{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T09:24:18Z","timestamp":1762161858248,"version":"3.37.3"},"reference-count":49,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T00:00:00Z","timestamp":1726444800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T00:00:00Z","timestamp":1726444800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Science and Technology Innovation 2030 - Brain Science and Brain-Inspired Intelligence Project","award":["2021ZD0200200","2021ZD0200200"],"award-info":[{"award-number":["2021ZD0200200","2021ZD0200200"]}]},{"name":"Equipment Development Project of the Chinese Academy of Sciences","award":["YJKYYQ20190040","YJKYYQ20190040"],"award-info":[{"award-number":["YJKYYQ20190040","YJKYYQ20190040"]}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"crossref","award":["62327805"],"award-info":[{"award-number":["62327805"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Neuroinform"],"DOI":"10.1007\/s12021-024-09687-1","type":"journal-article","created":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T01:02:11Z","timestamp":1726448531000},"page":"555-568","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["MBV-Pipe: A One-Stop Toolbox for Assessing Mouse Brain Morphological Changes for Cross-Scale Studies"],"prefix":"10.1007","volume":"22","author":[{"given":"Wentao","family":"Jiang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinyi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhengyi","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianzi","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,9,16]]},"reference":[{"issue":"6139","key":"9687_CR2","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1126\/science.1235381","volume":"340","author":"K Amunts","year":"2013","unstructured":"Amunts, K., Lepage, C., Borgeat, L., Mohlberg, H., Dickscheid, T., Rousseau, M. \u00c9., Bludau, S., Bazin, P. L., Lewis, L. B., Oros-Peusquens, A. M., Shah, N. J., Lippert, T., Zilles, K., & Evans, A. C. (2013). BigBrain: An ultrahigh-resolution 3D human brain model. Science, 340(6139), 1472\u20131475. https:\/\/doi.org\/10.1126\/science.1235381","journal-title":"Science"},{"issue":"3","key":"9687_CR1","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1016\/j.neuron.2016.10.046","volume":"92","author":"K Amunts","year":"2016","unstructured":"Amunts, K., Ebell, C., Muller, J., Telefont, M., Knoll, A., & Lippert, T. (2016). The human brain project: Creating a European research infrastructure to decode the human brain. Neuron, 92(3), 574\u2013581. https:\/\/doi.org\/10.1016\/j.neuron.2016.10.046","journal-title":"Neuron"},{"issue":"1","key":"9687_CR3","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.neuroimage.2007.07.007","volume":"38","author":"J Ashburner","year":"2007","unstructured":"Ashburner, J. (2007). A fast diffeomorphic image registration algorithm. Neuroimage, 38(1), 95\u2013113. https:\/\/doi.org\/10.1016\/j.neuroimage.2007.07.007","journal-title":"Neuroimage"},{"key":"9687_CR4","unstructured":"Ashburner, J., Barnes, G., Chen, C. C., Daunizeau, J., Flandin, G., Friston, K., Kiebel, S., Kilner, J., Litvak, V., & Moran, R. (2014). SPM12 manual. Wellcome Trust Centre for Neuroimaging, London, UK, 2464(4)."