| --- |
| license: cc-by-4.0 |
| task_categories: |
| - image-segmentation |
| tags: |
| - medical |
| - mri |
| - mpmri |
| - brain |
| - glioblastoma |
| - glioma |
| - brain-tumor |
| - tumor-segmentation |
| - brats |
| - nifti |
| - tcia |
| - upenn-gbm |
| pretty_name: UPENN-GBM (mpMRI + Tumor Segmentation) |
| size_categories: |
| - n<1K |
| dataset_info: |
| features: |
| - name: subject_id |
| dtype: string |
| - name: patient_id |
| dtype: string |
| - name: timepoint |
| dtype: string |
| - name: gt_source |
| dtype: string |
| - name: num_slices |
| dtype: int32 |
| - name: slice_index |
| dtype: int32 |
| - name: tumor_voxels |
| dtype: int64 |
| - name: modality |
| dtype: string |
| - name: image |
| dtype: image |
| - name: mask |
| dtype: image |
| - name: overlay |
| dtype: image |
| splits: |
| - name: manual |
| num_bytes: 5989524 |
| num_examples: 147 |
| - name: automated |
| num_bytes: 18932953 |
| num_examples: 464 |
| - name: unsegmented |
| num_bytes: 856502 |
| num_examples: 60 |
| download_size: 25763705 |
| dataset_size: 25778979 |
| configs: |
| - config_name: default |
| data_files: |
| - split: manual |
| path: data/manual-* |
| - split: automated |
| path: data/automated-* |
| - split: unsegmented |
| path: data/unsegmented-* |
| --- |
| |
| # UPENN-GBM — mpMRI + Tumor Segmentation |
|
|
| The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: structural |
| multi-parametric MRI (mpMRI) of de novo glioblastoma patients with tumor |
| sub-region segmentations. This is the **NIfTI** release from TCIA — images are |
| skull-stripped and co-registered to the SRI24 atlas, and the segmentations are |
| aligned to them. |
|
|
| > **This HuggingFace mirror is a segmentation-focused subset** of the full TCIA |
| > collection. It contains the structural mpMRI sequences and the tumor |
| > segmentations only. The DICOM package (139 GB), the DSC/DTI derivative maps, |
| > the skull-**unstripped** images, the histopathology WSIs (149 GB), and the |
| > radiomic-feature tables are **not** included here — obtain those from TCIA. |
|
|
| ## Dataset Details |
|
|
| | Field | Value | |
| |---|---| |
| | Modality | Brain mpMRI — T1, T1-Gd (T1CE), T2, T2-FLAIR | |
| | Body part | Brain (de novo glioblastoma) | |
| | Task | 3D multi-class tumor sub-region segmentation | |
| | Structural scans | 671 (630 patients; `_21` = follow-up timepoints) | |
| | Manual/expert masks | 147 (`images_segm`) — **recommended ground truth** | |
| | Automated masks | 611 (`automated_segm`) | |
| | Segmentable scans | 611 (have a manual and/or automated mask) | |
| | Volume geometry | 240 × 240 × 155, 1 mm isotropic, SRI24 atlas space | |
| | Format | NIfTI (`.nii.gz`) | |
| | License | CC BY 4.0 | |
|
|
| ## Label Scheme (BraTS convention) |
|
|
| | Value | Tumor sub-region | |
| |---|---| |
| | 0 | Background | |
| | 1 | Necrotic / non-enhancing tumor core (NCR/NET) | |
| | 2 | Peritumoral edematous / infiltrated tissue (ED) | |
| | 4 | GD-enhancing tumor (ET) | |
|
|
| Evaluation regions: **WT** (whole tumor) = 1+2+4, **TC** (tumor core) = 1+4, |
| **ET** (enhancing tumor) = 4. Note the enhancing-tumor label is **4** (native |
| BraTS/TCIA encoding), *not* 3 — verified across the released masks. |
|
|
| ## Mask Sources (two) |
|
|
| 1. **`images_segm` — manually-corrected expert segmentation (147 scans).** |
| Automated labels reviewed and corrected/approved by board-certified |
| neuroradiologists. **This is the recommended ground truth.** |
| 2. **`automated_segm` — automated segmentation (611 scans).** Label fusion |
| (STAPLE) of an ensemble of top BraTS-ranked deep models (DeepMedic, |
| DeepSCAN, nnU-Net). Silver/weak standard. |
|
|
| All 147 manually-corrected scans also have an automated mask. 60 scans |
| (follow-up `_21` timepoints) have neither and are image-only. |
|
|
| **Recommended GT policy (used by `subjects_manifest.json`):** prefer the manual |
| mask in `images_segm`; fall back to `automated_segm`; skip scans with neither. |
| |
| ## Structure |
| |
| ``` |
| images_structural/<subject>/<subject>_T1.nii.gz |
| images_structural/<subject>/<subject>_T1GD.nii.gz |
| images_structural/<subject>/<subject>_T2.nii.gz |
| images_structural/<subject>/<subject>_FLAIR.nii.gz |
| images_segm/<subject>_segm.nii.gz # manual/expert GT (147) |
| automated_segm/<subject>_automated_approx_segm.nii.gz # automated (611) |
| metadata/UPENN-GBM_clinical_info_v2.1.csv # clinical + genomic per subject |
| subjects_manifest.json # per-scan paths, mask availability, GT policy |
| ``` |
| |
| `<subject>` = `UPENN-GBM-NNNNN_TT`, where `TT` is the timepoint (`11` = baseline, |
| `21` = follow-up). `subjects_manifest.json` lists, for every structural scan, the |
| four modality paths, the manual/automated mask paths (if present), and the chosen |
| `gt_path`/`gt_source` — so loaders need not re-derive availability. |
| |
| ## Notes for Loaders |
| |
| - **Images and masks share an identical grid** (240×240×155, 1 mm iso, SRI24) — |
| no resampling or axis permutation is needed between a scan and its mask. |
| - The NIfTI images are SRI-registered and **do not** align with the TCIA DICOM |
| package by design. |
| - Multi-channel input: stack T1/T1GD/T2/FLAIR as channels (BraTS-style). |
| |
| ## Source |
| |
| - TCIA collection: https://www.cancerimagingarchive.net/collection/upenn-gbm/ |
| - DOI: `10.7937/TCIA.709X-DN49` |
| - Public, no registration required (TCIA fully public since 2025-07-07). |
| |
| ## Citation |
| |
| ```bibtex |
| @article{bakas2022upenngbm, |
| author = {Bakas, Spyridon and Sako, Chiharu and Akbari, Hamed and Bilello, Michel |
| and Sotiras, Aristeidis and Shukla, Gaurav and Rudie, Jeffrey D. and |
| Flores Santamar\'ia, Nadina and Fathi Kazerooni, Anahita and Pati, Sarthak |
| and others}, |
| title = {The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: |
| advanced MRI, clinical, genomics, \& radiomics}, |
| journal = {Scientific Data}, |
| volume = {9}, |
| number = {1}, |
| pages = {453}, |
| year = {2022}, |
| doi = {10.1038/s41597-022-01560-7} |
| } |
| ``` |
| |
