| --- |
| license: cc-by-3.0 |
| task_categories: |
| - image-segmentation |
| tags: |
| - medical |
| - mri |
| - brain |
| - glioblastoma |
| - tumor-segmentation |
| - neuro-oncology |
| - radiomics |
| - BraTS |
| configs: |
| - config_name: default |
| data_files: |
| - split: test |
| path: data/test-* |
| dataset_info: |
| features: |
| - name: patient_id |
| dtype: string |
| - name: study_date |
| dtype: string |
| - name: num_slices |
| dtype: int32 |
| - name: tumor_slice_idx |
| dtype: int32 |
| - name: tumor_voxels_upenn |
| dtype: int64 |
| - name: has_cwru_mask |
| dtype: bool |
| - name: T1 |
| dtype: image |
| - name: T1c |
| dtype: image |
| - name: T2 |
| dtype: image |
| - name: FLAIR |
| dtype: image |
| - name: seg_UPenn |
| dtype: image |
| - name: overlay_UPenn |
| dtype: image |
| - name: seg_CWRU |
| dtype: image |
| - name: overlay_CWRU |
| dtype: image |
| - name: age |
| dtype: string |
| - name: gender |
| dtype: string |
| - name: histopathology |
| dtype: string |
| - name: location |
| dtype: string |
| - name: extent_of_resection |
| dtype: string |
| - name: survival_days |
| dtype: string |
| - name: molecular_subtype |
| dtype: string |
| - name: idh1 |
| dtype: string |
| - name: mgmt |
| dtype: string |
| - name: egfr |
| dtype: string |
| - name: included_upenn |
| dtype: string |
| - name: included_cwru |
| dtype: string |
| splits: |
| - name: test |
| num_bytes: 4779075 |
| num_examples: 34 |
| download_size: 4795822 |
| dataset_size: 4779075 |
| --- |
| |
| # IvyGAP-Radiomics (SRI-atlas subset) |
|
|
| Multi-parametric brain-MRI **glioblastoma (GBM)** segmentation dataset: 4 co-registered, |
| skull-stripped MRI sequences per subject with **expert tumor sub-compartment masks** from |
| **two independent institutions**, plus precomputed radiomic features. From the TCIA |
| *Analysis Result* collection **IvyGAP-Radiomics** (Pati et al., 2020). |
|
|
| ## ⚠️ Scope — this is a preprocessed subset of the full Ivy GAP project |
| "IvyGAP-Radiomics" is **not** the complete Ivy Glioblastoma Atlas Project (Ivy GAP). It is a |
| derived analysis result containing only the **pre-operative** scans, **skull-stripped** and |
| **co-registered to the SRI24 atlas**, converted to NIfTI, with expert tumor masks and radiomic |
| features added. It does **not** include the original DICOM imaging (~140 GB), histology (ISH), |
| or gene-expression / genomic data of the parent Ivy GAP collection. Only the **SRI-atlas** |
| package is mirrored here (the alternate **MNI-atlas / CWRU-only** package is not included). |
|
|
| ## 🔴 Cross-dataset overlap with BraTS (evaluation-integrity hazard) |
| Pre-operative IvyGAP data is **included in the BraTS challenge training set** (together with |
| TCGA-GBM, TCGA-LGG, CPTAC-GBM), and these masks were produced with the **BraTS preprocessing |
| pipeline** (SRI24 atlas, skull-strip) and follow the **BraTS labeling convention**. **Do not** |
| benchmark these subjects against any BraTS-trained model, or alongside `Angelou0516/brats2023-*`, |
| without treating the results as non-held-out — there is likely train/test leakage. Subjects are |
| identified by Ivy GAP IDs (`W1`…`W55`); there is **no published BraTS-ID cross-reference column**, |
| so any mapping to BraTS subjects must be done externally via the Ivy GAP → BraTS name tables. |
|
|
| ## Two expert raters — no single gold standard (by design) |
| The dataset's purpose is **inter-rater reproducibility**. Each tumor was segmented independently |
