| --- |
| license: cc-by-3.0 |
| task_categories: |
| - image-segmentation |
| tags: |
| - medical |
| - mri |
| - t2-weighted |
| - prostate |
| - zonal-anatomy |
| - pi-rads |
| - tcia |
| - dicom-seg |
| pretty_name: PROSTATEx-Seg-Zones |
| size_categories: |
| - n<1K |
| dataset_info: |
| features: |
| - name: patient_id |
| dtype: string |
| - name: split |
| dtype: string |
| - name: image |
| dtype: image |
| - name: mask |
| dtype: image |
| - name: overlay |
| dtype: image |
| - name: preview_slice |
| dtype: int32 |
| - name: num_slices |
| dtype: int32 |
| - name: rows |
| dtype: int32 |
| - name: cols |
| dtype: int32 |
| - name: spacing_xyz |
| list: float32 |
| - name: zones_present |
| list: string |
| - name: voxels_per_zone_json |
| dtype: string |
| splits: |
| - name: train |
| num_bytes: 27847888 |
| num_examples: 98 |
| download_size: 27850346 |
| dataset_size: 27847888 |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/train-* |
| --- |
| |
| # PROSTATEx-Seg-Zones |
|
|
| Prostatic **zonal anatomy** segmentation on axial T2-weighted MRI. 98 patients, |
| each with a four-class label map covering the peripheral zone, transition zone, |
| prostatic urethra, and anterior fibromuscular stroma — the compartments a PI-RADS |
| v2 sector map is built on. |
|
|
| The upstream TCIA product is an *analysis result* containing DICOM-SEG objects and |
| **no images**. This mirror pairs each segmentation with its source T2 series from |
| the base SPIE-AAPM-NCI PROSTATEx collection and ships both as NIfTI, so the merge |
| does not have to be repeated downstream. |
|
|
| ## Dataset Details |
|
|
| | Field | Value | |
| |---|---| |
| | Modality | MRI, axial T2-weighted turbo spin-echo (`t2_tse_tra`) | |
| | Body part | Prostate | |
| | Task | Multi-class 3D segmentation (zonal anatomy) | |
| | Patients | 98 (one study, one T2 series, one segmentation each) | |
| | Classes | 4 + background, **mutually disjoint** | |
| | In-plane grid | 384x384 (82 cases), 320x320 (15), 640x640 (1) | |
| | Slices per volume | 19-25 | |
| | In-plane spacing | 0.5-0.5625 mm | |
| | Slice thickness | 3 mm (4.5 mm spacing typical) | |
| | Annotator | Single reader (`ContentCreator=Reader1`), reviewed by an expert urologist | |
| | Format | NIfTI (`.nii.gz`), converted from DICOM + DICOM-SEG | |
| | License | CC BY 3.0 Unported (commercial use permitted) | |
|
|
| ## Labels |
|
|
| | Value | Zone | SNOMED CT | |
| |---|---|---| |
| | 0 | background | — | |
| | 1 | Peripheral zone | 279706003 | |
| | 2 | Transition zone | 399384005 | |
| | 3 | Prostatic urethra | 71553001 | |
| | 4 | Anterior fibromuscular stroma | 717025007 | |
|
|
| There is **no central zone** — CZ is folded into the transition zone, consistent |
| with PI-RADS v2 practice. |
|
|
| The four zones are **strictly disjoint**: verified across all 98 cases that no |
| voxel carries two labels and `sum(per-zone counts) == |foreground|`. Consume this |
| as a single label map; per-target binary fan-out is not needed and would be wrong. |
|
|
| All four zones are non-empty in all 98 cases. They are, however, very unbalanced — |
| the urethra is ~2% and the anterior fibromuscular stroma ~3% of total foreground: |
|
|
| | Zone | Total voxels | Share of foreground | |
| |---|---|---| |
| | Transition zone | 5,532,407 | 65.2% | |
| | Peripheral zone | 2,508,037 | 29.6% | |
| | Anterior fibromuscular stroma | 261,059 | 3.1% | |
| | Prostatic urethra | 178,892 | 2.1% | |
|
|
| Expect low Dice on the last two. That is the class prior, not a defect. |
|
|
| ## Layout |
|
|
| ``` |
| volumes/ProstateX-0004/image.nii.gz # T2W volume (z, y, x) |
| volumes/ProstateX-0004/mask.nii.gz # uint8 label map, identical geometry |
| ... |
| metadata.jsonl # one record per case |
| label_map.json # label -> name + SNOMED code |
| ``` |
|
|
| `mask.nii.gz` carries the same origin, spacing and direction as its `image.nii.gz` |
| (set via `CopyInformation`), so the pair is voxel-aligned with no resampling. |
|
|
| Each `metadata.jsonl` record holds `patient_id`, `image`, `mask`, `split`, |
| `num_slices`, `rows`, `cols`, `spacing_xyz`, `voxels_per_zone`, `zones_present`, |
| and the originating `t2_series_uid` / `study_uid` / `seg_series_uid`. |
|
|
| ## Splits |
|
|
| **There is no official train/val/test split.** All 98 cases are published as a |
| flat pool and are labelled `train` in `metadata.jsonl`. Any split is your own |
| construction — group on `patient_id`. |
|
|
