{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:48:25Z","timestamp":1740138505039,"version":"3.37.3"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2016,2,24]],"date-time":"2016-02-24T00:00:00Z","timestamp":1456272000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"name":"NIH HHS\/United States","award":["R01NS066905"],"award-info":[{"award-number":["R01NS066905"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Neuroinform"],"published-print":{"date-parts":[[2016,7]]},"DOI":"10.1007\/s12021-016-9296-7","type":"journal-article","created":{"date-parts":[[2016,2,24]],"date-time":"2016-02-24T01:43:58Z","timestamp":1456278238000},"page":"305-317","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Heterogeneous Optimization Framework: Reproducible Preprocessing of Multi-Spectral Clinical MRI for Neuro-Oncology Imaging Research"],"prefix":"10.1007","volume":"14","author":[{"given":"Mikhail","family":"Milchenko","sequence":"first","affiliation":[]},{"given":"Abraham Z.","family":"Snyder","sequence":"additional","affiliation":[]},{"given":"Pamela","family":"LaMontagne","sequence":"additional","affiliation":[]},{"given":"Joshua S.","family":"Shimony","sequence":"additional","affiliation":[]},{"given":"Tammie L.","family":"Benzinger","sequence":"additional","affiliation":[]},{"given":"Sarah Jost","family":"Fouke","sequence":"additional","affiliation":[]},{"given":"Daniel S.","family":"Marcus","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,2,24]]},"reference":[{"key":"9296_CR1","unstructured":"Aerts, H.J.W.L. et al. (2014). Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nature Communications, 5, p.4006. Available at: http:\/\/www.nature.com\/ncomms\/2014\/140603\/ncomms5006\/full\/ncomms5006.html [Accessed July 15, 2014]."},{"key":"9296_CR2","doi-asserted-by":"crossref","unstructured":"Aribisala, B.S., He, J. & Blamire, A.M. (2011). Comparative study of standard space and real space analysis of quantitative MR brain data. Journal of magnetic resonance imaging: JMRI, 33(6), pp.1503\u20131509. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21591021 [Accessed August 18, 2014].","DOI":"10.1002\/jmri.22576"},{"key":"9296_CR3","doi-asserted-by":"crossref","unstructured":"Basser, P.J., Mattiello, J. & LeBihan, D. (1994). MR diffusion tensor spectroscopy and imaging. Biophysical Journal, 66(1), pp.259\u2013267. Available at: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=1275686&tool=pmcentrez&rendertype=abstract [Accessed September 20, 2013].","DOI":"10.1016\/S0006-3495(94)80775-1"},{"key":"9296_CR4","doi-asserted-by":"crossref","unstructured":"Buckner, R.L. et al. (2004). A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume. NeuroImage, 23(2), pp.724\u2013738. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15488422 [Accessed May 21, 2013].","DOI":"10.1016\/j.neuroimage.2004.06.018"},{"key":"9296_CR5","doi-asserted-by":"crossref","unstructured":"Cox, R.W., 1996. AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Computers and biomedical research, an international journal, 29(3), pp.162\u2013173. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/8812068 [Accessed August 12, 2014].","DOI":"10.1006\/cbmr.1996.0014"},{"key":"9296_CR6","doi-asserted-by":"crossref","unstructured":"Dale, A.M., Fischl, B. & Sereno, M.I. (1999). Cortical surface-based analysis. I. Segmentation and surface reconstruction. NeuroImage, 9(2), pp.179\u2013194. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/9931268 [Accessed June 7, 2013].","DOI":"10.1006\/nimg.1998.0395"},{"key":"9296_CR7","unstructured":"Das, S. et al., (2011). LORIS: a web-based data management system for multi-center studies. Frontiers in neuroinformatics, 5, p.37. Available at: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3262165&tool=pmcentrez&rendertype=abstract [Accessed July 9, 2014]."},{"key":"9296_CR8","doi-asserted-by":"crossref","unstructured":"Fennema-Notestine, C. et al. (2006). Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: effects of diagnosis, bias correction, and slice location. Human Brain Mapping, 27(2), pp.99\u2013113. Available at: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=2408865&tool=pmcentrez&rendertype=abstract [Accessed March 17, 2012].","DOI":"10.1002\/hbm.20161"},{"key":"9296_CR9","unstructured":"Fink, J. (2014). Docker: a Software as a Service, Operating System-Level Virtualization Framework. Code4lib Journal, (25), pp.3\u20135. Available at: http:\/\/journal.code4lib.org\/articles\/9669 ."