Number of Participants
Number of Studies
Number of Series
Number of Images
|Images Size (GB)||77.6 |
Instructions for Proper Use of the STL Files
The 3D surfaces of this dataset are in stereolithography format (binary representation). They are segmentations representing anatomic regions within the corresponding ultrasound (US) or MRI images. Each file is named "Prostate-MRI-US-Biopsy-XXXX-SURFACETYPE-seriesUID-YYYY.STL" where "XXXX" is the anonymized patient number and "YYYY" is the series instance UID of corresponding DICOM images. "SURFACETYPE" can be one of two identifiers, summarized below.
- If "SURFACETYPE" is "ProstateSurface," then the STL file is a segmentation of the prostate gland. These were contoured semi-automatically with Profuse (for MRI) or the Artemis fusion biopsy system (for US), both products of Eigen (Grass Valley, CA). Using these tools, the user manually traced the prostate on one or more image planes, and the remainder of gland was automatically segmented in 3D. The user was then able to adjust vertices of the 3D segmentation as necessary. These segmentations are generally of good quality, though their accuracy is user-dependent.
- If "SURFACETYPE" is "Target," then the STL file is a segmentation of a Region of Interest (ROI) suspicious for harboring prostate cancer. Zero, one, or more than one ROI may be present, and thus are designated "Target1," "Target2," etc. The ROIs corresponding to MRI were traced manually by a radiologist based on their interpretation of the patient's multiparametric MRI study. The ROIs corresponding to US images were acquired by registering the MRI prostate surface nonrigidly and semi-automatically to the US prostate surface. Therefore, the US ROIs are subject to misregistration, with average accuracy of 3-4 mm.
- Note that proximity to an ROI increases the likelihood of, but does not guarantee, prostate cancer. Also note that radiologists assigned each ROI a Likert-like suspicion score of 1-5, with 1 corresponding to very low suspicion of prostate cancer and 5 corresponding to very high suspicion of prostate cancer. These scores, which are roughly equivalent to the "PIRADS Version 2" scoring system, can be found in a spreadsheet included with the dataset.
The STL files can be visualized in 3D Slicer as follows:
1) Import the surface(s) either by drag-and-dropping or with File->Add Data
2) Within the "Models" module, adjust Display->Opacity of the prostate surface in order to visualize any ROI(s) within
3) To visualize surfaces in the context of corresponding MRI or US images, load the corresponding image series and then toggle the Slice Display->Visible radio button within the "models" module
4) To visualize surfaces in the context of biopsy cores, import the corresponding 3D slicer file named "BiopsyVectors.mrml" by drag-and-dropping or with File->Add Data.
The STL files, which are written in a standard format, can also be imported and visualized with most computer-aided design (CAD) and 3D printing software. Note that, if quantitative analysis is desired, the following transform was applied to US surfaces for 3D slicer compatibility and may need to be reversed for visualization alongside MRI or US images using other software.
Transform: [0 1 0 0 0 1 1 0 0]
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