{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T16:07:03Z","timestamp":1753891623003,"version":"3.41.2"},"reference-count":22,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T00:00:00Z","timestamp":1711411200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004488","name":"Hrvatska Zaklada za Znanost","doi-asserted-by":"publisher","award":["IP-06-2016-1892"],"award-info":[{"award-number":["IP-06-2016-1892"]}],"id":[{"id":"10.13039\/501100004488","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["KK.01.1.1.07.0071"],"award-info":[{"award-number":["KK.01.1.1.07.0071"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Neuroinform."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Magnetic resonance imaging (MRI) is invaluable for understanding brain disorders, but data complexity poses a challenge in experimental research. In this study, we introduce suMRak, a MATLAB application designed for efficient preclinical brain MRI analysis. SuMRak integrates brain segmentation, volumetry, image registration, and parameter map generation into a unified interface, thereby reducing the number of separate tools that researchers may require for straightforward data handling.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods and implementation<\/jats:title><jats:p>All functionalities of suMRak are implemented using the MATLAB App Designer and the MATLAB-integrated Python engine. A total of six helper applications were developed alongside the main suMRak interface to allow for a cohesive and streamlined workflow. The brain segmentation strategy was validated by comparing suMRak against manual segmentation and ITK-SNAP, a popular open-source application for biomedical image segmentation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>When compared with the manual segmentation of coronal mouse brain slices, suMRak achieved a high S\u00f8rensen\u2013Dice similarity coefficient (0.98 \u00b1 0.01), approaching manual accuracy. Additionally, suMRak exhibited significant improvement (<jats:italic>p<\/jats:italic> = 0.03) when compared to ITK-SNAP, particularly for caudally located brain slices. Furthermore, suMRak was capable of effectively analyzing preclinical MRI data obtained in our own studies. Most notably, the results of brain perfusion map registration to T2-weighted images were shown, improving the topographic connection to anatomical areas and enabling further data analysis to better account for the inherent spatial distortions of echoplanar imaging.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>SuMRak offers efficient MRI data processing of preclinical brain images, enabling researchers' consistency and precision. Notably, the accelerated brain segmentation, achieved through K-means clustering and morphological operations, significantly reduces processing time and allows for easier handling of larger datasets.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fninf.2024.1358917","type":"journal-article","created":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T04:28:17Z","timestamp":1711427297000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["suMRak: a multi-tool solution for preclinical brain MRI data analysis"],"prefix":"10.3389","volume":"18","author":[{"given":"Rok","family":"Ister","sequence":"first","affiliation":[]},{"given":"Marko","family":"Sternak","sequence":"additional","affiliation":[]},{"given":"Sini\u0161a","family":"\u0160koki\u0107","sequence":"additional","affiliation":[]},{"given":"Sre\u0107ko","family":"Gajovi\u0107","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,3,26]]},"reference":[{"key":"B1","unstructured":"Allen Mouse Brain Atlas2004"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.5555\/1283383.1283494","article-title":"\u201cK-means++: the advantages of careful seeding,\u201d","author":"Arthur","year":"2007","journal-title":"Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms"},{"key":"B3","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1161\/01.STR.0000056169.45365.15","article-title":"Neuroprotective effect of SolCD39, a novel platelet aggregation inhibitor, on transient middle cerebral artery occlusion in rats","volume":"34","author":"Belayev","year":"2003","journal-title":"Stroke"},{"key":"B4","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s13311-010-0002-4","article-title":"MRI in rodent models of brain disorders","volume":"8","author":"Denic","year":"2011","journal-title":"Neurotherapeutics"},{"key":"B5","doi-asserted-by":"publisher","first-page":"297","DOI":"10.2307\/1932409","article-title":"Measures of the amount of ecologic association between species","volume":"26","author":"Dice","year":"1945","journal-title":"Ecology"},{"key":"B6","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.neuroimage.2008.03.037","article-title":"High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl\/6J mice","volume":"42","author":"Dorr","year":"2008","journal-title":"Neuroimage"},{"key":"B7","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1161\/01.STR.0000113692.38574.57","article-title":"Noninvasive quantification of brain edema and the space-occupying effect in rat stroke models using magnetic resonance imaging","volume":"35","author":"Gerriets","year":"2004","journal-title":"Stroke"},{"key":"B8","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1007\/BF00133570","article-title":"Snakes: active contour models","volume":"1","author":"Kass","year":"1988","journal-title":"Int. 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