},{"issue":"1","key":"9687_CR5","doi-asserted-by":"publisher","first-page":"5699","DOI":"10.1038\/s41467-019-13575-7","volume":"10","author":"DA Barri\u00e8re","year":"2019","unstructured":"Barri\u00e8re, D. A., Magalh\u00e3es, R., Novais, A., Marques, P., Selingue, E., Geffroy, F., Marques, F., Cerqueira, J., Sousa, J. C., Boumezbeur, F., Bottlaender, M., Jay, T. M., Cachia, A., Sousa, N., & M\u00e9riaux, S. (2019). The SIGMA rat brain templates and atlases for multimodal MRI data analysis and visualization. Nature Communications, 10(1), 5699. https:\/\/doi.org\/10.1038\/s41467-019-13575-7","journal-title":"Nature Communications"},{"issue":"9","key":"9687_CR6","doi-asserted-by":"publisher","first-page":"2554","DOI":"10.1109\/TIP.2011.2126587","volume":"20","author":"N Chou","year":"2011","unstructured":"Chou, N., Wu, J., Bingren, B., Anqi, J., & Kai-Hsiang Chuang. (2011). Robust automatic rodent brain extraction using 3-D pulse-coupled neural networks (PCNN). IEEE Transactions on Image Processing, 20(9), 2554\u20132564. https:\/\/doi.org\/10.1109\/TIP.2011.2126587","journal-title":"IEEE Transactions on Image Processing"},{"issue":"3","key":"9687_CR7","doi-asserted-by":"publisher","first-page":"e13169","DOI":"10.1111\/adb.13169","volume":"27","author":"JR Coleman","year":"2022","unstructured":"Coleman, J. R., Madularu, D., Ortiz, R. J., Athanassiou, M., Knudsen, A., Alkislar, I., Cai, X., Kulkarni, P. P., Cushing, B. S., & Ferris, C. F. (2022). Changes in brain structure and function following chronic exposure to inhaled vaporised cannabis during periadolescence in female and male mice: A multimodal MRI study. Addiction Biology, 27(3), e13169. https:\/\/doi.org\/10.1111\/adb.13169","journal-title":"Addiction Biology"},{"issue":"41","key":"9687_CR8","doi-asserted-by":"publisher","first-page":"eadg3844","DOI":"10.1126\/sciadv.adg3844","volume":"9","author":"I Costantini","year":"2023","unstructured":"Costantini, I., Morgan, L., Yang, J., Balbastre, Y., Varadarajan, D., Pesce, L., Scardigli, M., Mazzamuto, G., Gavryusev, V., Castelli, F. M., Roffilli, M., Silvestri, L., Laffey, J., Raia, S., Varghese, M., Wicinski, B., Chang, S., Chen, I. A., Wang, H., & Hof, P. R. (2023). A cellular resolution atlas of Broca\u2019s area. Science Advances, 9(41), eadg3844. https:\/\/doi.org\/10.1126\/sciadv.adg3844","journal-title":"Science Advances"},{"issue":"1","key":"9687_CR9","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1007\/s10561-013-9380-2","volume":"15","author":"AT Davenport","year":"2014","unstructured":"Davenport, A. T., Grant, K. A., Szeliga, K. T., Friedman, D. P., & Daunais, J. B. (2014). Standardized method for the harvest of nonhuman primate tissue optimized for multiple modes of analyses. Cell and Tissue Banking, 15(1), 99\u2013110. https:\/\/doi.org\/10.1007\/s10561-013-9380-2","journal-title":"Cell and Tissue Banking"},{"key":"9687_CR10","doi-asserted-by":"crossref","unstructured":"Eid, L., & Parent, M. (2017). Preparation of non-human primate brain tissue for pre-embedding immunohistochemistry and electron microscopy. Journal of Visualized Experiments.","DOI":"10.3791\/55397-v"},{"issue":"2","key":"9687_CR11","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1016\/j.neuroimage.2012.01.021","volume":"62","author":"B Fischl","year":"2012","unstructured":"Fischl, B. (2012). FreeSurfer NeuroImage, 62(2), 774\u2013781. https:\/\/doi.org\/10.1016\/j.neuroimage.2012.01.021.","journal-title":"FreeSurfer NeuroImage"},{"issue":"42","key":"9687_CR12","doi-asserted-by":"publisher","first-page":"eabc8098","DOI":"10.1126\/sciadv.abc8098","volume":"6","author":"CW Fung","year":"2020","unstructured":"Fung, C. W., Guo, J., Fu, H., Figueroa, H. Y., Konofagou, E. E., & Duff, K. E. (2020). Atrophy associated with tau pathology precedes overt cell death in a mouse model of progressive tauopathy. Science Advances, 6(42), eabc8098. https:\/\/doi.org\/10.1126\/sciadv.abc8098","journal-title":"Science Advances"},{"key":"9687_CR13","doi-asserted-by":"publisher","first-page":"3564","DOI":"10.3791\/3564","volume":"65","author":"GJ Gage","year":"2012","unstructured":"Gage, G. J., Kipke, D. R., & Shain, W. (2012). Whole animal perfusion fixation for rodents. Journal of Visualized Experiments, 65, 3564. https:\/\/doi.org\/10.3791\/3564","journal-title":"Journal of Visualized Experiments"},{"key":"9687_CR14","doi-asserted-by":"crossref","unstructured":"Gong, H. (2017). Precise cerebral vascular atlas in stereotaxic coordinates of whole mouse brain. Frontiers in Neuroanatomy, 11.","DOI":"10.3389\/fnana.2017.00128"},{"key":"9687_CR15","doi-asserted-by":"publisher","unstructured":"Holmes, H. E., Powell, N. M., Ma, D., Ismail, O., Harrison, I. F., Wells, J. A., Colgan, N., O\u2019Callaghan, J. M., Johnson, R. A., Murray, T. K., Ahmed, Z., Heggenes, M., Fisher, A., Cardoso, M. J., Modat, M., O\u2019Neill, M. J., Collins, E. C., Fisher, E. M. C., Ourselin, S., & Lythgoe, M. F. (2017). Comparison of in vivo and ex vivo MRI for the detection of structural abnormalities in a mouse model of tauopathy. Frontiers in Neuroinformatics, 11. https:\/\/doi.org\/10.3389\/fninf.2017.00020","DOI":"10.3389\/fninf.2017.00020"},{"issue":"1","key":"9687_CR16","doi-asserted-by":"publisher","first-page":"4320","DOI":"10.1038\/s41467-023-39916-1","volume":"14","author":"AFD Howard","year":"2023","unstructured":"Howard, A. F. D., Huszar, I. N., Smart, A., Cottaar, M., Daubney, G., Hanayik, T., Khrapitchev, A. A., Mars, R. B., Mollink, J., Scott, C., Sibson, N. R., Sallet, J., Jbabdi, S., & Miller, K. L. (2023). An open resource combining multi-contrast MRI and microscopy in the macaque brain. Nature Communications, 14(1), 4320. https:\/\/doi.org\/10.1038\/s41467-023-39916-1","journal-title":"Nature Communications"},{"key":"9687_CR18","doi-asserted-by":"publisher","first-page":"1149674","DOI":"10.3389\/fnana.2023.1149674","volume":"17","author":"R Insausti","year":"2023","unstructured":"Insausti, R., Insausti, A. M., Mu\u00f1oz L\u00f3pez, M., Medina Lorenzo, I., Arroyo-Jim\u00e9nez, M. D. M., Marcos Rabal, M. P., De La Rosa-Prieto, C., Delgado-Gonz\u00e1lez, J. C., Mont\u00f3n Etxeberria, J., Cebada-S\u00e1nchez, S., Raspe\u00f1o-Garc\u00eda, J. F., De I\u00f1iguez, M. M., Molina Romero, F. J., Benavides-Piccione, R., Tapia-Gonz\u00e1lez, S., Wisse, L. E. M., Ravikumar, S., Wolk, D. A., DeFelipe, J., & Artacho-P\u00e9rula, E. (2023). Ex vivo, in situ perfusion protocol for human brain fixation compatible with microscopy, MRI techniques, and anatomical studies. Frontiers in Neuroanatomy, 17, 1149674. https:\/\/doi.org\/10.3389\/fnana.2023.1149674","journal-title":"Frontiers in Neuroanatomy"},{"issue":"6133","key":"9687_CR19","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1126\/science.1239276","volume":"340","author":"TR Insel","year":"2013","unstructured":"Insel, T. R., Landis, S. C., & Collins, F. S. (2013). The NIH BRAIN initiative. Science, 340(6133), 687\u2013688. https:\/\/doi.org\/10.1126\/science.1239276","journal-title":"Science"},{"issue":"2","key":"9687_CR20","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1016\/j.neuroimage.2011.09.015","volume":"62","author":"M Jenkinson","year":"2012","unstructured":"Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M. (2012). FSL. NeuroImage, 62(2), 782\u2013790. https:\/\/doi.org\/10.1016\/j.neuroimage.2011.09.015.","journal-title":"FSL NeuroImage"},{"key":"9687_CR21","doi-asserted-by":"publisher","first-page":"83","DOI":"10.3389\/fnana.2018.00083","volume":"12","author":"D Keller","year":"2018","unstructured":"Keller, D., Er\u00f6, C., & Markram, H. (2018). Cell densities in the mouse brain: A systematic review. Frontiers in Neuroanatomy, 12, 83. https:\/\/doi.org\/10.3389\/fnana.2018.00083","journal-title":"Frontiers in Neuroanatomy"},{"key":"9687_CR22","doi-asserted-by":"publisher","first-page":"e05793","DOI":"10.7554\/eLife.05793","volume":"4","author":"N Korogod","year":"2015","unstructured":"Korogod, N., Petersen, C. C., & Knott, G. W. (2015). Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation. eLife, 4, e05793. https:\/\/doi.org\/10.7554\/eLife.05793","journal-title":"eLife"},{"key":"9687_CR23","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.nbd.2017.12.014","volume":"111","author":"Y Lee","year":"2018","unstructured":"Lee, Y., Rodriguez, O. C., Albanese, C., Santos, V. R., De Oliveira, C., Donatti, J. A., Fernandes, A. L. F., Garcia-Cairasco, A., N\u2019Gouemo, N., P., & Forcelli, P. A. (2018). Divergent brain changes in two audiogenic rat strains: A voxel-based morphometry and diffusion tensor imaging comparison of the genetically epilepsy prone rat (GEPR-3) and the wistar audiogenic rat (WAR). Neurobiology of Disease, 111, 80\u201390. https:\/\/doi.org\/10.1016\/j.nbd.2017.12.014","journal-title":"Neurobiology of Disease"},{"key":"9687_CR24","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.jneumeth.2016.03.001","volume":"264","author":"X Li","year":"2016","unstructured":"Li, X., Morgan, P. S., Ashburner, J., Smith, J., & Rorden, C. (2016). The first step for neuroimaging data analysis: DICOM to NIfTI conversion. Journal of Neuroscience Methods, 264, 47\u201356. https:\/\/doi.org\/10.1016\/j.jneumeth.2016.03.001","journal-title":"Journal of Neuroscience Methods"},{"issue":"1","key":"9687_CR25","doi-asserted-by":"publisher","first-page":"12219","DOI":"10.1038\/s41598-019-48489-3","volume":"9","author":"J Lohmeier","year":"2019","unstructured":"Lohmeier, J., Kaneko, T., Hamm, B., Makowski, M. R., & Okano, H. (2019). atlasBREX: Automated template-derived brain extraction in animal MRI. Scientific Reports, 9(1), 12219. https:\/\/doi.org\/10.1038\/s41598-019-48489-3","journal-title":"Scientific Reports"},{"issue":"4","key":"9687_CR26","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1002\/hbm.25274","volume":"42","author":"E Lommers","year":"2021","unstructured":"Lommers, E., Guillemin, C., Reuter, G., Fouarge, E., Delrue, G., Collette, F., Degueldre, C., Balteau, E., Maquet, P., & Phillips, C. (2021). Voxel-based quantitative MRI reveals spatial patterns of grey matter alteration in multiple sclerosis. Human Brain Mapping, 42(4), 1003\u20131012. https:\/\/doi.org\/10.1002\/hbm.25274","journal-title":"Human Brain Mapping"},{"issue":"3","key":"9687_CR27","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1111\/bdi.13286","volume":"25","author":"GS Malhi","year":"2023","unstructured":"Malhi, G. S., Das, P., Outhred, T., Bell, E., Gessler, D., Bryant, R., & Mannie, Z. (2023). Significant age by childhood trauma interactions on grey matter volumes: A whole brain VBM analysis. Bipolar Disorders, 25(3), 209\u2013220. https:\/\/doi.org\/10.1111\/bdi.13286","journal-title":"Bipolar Disorders"},{"issue":"1","key":"9687_CR28","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.jneumeth.2009.01.001","volume":"179","author":"PR Manger","year":"2009","unstructured":"Manger, P. R., Pillay, P., Maseko, B. C., Bhagwandin, A., Gravett, N., Moon, D. J., Jillani, N., & Hemingway, J. (2009). Acquisition of brains from the African elephant (Loxodonta africana): Perfusion-fixation and dissection. Journal of Neuroscience Methods, 179(1), 16\u201321. https:\/\/doi.org\/10.1016\/j.jneumeth.2009.01.001","journal-title":"Journal of Neuroscience Methods"},{"key":"9687_CR29","doi-asserted-by":"publisher","first-page":"e61279","DOI":"10.7554\/eLife.61279","volume":"10","author":"LP