Child pages
  • Prostate MRI and Ultrasound With Pathology and Coordinates of Tracked Biopsy (Prostate-MRI-US-Biopsy)
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 90 Next »

Summary


These two images show biopsy data displayed in 3D alongside MRI contours. The image on the left captures the entire 3D slicer screen.  The image on the right succinctly exemplifies most aspects of the dataset.

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. 

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.   

Note: Some Private Tags in this collection are critical to properly displaying the STL surface and the Prostate anatomy.  Private Tag (1129,"Eigen Artemis",1016) DS VoxelSize is especially important for multi-frame US cases.    


Acknowledgements

We would like to acknowledge the individuals and institutions that have provided data for this collection:

  • This work was supported in part by the National Cancer Institute Award R01CA158627, Prostate  Cancer SPORE at University of California-Los Angeles P50CA092131, the Beckman Coulter  Foundation, Jean Perkins Foundation, and Steven C. Gordon Family Foundation
  • TBD:  Harmonization of the components of this dataset, including into standard DICOM representation, was supported in part by the NCI Imaging Data Commons consortium. NCI Imaging Data Commons consortium is supported by the contract number 19X037Q from Leidos Biomedical Research under Task Order HHSN26100071 from NC


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) 78.7 (GB)

Target Data (XLSX) 138 (KB)

Biopsy Data (XLSX) 4.4 (MB)

STL Files (ZIP) 274 (MB)

Bipsy Overlays (ZIP) 333 (MB)

Click the Versions tab for more info about data releases.


Detailed Description

Image Statistics


Modalities

MR, US

Number of Participants

1151

Number of Studies

2795

Number of Series

2795

Number of Images

61,135

Images Size (GB)78.7 

Citations & Data Usage Policy

Users of this data must abide by the Creative Commons Attribution 3.0 Unported License under which it has been published. Attribution should include references to the following citations:

Data 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. https://doi.org/10.7937/TCIA.2020.A61IOC1A

Publication 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 U rology 189, no. 1 (2013): 86-92

TCIA 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):  2020/04/20

Data TypeDownload all or Query/Filter
Images (DICOM) 78.7 (GB)
Target Data (XLSX) 138 (KB)
Biopsy Data (XLSX) 4.4 (MB)

STL Files (ZIP) 274 (MB)

Biopsy Overlays (ZIP) 333 (MB) 

Added new subjects.












  • No labels