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Localtab Group

titleData Access

Data Access

Click the  Download button to save a ".tcia" manifest file to your computer, which you must open with the NBIA Data Retriever . Click the Search button to open our Data Portal, where you can browse the data collection and/or download a subset of its contents.

Data TypeDownload all or Query/Filter
Images (DICOM) 77.6 (GB)

Target Data (XLSX) 131 (KB)

Biopsy Data (XLSX) 4.25 (MB)

STL Files (ZIP) 274 (MB)

(Click the "Detailed Description" tab above for usage instructions)

Bipsy Biopsy Overlays (ZIP) 333 (MB)

titleDetailed Description

Detailed Description

Image Statistics



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]

Click the Versions tab for more info about data releases.

titleCitations & Data Usage Policy

Citations & Data Usage Policy

Tcia license 4 international

titleData Citation

Natarajan, S., Priester, A., Margolis, D., Huang, J., & Marks, L. (2020). Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy) [Data set]. The Cancer Imaging Archive.

titlePublication Citation

Sonn, Geoffrey A., Shyam Natarajan, Daniel JA Margolis, Malu MacAiran, Patricia Lieu, Jiaoti  Huang, Frederick J. Dorey, and Leonard S. Marks. "Targeted biopsy in the detection of prostate  cancer using an office based magnetic resonance ultrasound fusion device."  The Journal of Urology 189, no. 1 (2013): 86-92

titleTCIA Citation

Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. DOI: 10.1007/s10278-013-9622-7

Other Publications Using This Data

TCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk.


Version 1 (Current):  2020/09/11

Data TypeDownload all or Query/Filter
Images (DICOM) 77.6 (GB)
Target Data (XLSX) 131 (KB)
Biopsy Data (XLSX) 4.25 (MB)

STL Files (ZIP) 274 (MB)

(Click the "Detailed Description" tab above for usage instructions)

Biopsy Overlays (ZIP) 333 (MB) 

Added new subjects.