Upload README.md with huggingface_hub

README.md

@@ -0,0 +1,134 @@
+---
+license: cc-by-4.0
+task_categories:
+  - image-segmentation
+tags:
+  - medical
+  - mri
+  - mpmri
+  - prostate
+  - prostate-cancer
+  - test-retest
+  - repeatability
+  - dicom
+  - tcia
+pretty_name: QIN-PROSTATE-Repeatability
+size_categories:
+  - n<1K
+---
+
+# QIN-PROSTATE-Repeatability
+
+Annotated test-retest multi-parametric MRI of the prostate. Fifteen treatment-naive
+subjects each scanned twice within two weeks on the same 3T scanner with an
+endorectal coil, yielding 30 imaging studies. Each study contains T2-weighted axial,
+diffusion-weighted (b=0, b=1400), apparent diffusion coefficient (ADC), and dynamic
+contrast-enhanced (DCE) subtraction series, with manual whole-gland, peripheral-zone,
+suspected-lesion, and normal-PZ segmentations stored as DICOM SEG.
+
+## Dataset Details
+
+| Field | Value |
+|---|---|
+| Modality | Multi-parametric MRI @ 3T (endorectal coil) |
+| Sequences | T2W axial, DWI (b=0, b=1400), ADC, DCE subtraction |
+| Body part | Prostate |
+| Task | Multi-class 3D segmentation |
+| Subjects | 15 |
+| Studies | 30 (each subject scanned twice — test/retest) |
+| MR series | 150 |
+| SEG series | 90 (3 per study — T2W/ADC/DCE) |
+| SR series | 90 (DICOM Structured Reports, TID 1500) |
+| MR images | 38,320 DICOM slices |
+| Format | DICOM (images) + DICOM SEG (segmentations) + DICOM SR (measurements) |
+| License | CC BY 4.0 |
+
+No predefined train/val/test split — this is a repeatability cohort. The natural
+split is two timepoints per subject (Time Point 1 vs Time Point 2). All 15
+subjects are treatment-naive; 11 have at least one suspected lesion (yielding 22
+lesion-positive study-timepoints).
+
+## Segmentation Classes
+
+A single radiologist (10+ years abdominal-MRI experience) annotated each study in
+3D Slicer, blinded to subject ID and to baseline/repeat status. `SegmentAlgorithmType`
+in every SEG is `MANUAL`. Per study:
+
+1. **Whole prostate gland**     — annotated on T2W/ADC/DCE
+2. **Whole peripheral zone**    — annotated on T2W/ADC/DCE
+3. **Suspected lesion (tumor)** — annotated when present (22 of 30 study-timepoints)
+4. **Normal PZ tissue**         — annotated on ADC only
+
+Bundled DICOM SEG objects are the canonical and only ground truth — no alternative
+mask source exists for this collection.
+
+## Structure
+
+```
+images/<PatientID>/<StudyInstanceUID>/<SeriesInstanceUID>/*.dcm           # MR
+segmentations/<PatientID>/<StudyInstanceUID>/<SeriesInstanceUID>/*.dcm    # SEG (multi-frame)
+structured_reports/<PatientID>/<StudyInstanceUID>/<SeriesInstanceUID>/*.dcm  # SR (TID 1500)
+series_to_patient.json                                                    # series-level metadata
+```
+
+Each SEG SOP references its source-image series via DICOM metadata
+(`DerivationImageSequence -> SourceImageSequence -> ReferencedSOPInstanceUID`).
+SR objects (TID 1500/1411) carry per-ROI volume (mm³) and mean ADC (µm²/s) with
+`Time Point` (1 or 2) and `Tracking UID` linkage to the segmented ROIs.
+
+## Important Notes for Loaders
+
+- **mpMRI is NOT co-registered.** T2W, DWI, ADC, and DCE have different geometries.
+  Use T2W axial as the geometric reference and resample/align other modalities to it
+  rather than stacking as channels.
+- **DICOM SEG ⇄ ITK conversion** is needed to get a labelmap volume; use
+  `dcmqi`'s `segimage2itkimage` or `pydicom-seg`.
+- **Test/retest pairs**: each subject has two studies (TP1 vs TP2). Decide whether
+  to treat as 30 independent samples or 15 paired samples for evaluation.
+- **Lesion mask absent** in 4 subjects (8 study-timepoints) — handle missing-class
+  gracefully.
+
+## Source
+
+- TCIA collection: https://www.cancerimagingarchive.net/collection/qin-prostate-repeatability/
+- DOI: `10.7937/K9/TCIA.2018.MR1CKGND`
+- Companion paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC6278692/
+
+## Citation
+
+```bibtex
+@article{fedorov2018qinprostate,
+  author  = {Fedorov, Andrey and Schwier, Michael and Clunie, David and
+             Herz, Christian and Pieper, Steve and Kikinis, Ron and
+             Tempany, Clare and Fennessy, Fiona},
+  title   = {An annotated test-retest collection of prostate multiparametric MRI},
+  journal = {Scientific Data},
+  volume  = {5},
+  pages   = {180281},
+  year    = {2018},
+  doi     = {10.1038/sdata.2018.281}
+}
+
+@misc{qinprostaterepeatability2018tcia,
+  author    = {Fedorov, A. and Schwier, M. and Clunie, D. and Herz, C. and
+               Pieper, S. and Kikinis, R. and Tempany, C. and Fennessy, F.},
+  title     = {Data From QIN-PROSTATE-Repeatability [Dataset]},
+  year      = {2018},
+  publisher = {The Cancer Imaging Archive},
+  doi       = {10.7937/K9/TCIA.2018.MR1CKGND}
+}
+
+@article{fedorov2017repeatability,
+  author  = {Fedorov, Andrey and Vangel, Mark G. and Tempany, Clare M. and
+             Fennessy, Fiona M.},
+  title   = {Multiparametric Magnetic Resonance Imaging of the Prostate:
+             Repeatability of Volume and Apparent Diffusion Coefficient
+             Quantification},
+  journal = {Investigative Radiology},
+  volume  = {52},
+  number  = {9},
+  pages   = {538--546},
+  year    = {2017},
+  doi     = {10.1097/RLI.0000000000000382}
+}
+```