| ## Provenance and integrity notes |
|
|
| **Source images are a separate download.** The Zone Segmentations product (149 MB) |
| contains segmentations only. The corresponding 2,020 T2 DICOM (585 MB) come from |
| the base PROSTATEx collection via TCIA's "Corresponding Original files" manifest. |
| Both are CC BY 3.0. |
|
|
| **T2 series were resolved via `ReferencedSeriesSequence`, never by |
| `SeriesDescription`.** All 98 SEGs reference a series described `t2_tse_tra`, but |
| 14 of the 98 studies contain two MR series carrying that identical description — |
| matching on the description silently selects the wrong volume in ~14% of cases. |
|
|
| **Slice placement is by source SOP Instance UID.** Each SEG frame was placed at |
| the index of its `DerivationImageSequence` source instance within the geometrically |
| sorted T2 stack. DICOM-SEG frame order is not anatomical order, and |
| `ReferencedInstanceSequence` is not guaranteed sorted. |
|
|
| **Relationship to PROSTATEx-Seg-HiRes.** A second TCIA analysis result |
| (`10.7937/TCIA.2019.DEG7ZG1U`) provides 66 cases of **whole-gland binary** |
| segmentation built by fusing axial/sagittal/coronal delineations. Those 66 |
| patients are a strict subset of these 98, but the two are different products, not |
| two tiers of one annotation — HiRes has no zone labels, and its masks are not |
| voxel-aligned to any TCIA series (e.g. ProstateX-0020: 116 planes at 0.6 mm versus |
| the T2 series' 21 at 3 mm). For zonal work, this dataset is the reference. |
|
|
| ### ⚠️ Patient overlap with PI-CAI |
|
|
| All 98 patients come from the SPIE-AAPM-NCI PROSTATEx collection (346 patients). |
| The **PI-CAI** public training set incorporates 328 ProstateX cases, so effectively |
| every patient here also appears in PI-CAI, and the PI-CAI organisers explicitly |
| recommend not using both together. |
|
|
| This overlap is **not programmatically excludable**: PI-CAI re-anonymised to |
| sequential identifiers and publishes no ProstateX↔PI-CAI mapping. De-duplication |
| would require image-level matching (T2 geometry or voxel hashing). |
|
|
| The label content does not collide — PI-CAI annotates csPCa *lesions* and whole |
| gland, this dataset annotates *zonal anatomy* — so the two are complementary in |
| what they measure. But do not treat them as independent cohorts when aggregating |
| patient-level statistics. The `patient_id` field preserves the canonical |
| `ProstateX-####` identifier for cross-referencing against any PROSTATEx-derived |
| set. |
|
|
| Other prostate datasets checked: **PROSTATEx-2** shares this image archive |
| (different task). **Prostate158**, **PROMISE12**, **MSD Task05_Prostate**, |
| **NCI-ISBI 2013**, **QIN-PROSTATE-Repeatability**, and **Prostate-MRI-US-Biopsy** |
| draw on different TCIA collections or institutions with no documented patient |
| overlap. |
| |
| ## Citation |
| |
| ```bibtex |
| @inproceedings{meyer2019prostatezones, |
| title = {Towards Patient-Individual {PI-RADS} v2 Sector Map: {CNN} for |
| Automatic Segmentation of Prostatic Zones from {T2}-Weighted {MRI}}, |
| author = {Meyer, Anneke and Rak, Marko and Schindele, Daniel and |
| Blaschke, Simon and Schostak, Martin and Fedorov, Andriy and |
| Hansen, Christian}, |
| booktitle = {IEEE International Symposium on Biomedical Imaging (ISBI)}, |
| pages = {696--700}, |
| year = {2019}, |
| doi = {10.1109/ISBI.2019.8759572} |
| } |
| |
| @misc{meyer2020prostatexzones, |
| title = {{PROSTATEx} Zone Segmentations}, |
| author = {Meyer, Anneke and Schindele, Daniel and von Reibnitz, Daniel and |
| Rak, Marko and Schostak, Martin and Hansen, Christian}, |
| year = {2020}, |
| publisher = {The Cancer Imaging Archive}, |
| doi = {10.7937/TCIA.NBB4-4655} |
| } |
| |
| @misc{litjens2017prostatex, |
| title = {{SPIE-AAPM-NCI PROSTATEx} Challenges ({PROSTATEx})}, |
| author = {Litjens, Geert and Debats, Oscar and Barentsz, Jelle and |
| Karssemeijer, Nico and Huisman, Henkjan}, |
| year = {2017}, |
| publisher = {The Cancer Imaging Archive}, |
| doi = {10.7937/K9TCIA.2017.MURS5CL} |
| } |
| |
| @article{clark2013tcia, |
| title = {The Cancer Imaging Archive ({TCIA}): Maintaining and Operating a |
| Public Information Repository}, |
| author = {Clark, Kenneth and Vendt, Bruce and Smith, Kirk and others}, |
| journal = {Journal of Digital Imaging}, |
| volume = {26}, |
| number = {6}, |
| pages = {1045--1057}, |
| year = {2013}, |
| doi = {10.1007/s10278-013-9622-7} |
| } |
| ``` |
| |