| by board-certified neuroradiologists at **two institutions**: |
| - **UPenn** (Hospital of the University of Pennsylvania) — **34 subjects** |
| - **CWRU** (Case Western Reserve University) — **31 subjects** |
|
|
| **31 subjects are paired** (annotated by both). The paper anoints **neither** rater as "the" |
| ground truth — both are equally-valid expert annotations. Both mask sets are provided here. |
| For a single-GT workflow, the recommended default is **UPenn** (broader coverage: 34 vs 31). |
| Subjects without a CWRU mask: **W6, W30, W54**. |
|
|
| ## Labels (BraTS convention) |
| | value | sub-compartment | |
| |------:|-----------------| |
| | 0 | background | |
| | 1 | NCR/NET — necrotic & non-enhancing tumor core | |
| | 2 | ED — peritumoral edema / invaded tissue | |
| | 4 | ET — enhancing tumor | |
|
|
| Composite regions: **TC** (tumor core) = {1,4}; **WT** (whole tumor) = {1,2,4}; **ET** = {4}. |
| Mask dtypes as released: UPenn `uint16`, CWRU `float32` — both encode the integer labels above |
| (content is preserved byte-for-byte; cast to integer when loading). |
|
|
| ## Geometry |
| All volumes are **240 × 240 × 155 @ 1.0 mm isotropic** in **SRI24** space, skull-stripped, |
| LPS orientation. One pre-operative study per subject. |
|
|
| ## Structure |
| ``` |
| W{n}/ # one folder per subject, at the repo root |
| W{n}_t1.nii.gz # native T1 |
| W{n}_t1c.nii.gz # post-contrast T1 (T1-Gd; original token "t1gd") |
| W{n}_t2.nii.gz # T2 |
| W{n}_flair.nii.gz # T2-FLAIR |
| W{n}_seg-UPenn.nii.gz # UPenn expert mask (all 34 subjects) |
| W{n}_seg-CWRU.nii.gz # CWRU expert mask (31 subjects) |
| atlas/spgr_unstrip_lps.nii.gz # SRI24 reference template |
| data/test-*.parquet # Dataset Viewer preview only (rendered slices + metadata) |
| radiomic_features/ # CaPTk/IBSI features per rater, feature parameters, reproducibility correlations |
| ivygap_metadata.csv # per-subject clinical & molecular metadata (see below) |
| subject_study_dates.csv # subject -> original study date + which rater masks exist |
| ``` |
|
|
| ## `ivygap_metadata.csv` |
| Per-subject metadata keyed by `Patient` (W-ID). Columns include `Included_Upenn`, |
| `Included_CWRU`, `4_Modalities` (inclusion flags), `Age`, `gender`, `Histopathology`, |
| `location`, `EoR` (extent of resection), `Surgery`, `survival_days`, `Molecular_subtype`, |
| `IDH1`, `1p19q_deletion`, `MGMT`/`MGMT PCR`, `EGFR`/`EGFR vIII`, `PTEN`, `KPS(initial)`, |
| time-to-progression / last-follow-up, and cause of death. (The CSV also lists a few subjects |
| that lack 4-modality imaging and are therefore **not** present under `data/`.) |
|
|
| ## Provenance, license & citation |
| - **Provenance:** Official TCIA Analysis Result (author-provided), DOI **10.7937/9j41-7d44**. |
| SRI-atlas package downloaded via TCIA IBM-Aspera faspex5. |
| - **License:** **CC BY 3.0** (TCIA Analysis Results) + the TCIA Data Usage Policy. |
| - **Data citation:** Pati, S., Verma, R., Akbari, H., Bilello, M., Hill, V.B., Sako, C., Correa, R., |
| Beig, N., Venet, L., Thakur, S., Serai, P., Ha, S.M., Blake, G.D., Shinohara, R.T., Tiwari, P., |
| Bakas, S. (2020). *Data from the Multi-Institutional Paired Expert Segmentations and Radiomic |
| Features of the Ivy GAP Dataset.* The Cancer Imaging Archive. DOI 10.7937/9j41-7d44. |
| - **Publication:** Pati S, et al. *Reproducibility analysis of multi-institutional paired expert |
| annotations and radiomic features of the Ivy GAP dataset.* Medical Physics 2020;47(12):6039–6052. |
| DOI 10.1002/mp.14556. |
|
|