Munting","year":"2021","unstructured":"Munting, L. P., Derieppe, M., Suidgeest, E., Hirschler, L., Van Osch, M. J., De Senneville, D., B., & Van Der Weerd, L. (2021). Cerebral blood flow and cerebrovascular reactivity are preserved in a mouse model of cerebral microvascular amyloidosis. eLife, 10, e61279. https:\/\/doi.org\/10.7554\/eLife.61279","journal-title":"eLife"},{"issue":"1","key":"9687_CR30","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.cell.2021.11.037","volume":"185","author":"J Ngai","year":"2022","unstructured":"Ngai, J. (2022). BRAIN 2.0: Transforming neuroscience. Cell, 185(1), 4\u20138. https:\/\/doi.org\/10.1016\/j.cell.2021.11.037","journal-title":"Cell"},{"issue":"7495","key":"9687_CR31","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature13186","volume":"508","author":"SW Oh","year":"2014","unstructured":"Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., Wang, Q., Lau, C., Kuan, L., Henry, A. M., Mortrud, M. T., Ouellette, B., Nguyen, T. N., Sorensen, S. A., Slaughterbeck, C. R., Wakeman, W., Li, Y., Feng, D., Ho, A., & Zeng, H. (2014). A mesoscale connectome of the mouse brain. Nature, 508(7495), 207\u2013214. https:\/\/doi.org\/10.1038\/nature13186","journal-title":"Nature"},{"issue":"1","key":"9687_CR32","doi-asserted-by":"publisher","first-page":"2615","DOI":"10.1038\/s41467-018-04921-2","volume":"9","author":"LR Qiu","year":"2018","unstructured":"Qiu, L. R., Fernandes, D. J., Szulc-Lerch, K. U., Dazai, J., Nieman, B. J., Turnbull, D. H., Foster, J. A., Palmert, M. R., & Lerch, J. P. (2018). Mouse MRI shows brain areas relatively larger in males emerge before those larger in females. Nature Communications, 9(1), 2615. https:\/\/doi.org\/10.1038\/s41467-018-04921-2","journal-title":"Nature Communications"},{"key":"9687_CR33","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.neuroimage.2013.07.084","volume":"86","author":"J Radua","year":"2014","unstructured":"Radua, J., Canales-Rodr\u00edguez, E. J., Pomarol-Clotet, E., & Salvador, R. (2014). Validity of modulation and optimal settings for advanced voxel-based morphometry. Neuroimage, 86, 81\u201390. https:\/\/doi.org\/10.1016\/j.neuroimage.2013.07.084","journal-title":"Neuroimage"},{"issue":"1","key":"9687_CR34","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/s41597-023-01942-5","volume":"10","author":"N Rahman","year":"2023","unstructured":"Rahman, N., Xu, K., Budde, M. D., Brown, A., & Baron, C. A. (2023). A longitudinal microstructural MRI dataset in healthy C57Bl\/6 mice at 9.4 Tesla. Scientific Data, 10(1), 94. https:\/\/doi.org\/10.1038\/s41597-023-01942-5","journal-title":"Scientific Data"},{"key":"9687_CR35","doi-asserted-by":"publisher","unstructured":"Raichle, M. E. (1983). The pathophysiology of brain ischemia. https:\/\/doi.org\/10.1002\/ana.410130103","DOI":"10.1002\/ana.410130103"},{"key":"9687_CR36","doi-asserted-by":"publisher","first-page":"116894","DOI":"10.1016\/j.neuroimage.2020.116894","volume":"217","author":"H Rallapalli","year":"2020","unstructured":"Rallapalli, H., Darwin, B. C., Toro-Montoya, E., Lerch, J. P., & Turnbull, D. H. (2020). Longitudinal MEMRI analysis of brain phenotypes in a mouse model of Niemann-pick type C disease. Neuroimage, 217, 116894. https:\/\/doi.org\/10.1016\/j.neuroimage.2020.116894","journal-title":"Neuroimage"},{"issue":"1","key":"9687_CR37","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1038\/s41467-022-28591-3","volume":"13","author":"F Rocchi","year":"2022","unstructured":"Rocchi, F., Canella, C., Noei, S., Gutierrez-Barragan, D., Coletta, L., Galbusera, A., Stuefer, A., Vassanelli, S., Pasqualetti, M., Iurilli, G., Panzeri, S., & Gozzi, A. (2022). Increased fMRI connectivity upon chemogenetic inhibition of the mouse prefrontal cortex. Nature Communications, 13(1), 1056. https:\/\/doi.org\/10.1038\/s41467-022-28591-3","journal-title":"Nature Communications"},{"key":"9687_CR38","unstructured":"Sawiak, S. J., Wood, N. I., Williams, G. B., Morton, A. J., & Carpenter, T. A. (2009). SPMMouse: A new toolbox for SPM in the animal brain."