From the National Cancer Institute’s Image Data Commons archive, we obtained the dataset titled Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy).
Summary of Dataset (from Cancer Imaging Archive):
This dataset was derived from tracked biopsy sessions using the Artemis biopsy system, many of which included image fusion with MRI targets. Patients received a 3D transrectal ultrasound scan, after which nonrigid registration (e.g. “fusion”) was performed between real-time ultrasound and preoperative MRI, enabling biopsy cores to be sampled from MR regions of interest. Most cases also included sampling of systematic biopsy cores using a 12-core digital template. The Artemis system tracked targeted and systematic core locations using encoder kinematics of a mechanical arm, and recorded locations relative to the Ultrasound scan. MRI biopsy coordinates were also recorded for most cases. STL files and biopsy overlays are available and can be visualized in 3D Slicer with the SlicerHeart extension. Spreadsheets summarizing biopsy and MR target data are also available. See the Detailed Description tab below for more information.
MRI targets were defined using multiparametric MRI, e.g. t2-weighted, diffusion-weighted, and perfusion-weighted sequences, and scored on a Likert-like scale with close correspondence to PIRADS version 2. t2-weighted MRI was used to trace ROI contours, and is the only sequence provided in this dataset. MR imaging was performed on a 3 Tesla Trio, Verio or Skyra scanner (Siemens, Erlangen, Germany). A transabdominal phased array was used in all cases, and an endorectal coil was used in a subset of cases. The majority of pulse sequences are 3D T2:SPC, with TR/TE 2200/203, Matrix/FOV 256 × 205/14 × 14 cm, and 1.5mm slice spacing. Some cases were instead 3D T2:TSE with TR/TE 3800–5040/101, and a small minority were imported from other institutions (various T2 protocols.)
Ultrasound scans were performed with Hitachi Hi-Vision 5500 7.5 MHz or the Noblus C41V 2-10 MHz end-fire probe. 3D scans were acquired by rotation of the end-fire probe 200 degrees about its axis, and interpolating to resample the volume with isotropic resolution.
Patients with suspicion of prostate cancer due to elevated PSA and/or suspicious imaging findings were consecutively accrued. Any consented patient who underwent or had planned to receive a routine, standard-of-care prostate biopsy at the UCLA Clark Urology Center was included.
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. DOI: 10.7937/TCIA.2020.A61IOC1A
Sonn GA, Natarajan S, Margolis DJ, MacAiran M, Lieu P, Huang J, Dorey FJ, Marks LS. Targeted biopsy in the detection of prostate cancer using an office based magnetic resonance ultrasound fusion device. Journal of Urology 189, no. 1 (2013): 86-91. DOI: 10.1016/j.juro.2012.08.095
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
Data source files:
- Images – DICOM 77GB (67K files)
- Target Data (XLSX) 131 (KB)
- Biopsy Data (XLSX) 4.25 (MB)
- STL Files (ZIP) 274 (MB)
- Biopsy Overlays (ZIP) 333 (MB)
Number of Participants
Number of Studies
Number of Series
Number of Images
|Images Size (GB)||77.6|
While the original dataset had anonymized health information for over 1000 patients, it was distributed across several files and sources. Key to joining the correct information was a unique Patient Identifier assigned to each record.
PATIENT DATA exploratory analysis
Input Feature: Patient Weight in Kilograms
Input Feature: Patient Height in M
Target Feature: Cancerous Percentage of Biopsy
While several parts of the dataset related to patient diagnostics, such as their medical scans or blood tests, even more important was their outcomes related to cancer. The dataset did not indicate directly whether a patient received a diagnosis of prostate cancer or its severity. Rather, it had information relating to the amount and score of cancer found during biopsy. In order to generate a useful set of target labels for supervised training, a patient was labeled as “cancerous” if any of their biopsies had a percentage of cancer greater than zero.
Input Feature: Patient Age in Years
Input Feature: Prostate Specific Antigen (PSA)
Blood Concentration in nanograms per milliliter
PSA is a protein produced by the prostate in both healthy and cancerous individuals. In many cases, a blood test measuring PSA concentration will be the first line of prostate cancer detection. It is thought that prostate cancer leads to higher PSA production and thus concentration in the blood, but its use as a screening procedure is often interchanged with the digital rectal exam.