-registered (nonlinear) to the T2-FLAIR reference space at **1 mm isotropic**.
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+ - **Skull-stripped** with a deep-learning brain-extraction method.
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+ - Intensities are *not* N4 bias-corrected in this subset (the full release also offers `_bias` variants).
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+
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+ ## License
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+
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+ **CC BY 4.0** (Creative Commons Attribution 4.0 International). You must give appropriate credit.
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+
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+ ## Citation
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+
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+ Calabrese E, Villanueva-Meyer JE, Rudie JD, et al. *The University of California San Francisco Preoperative
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+ Diffuse Glioma MRI Dataset.* Radiology: Artificial Intelligence. 2022;4(6):e220058.
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+ https://doi.org/10.1148/ryai.220058
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+
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+ Data (TCIA): Calabrese, E., et al. (2022). *UCSF-PDGM* (Version 5) [Data set]. The Cancer Imaging Archive.
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+ https://doi.org/10.7937/tcia.bdgf-8v37 — collection page: https://www.cancerimagingarchive.net/collection/ucsf-pdgm/
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+
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+ ## Provenance
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+
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+ Structural subset extracted from **UCSF-PDGM Version 5** (TCIA), retaining only the T1/T1c/T2/FLAIR images and the
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+ `tumor_segmentation` mask from each patient's NIfTI package. Re-distributed here under the source CC BY 4.0 license.
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