Dataset Open Access

Annotated MRI and ultrasound volume images of the prostate

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

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  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.16396", 
  "author": [
      "given": "Andrey", 
      "family": "Fedorov"
      "given": "Paul L", 
      "family": "Nguyen"
      "given": "Kemal", 
      "family": "Tuncali"
      "given": "Clare", 
      "family": "Tempany"
  "issued": {
    "date-parts": [
  "abstract": "<p><strong>Introduction</strong></p>\n\n<p>The <em>Surgical Planning Laboratory (SPL) </em>and the <em>National Center for Image Guided Therapy (NCIGT) </em>are making this dataset available as a resource to aid in the development of algorithms and tools for deformable registration,&nbsp;segmentation and analysis of prostate magnetic resonance imaging (MRI) and ultrasound&nbsp;(US) images. &nbsp;</p>\n\n<p><strong>Description</strong></p>\n\n<p>This dataset contains anonymized images of the human prostate (N=3 patients) collected during two sessions for each patient:</p>\n\n<ol>\n\t<li>MRI&nbsp;examination of the prostate for the purposes of disease staging.</li>\n\t<li>US&nbsp;examination of the prostate for the purposes of volumetric examination in preparation to the brachytherapy implant.</li>\n</ol>\n\n<p>These are three-dimensional (multi-slice) scalar images.</p>\n\n<p>Image files are stored using NRRD file format (files with .nrrd extension), see details at Each image file includes a code for the case number (internal numbering at the research site) and the modality (US or MR).</p>\n\n<p>Image annotations were prepared by Dr. Fedorov (no professional training in radiology)&nbsp;and Dr. Tuncali (10+ in prostate imaging interpretation). Annotations include</p>\n\n<ol>\n\t<li>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 &quot;-label&quot; suffix.</li>\n\t<li>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&nbsp;(.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.</li>\n</ol>\n\n<p><strong>Viewing the collection</strong></p>\n\n<p>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, with the pre-compiled binaries available for all major operating systems. You can download 3D Slicer at</p>\n\n<p><strong>Acknowledgments </strong></p>\n\n<p>Preparation of this data collection was made possible thanks to the&nbsp;funding from the National Institutes of Health (NIH) through grants R01 CA111288 and P41 RR019703.</p>\n\n<p><strong>Contact</strong></p>\n\n<p>Andrey Fedorov,</p>", 
  "title": "Annotated MRI and ultrasound volume images of the prostate", 
  "type": "dataset", 
  "id": "16396"
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