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Challenges to accurate correlation include matching the pathology sectioning plane with the <jats:italic>in vivo<\/jats:italic> imaging slice plane and correction for the deformation that occurs between <jats:italic>in vivo<\/jats:italic> imaging and histology. A methodology is presented for matching of the histological sectioning angle and position to the <jats:italic>in vivo<\/jats:italic> imaging slices.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods:<\/jats:title><jats:p>Patients (<jats:italic>n<\/jats:italic> = 4) with biochemical failure following external beam radiotherapy underwent diagnostic MRI to confirm localized recurrence of prostate cancer, followed by salvage radical prostatectomy. High\u2010resolution 3\u2010D MRI of the <jats:italic>ex vivo<\/jats:italic> specimens was acquired to determine the pathology sectioning angle that best matched the <jats:italic>in vivo<\/jats:italic> imaging slice plane, using matching anatomical features and implanted fiducials. A novel sectioning device was developed to guide sectioning at the correct angle, and to assist the insertion of reference dye marks to aid in histopathology reconstruction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results:<\/jats:title><jats:p>The percentage difference in the positioning of the urethra in the <jats:italic>ex vivo<\/jats:italic> pathology sections compared to the positioning in <jats:italic>in vivo<\/jats:italic> images was reduced from 34% to 7% through slicing at the best match angle. Reference dye marks were generated, which were visible in <jats:italic>ex vivo<\/jats:italic> imaging, in the tissue sections before and after processing, and in histology sections.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions:<\/jats:title><jats:p>The method achieved an almost fivefold reduction in the slice\u2010matching error and is readily implementable in combination with standard MRI technology. The technique will be employed to generate datasets for correlation of whole\u2010specimen prostate histopathology with <jats:italic>in vivo<\/jats:italic> diagnostic MRI using 3\u2010D deformable registration, allowing assessment of the sensitivity and specificity of MRI parameters for prostate cancer. Although developed specifically for prostate, the method is readily adaptable to other types of whole tissue specimen, such as mastectomy or liver resection.<\/jats:p><\/jats:sec>","DOI":"10.1118\/1.4941016","type":"journal-article","created":{"date-parts":[[2016,2,4]],"date-time":"2016-02-04T18:02:34Z","timestamp":1454608954000},"page":"1065-1072","update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":11,"title":["Technical Note: Method to correlate whole\u2010specimen histopathology of radical prostatectomy with diagnostic MR imaging"],"prefix":"10.1002","volume":"43","author":[{"given":"Deirdre M.","family":"McGrath","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Warren D.","family":"Foltz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Navid","family":"Samavati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A. 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