},{"issue":"1","key":"9687_CR39","doi-asserted-by":"publisher","first-page":"7290","DOI":"10.2310\/7290.2009.00004","volume":"8","author":"AEH Scheenstra","year":"2009","unstructured":"Scheenstra, A. E. H., Van De Ven, R. C. G., Van Der Weerd, L., Van Den Maagdenberg, A. M. J. M., Dijkstra, J., & Reiber, J. H. C. (2009). Automated segmentation of in Vivo and Ex vivo mouse brain magnetic resonance images. Molecular Imaging, 8(1), 7290. 2009.00004","journal-title":"Molecular Imaging"},{"issue":"6","key":"9687_CR40","doi-asserted-by":"publisher","first-page":"1468","DOI":"10.1002\/jmri.23927","volume":"37","author":"S Shen","year":"2013","unstructured":"Shen, S., & Sterr, A. (2013). Is DARTEL-based Voxel\u2010based morphometry affected by width of smoothing kernel and group size? A study using simulated atrophy. Journal of Magnetic Resonance Imaging, 37(6), 1468\u20131475. https:\/\/doi.org\/10.1002\/jmri.23927","journal-title":"Journal of Magnetic Resonance Imaging"},{"issue":"2","key":"9687_CR41","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1007\/s00429-010-0299-0","volume":"216","author":"A Sierra","year":"2011","unstructured":"Sierra, A., Laitinen, T., Lehtim\u00e4ki, K., Rieppo, L., Pitk\u00e4nen, A., & Gr\u00f6hn, O. (2011). Diffusion tensor MRI with tract-based spatial statistics and histology reveals undiscovered lesioned areas in kainate model of epilepsy in rat. Brain Structure and Function, 216(2), 123\u2013135. https:\/\/doi.org\/10.1007\/s00429-010-0299-0","journal-title":"Brain Structure and Function"},{"issue":"1","key":"9687_CR43","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.neuroimage.2008.03.061","volume":"44","author":"S Smith","year":"2009","unstructured":"Smith, S., & Nichols, T. (2009). Threshold-free cluster enhancement: Addressing problems of smoothing, threshold dependence and localisation in cluster inference. Neuroimage, 44(1), 83\u201398. https:\/\/doi.org\/10.1016\/j.neuroimage.2008.03.061","journal-title":"Neuroimage"},{"issue":"4","key":"9687_CR42","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.1016\/j.neuroimage.2006.02.024","volume":"31","author":"SM Smith","year":"2006","unstructured":"Smith, S. M., Jenkinson, M., Johansen-Berg, H., Rueckert, D., Nichols, T. E., Mackay, C. E., Watkins, K. E., Ciccarelli, O., Cader, M. Z., Matthews, P. M., & Behrens, T. E. J. (2006). Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data. Neuroimage, 31(4), 1487\u20131505. https:\/\/doi.org\/10.1016\/j.neuroimage.2006.02.024","journal-title":"Neuroimage"},{"issue":"4","key":"9687_CR44","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/s41592-020-0792-1","volume":"17","author":"MI Todorov","year":"2020","unstructured":"Todorov, M. I., Paetzold, J. C., Schoppe, O., Tetteh, G., Shit, S., Efremov, V., Todorov-V\u00f6lgyi, K., D\u00fcring, M., Dichgans, M., Piraud, M., Menze, B., & Ert\u00fcrk, A. (2020). Machine learning analysis of whole mouse brain vasculature. Nature Methods, 17(4), 442\u2013449. https:\/\/doi.org\/10.1038\/s41592-020-0792-1","journal-title":"Nature Methods"},{"key":"9687_CR45","doi-asserted-by":"publisher","first-page":"116137","DOI":"10.1016\/j.neuroimage.2019.116137","volume":"202","author":"JD