Dataset Open Access

Annotated MRI and ultrasound volume images of the prostate

Fedorov, Andrey; Nguyen, Paul L; Tuncali, Kemal; Tempany, Clare

Introduction

The Surgical Planning Laboratory (SPL) and the National Center for Image Guided Therapy (NCIGT) are making this dataset available as a resource to aid in the development of algorithms and tools for deformable registration, segmentation and analysis of prostate magnetic resonance imaging (MRI) and ultrasound (US) images.  

Description

This dataset contains anonymized images of the human prostate (N=3 patients) collected during two sessions for each patient:

  1. MRI examination of the prostate for the purposes of disease staging.
  2. US examination of the prostate for the purposes of volumetric examination in preparation to the brachytherapy implant.

These are three-dimensional (multi-slice) scalar images.

Image files are stored using NRRD file format (files with .nrrd extension), see details at http://teem.sourceforge.net/nrrd/format.html. Each image file includes a code for the case number (internal numbering at the research site) and the modality (US or MR).

Image annotations were prepared by Dr. Fedorov (no professional training in radiology) and Dr. Tuncali (10+ in prostate imaging interpretation). Annotations include

  1. Manual contouring (segmentation) of the whole prostate gland, performed in 3D Slicer software. These segmentation images are coded in the same fashion as the image files, and saved in NRRD format, with "-label" suffix.
  2. Manually placed points (fiducials) corresponding to the location of urethra entry into the prostate at base (coded as UB), verumontanum (VM), urethra entry into the prostate at apex (UA), as well as centroids of cysts and calcifications. UB, UA and VM locations are annotated both in MR and US for all cases, while cysts and calcifications are annotated when applicable. Fiducial points are stored in comma-separated CSV-style format adopted by 3D Slicer software (.fcsv file extension). There is one row per point in these files, encoding the location of the point in RAS coordinate space relative to the image data, and the name of the point.

Viewing the collection

We tested visualization of images, segmentations and fiducials in 3D Slicer software, and thus recommend 3D Slicer as the platform for visualization. 3D Slicer is a free open source platform (see http://slicer.org), with the pre-compiled binaries available for all major operating systems. You can download 3D Slicer at http://download.slicer.org.

Acknowledgments

Preparation of this data collection was made possible thanks to the funding from the National Institutes of Health (NIH) through grants R01 CA111288 and P41 RR019703.

Contact

Andrey Fedorov, fedorov@bwh.harvard.edu

Files (34.1 MB)
Name Size
Case10-MR-fiducials.fcsv
md5:3f1da94b3345aab37b5cd0d7757b1962
444 Bytes Download
Case10-MR-label.nrrd
md5:a736ddcf07eb745d01154497e55d75a2
18.4 kB Download
Case10-MR.nrrd
md5:ee6186f1a803e9abf3406071baaab2e2
10.1 MB Download
Case10-US-fiducials.fcsv
md5:2068287af10a687b24c83dfa016eb130
444 Bytes Download
Case10_US_resampled-label.nrrd
md5:70596dad2c0a2e47f65f8d336f434fc6
18.4 kB Download
Case10_US_resampled.nrrd
md5:b15d1b0a4081e8c105ca6f20d799fbb3
900.8 kB Download
Case12-MR-fiducials.fcsv
md5:374ab22fc2bc3d5b72e396ab0c853a18
545 Bytes Download
Case12-MR-label.nrrd
md5:0a0b695108e36bbf6865aae6bc2b046c
19.9 kB Download
Case12-MR.nrrd
md5:b49c836ccf430f005bdc65b250914d71
10.7 MB Download
Case12-US-fiducials.fcsv
md5:3a5d5ecacd15ed4b31ab4f21b13cadd9
545 Bytes Download
Case12_US_resampled-label.nrrd
md5:5c3fad7b196ce8b96651f5152952372d
19.5 kB Download
Case12_US_resampled.nrrd
md5:0110214af0c2aa0cccc685a7155b41e9
1.0 MB Download
Case9-MR-fiducials.fcsv
md5:42067dbf898a633e97fba810f78bcc4f
644 Bytes Download
Case9-MR-label.nrrd
md5:e988da285a1aff988a23de9285ba1d9d
20.6 kB Download
Case9-MR.nrrd
md5:7ab22368b5930ab67daffee9f362b01a
10.1 MB Download
Case9-US-fiducials.fcsv
md5:fe4e618f68d96cac92b2aa925adc088d
642 Bytes Download
Case9_US_resampled-label.nrrd
md5:4bd972e270444e5b014996d73eed957f
20.7 kB Download
Case9_US_resampled.nrrd
md5:7ceff4fabe26807ac511e2ca2fafe1af
1.2 MB Download
  • Fedorov, Andriy, Siavash Khallaghi, C Antonio Sánchez, Andras Lasso, Sidney Fels, Kemal Tuncali, Emily Neubauer Sugar, et al. 2015. “Open-Source Image Registration for MRI–TRUS Fusion-Guided Prostate Interventions.” International Journal of Computer Assisted Radiology and Surgery, April. Springer Berlin Heidelberg, 1–10. doi:10.1007/s11548-015-1180-7.

  • Fedorov, A., Beichel, R., Kalpathy-Cramer, J., Finet, J., Fillion -Robin, J. C., Pujol, S., ... & Kikinis, R. (2012). 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magnetic resonance imaging, 30(9), 1323-1341.

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