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Prostate and pelvis, segmentation

PROSTATEx gland zones

Transverse T2 MR of the prostate of one man examined for prostate cancer at 3 T without an endorectal coil, the peripheral zone and the rest of the gland drawn by radiologists (PROSTATEx masks).

20 test casesprostateimage MR
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Read before comparing (9)
  • Images. The repository's axial T2 of each exam, the series its readers drew on, taken as it is: Siemens 3 T at Radboud University Medical Centre, values with no common scale between exams. Slices are 3 mm apart on 194 of the 204 exams and 3.5 to 4.5 mm on 10; pixels are 0.5 mm on 184.
  • Truth. Two radiology residents and two board-certified radiologists of the University of Naples Federico II drew the zones by hand, slice by slice; a program then cleaned stray clusters, patching the peripheral zone on 67 exams and the rest on 133. Neither paper says who drew which exam, nor whether an exam was read twice: graded expert.
  • Labels. 1 is the peripheral zone, 2 the rest of the gland (transition zone, central zone and anterior stroma), ProstateISBI2013's central gland. They never overlap, and together make the repository's whole-gland mask but for at most 0.04 mL on 57 exams, left as background. On ProstateX-0009 and development case ProstateX-0079 they start on the lowest slice: the apex may go on below the field of view.
  • Lesions. The 299 lesion masks are left out: painted over the zones, they would take voxels from them and add a small, noisy structure drawn only where the challenge listed a finding.
  • Second reading. Another group's zones on TCIA (PROSTATEx-Seg-Zones) agree with these labels, on the four test cases that have them, at a Dice of 0.69 to 0.78 on the peripheral zone, 0.90 to 0.95 on the rest and 0.93 to 0.95 on the whole gland. A method should not be expected far past that, most on the peripheral zone.
  • TotalSegmentator. Version 2.18 (total_mr) has no zones: on ProstateX-0095 its prostate overlaps the union of the two labels at a Dice of 0.79, and a method that writes only the gland scores 0 on both labels.
  • Overlap. ProstateX-0082 is ProstateISBI2013's Prostate3T-03-0001 voxel for voxel and is left out. Its nine other Radboud images match no PROSTATEx T2 by voxels, nor any exam by study time or by age, weight and height, though a later visit under a PROSTATEx number cannot be ruled out. PROMISE12's Radboud cases lie on a grid no PROSTATEx T2 has.
  • PI-CAI. PROSTATEx is inside PI-CAI's public training and development set: a dataset built from PI-CAI should leave these patients out, at least the 38 built here. The 142 exams of the PROSTATEx test set have no masks.
  • Source. prepare.py pins the repository's commit 21b9dfd. The masks fit the dcm2niix volumes the repository gives, which the corpus uses.

No method has a result on every case of this dataset yet.

Case by case

Click a score to look at that result: the image, the truth in green and the method's map in red. Underlined scores have their image; for the others you see the case without the result.

About the data

The first test case of PROSTATEx gland zones
The first test caseClick to look at every case.
Test cases
20 test exams drawn with seed 2026 among the 185 of the pool outside development, then 18 development exams, the last of the same seeded order. The pool is the 204 exams of the PROSTATEx training set, one a patient, less ProstateX-0082, which is ProstateISBI2013's test case Prostate3T-03-0001: 203.
Truth
contours by experts the peripheral zone and the rest of the gland (transition zone, central zone and anterior stroma together), drawn by hand slice by slice on the axial T2 by two radiology residents and two board-certified radiologists of the University of Naples Federico II, then cleaned of stray clusters by a program (PROSTATEx masks)
Licence
CC BY 4.0 (the repository: masks and the T2 volumes it redistributes); CC BY 3.0 (the PROSTATEx images, TCIA)
18 cases for tuning, never tested

ProstateX-0079, ProstateX-0091, ProstateX-0186, ProstateX-0051, ProstateX-0012, ProstateX-0135, ProstateX-0105, ProstateX-0015, ProstateX-0170, ProstateX-0165, ProstateX-0160, ProstateX-0176, ProstateX-0137, ProstateX-0183, ProstateX-0108, ProstateX-0092, ProstateX-0034, ProstateX-0088