Tournier","year":"2019","unstructured":"Tournier, J. D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C. H., & Connelly, A. (2019). MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. Neuroimage, 202, 116137. https:\/\/doi.org\/10.1016\/j.neuroimage.2019.116137","journal-title":"Neuroimage"},{"issue":"6","key":"9687_CR46","doi-asserted-by":"publisher","first-page":"1310","DOI":"10.1109\/TMI.2010.2046908","volume":"29","author":"NJ Tustison","year":"2010","unstructured":"Tustison, N. J., Avants, B. B., Cook, P. A., Zheng, Y., Egan, A., Yushkevich, P. A., & Gee, J. C. (2010). N4ITK: Improved N3 Bias correction. IEEE Transactions on Medical Imaging, 29(6), 1310\u20131320. https:\/\/doi.org\/10.1109\/TMI.2010.2046908","journal-title":"IEEE Transactions on Medical Imaging"},{"key":"9687_CR47","doi-asserted-by":"publisher","unstructured":"Van Hecke, W., Emsell, L., & Sunaert, S. (Eds.). (2016). Diffusion tensor imaging: A practical handbook. Springer. https:\/\/doi.org\/10.1007\/978-1-4939-3118-7","DOI":"10.1007\/978-1-4939-3118-7"},{"issue":"4","key":"9687_CR49","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1016\/j.neuroimage.2011.01.038","volume":"55","author":"Y Wang","year":"2011","unstructured":"Wang, Y., Gupta, A., Liu, Z., Zhang, H., Escolar, M. L., Gilmore, J. H., Gouttard, S., Fillard, P., Maltbie, E., Gerig, G., & Styner, M. (2011). DTI registration in atlas based fiber analysis of infantile Krabbe disease. Neuroimage, 55(4), 1577\u20131586. https:\/\/doi.org\/10.1016\/j.neuroimage.2011.01.038","journal-title":"Neuroimage"},{"issue":"4","key":"9687_CR48","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1016\/j.cell.2020.04.007","volume":"181","author":"Q Wang","year":"2020","unstructured":"Wang, Q., Ding, S. L., Li, Y., Royall, J., Feng, D., Lesnar, P., Graddis, N., Naeemi, M., Facer, B., Ho, A., Dolbeare, T., Blanchard, B., Dee, N., Wakeman, W., Hirokawa, K. E., Szafer, A., Sunkin, S. M., Oh, S. W., Bernard, A., & Ng, L. (2020). The Allen Mouse Brain Common coordinate Framework: A 3D reference Atlas. Cell, 181(4), 936\u2013953e20. https:\/\/doi.org\/10.1016\/j.cell.2020.04.007","journal-title":"Cell"},{"issue":"11","key":"9687_CR17","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1109\/TMI.2007.906784","volume":"26","author":"H Zhang","year":"2007","unstructured":"Zhang, H., Avants, B. B., Yushkevich, P. A., Woo, J. H., Wang, S., McCluskey, L. F., Elman, L. B., Melhem, E. R., & Gee, J. C. (2007). High-dimensional spatial normalization of Diffusion Tensor images improves the detection of White Matter differences: An Example Study using amyotrophic lateral sclerosis. IEEE Transactions on Medical Imaging, 26(11), 1585\u20131597. https:\/\/doi.org\/10.1109\/TMI.2007.906784","journal-title":"IEEE Transactions on Medical Imaging"}],"container-title":["Neuroinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12021-024-09687-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s12021-024-09687-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12021-024-09687-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T08:53:05Z","timestamp":1732092785000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s12021-024-09687-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,16]]},"references-count":49,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2024,10]]}},"alternative-id":["9687"],"URL":"https:\/\/doi.org\/10.1007\/s12021-024-09687-1","relation":{},"ISSN":["1559-0089"],"issn-type":[{"type":"electronic","value":"1559-0089"}],"subject":[],"published":{"date-parts":[[2024,9,16]]},"assertion":[{"value":"26 August 2024","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 September 2024","order":2,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}]}}