},{"key":"9296_CR10","doi-asserted-by":"crossref","unstructured":"Fischl, B., Sereno, M.I. & Dale, A.M. (1999). Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. NeuroImage, 9(2), pp.195\u2013207. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/9931269 [Accessed June 7, 2013].","DOI":"10.1006\/nimg.1998.0396"},{"key":"9296_CR11","unstructured":"Fouke, S.J. et al. (2013). The comprehensive neuro-oncology data repository (CONDR): A research infrastructure to develop and validate imaging biomarkers. Neurosurgery. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24089052 [Accessed October 14, 2013]."},{"key":"9296_CR12","doi-asserted-by":"crossref","unstructured":"Friston, K., 2007. Statistical parametric mapping: the analysis of funtional brain images, Amsterdam;;Boston: Elsevier\/Academic Press.","DOI":"10.1016\/B978-012372560-8\/50002-4"},{"key":"9296_CR13","doi-asserted-by":"crossref","unstructured":"Gholipour, A. et al. (2007). Brain functional localization: a survey of image registration techniques. IEEE Transactions on Medical Imaging, 26(4), pp.427\u2013451. Available at: http:\/\/ieeexplore.ieee.org\/xpls\/abs_all.jsp?arnumber=4141192 [Accessed October 17, 2012].","DOI":"10.1109\/TMI.2007.892508"},{"key":"9296_CR14","unstructured":"Glauche, V., (2014) MATLAB Batch System. Available at: http:\/\/sourceforge.net\/p\/matlabbatch\/wiki\/Home\/ ."},{"key":"9296_CR15","doi-asserted-by":"crossref","unstructured":"Hajnal, J. V. et al. (1995). A registration and interpolation procedure for subvoxel matching of serially acquired MR images. Journal of Computer Assisted Tomography, 19(2), pp.289\u2013296. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/7890857 [Accessed October 2, 2013].","DOI":"10.1097\/00004728-199503000-00022"},{"key":"9296_CR16","doi-asserted-by":"crossref","unstructured":"Hlaihel, C. et al. (2010). Predictive value of multimodality MRI using conventional, perfusion, and spectroscopy MR in anaplastic transformation of low-grade oligodendrogliomas. Journal of Neuro-Oncology, 97(1), pp.73\u201380. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19727562 [Accessed October 10, 2012].","DOI":"10.1007\/s11060-009-9991-4"},{"key":"9296_CR17","doi-asserted-by":"crossref","unstructured":"Joshi, A. et al. (2011). Unified framework for development, deployment and robust testing of neuroimaging algorithms. Neuroinformatics, 9(1), pp.69\u201384. Available at: http:\/\/www.springerlink.com\/content\/m763304211482j8r\/ [Accessed August 27, 2012].","DOI":"10.1007\/s12021-010-9092-8"},{"key":"9296_CR18","doi-asserted-by":"crossref","unstructured":"Kumar, V. et al. (2012). Radiomics: the process and the challenges. Magnetic Resonance Imaging, 30(9), pp.1234\u20131248. Available at: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3563280&tool=pmcentrez&rendertype=abstract [Accessed October 6, 2014].","DOI":"10.1016\/j.mri.2012.06.010"},{"key":"9296_CR19","unstructured":"LaMontagne, P. et al. (2013). Reliability of Quantitative Biomarkers of Tumor Progression Based on Multispectral MRI in Glioblastoma Patients. In Neuro-Oncology. Oxford University Press, pp. iii191\u2013iii205. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3823904\/ [Accessed September 17, 2015]."},{"key":"9296_CR20","doi-asserted-by":"crossref","unstructured":"Law, M. et al. (2008). Gliomas: predicting time to progression or survival with cerebral blood volume measurements at dynamic susceptibility-weighted contrast-enhanced perfusion MR imaging. Radiology, 247(2), pp.490\u2013498. Available at: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3774106&tool=pmcentrez&rendertype=abstract [Accessed October 9, 2013].","DOI":"10.1148\/radiol.2472070898"},{"key":"9296_CR21","unstructured":"Lee, J.J. et al. (2010). Dynamic susceptibility contrast MRI with localized arterial input functions. Magnetic resonance in medicine: official journal of the Society of Magnetic Resonance in Medicine\/Society of Magnetic Resonance in Medicine, 63(5), pp.1305\u20131314. Available at: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3014609&tool=pmcentrez&rendertype=abstract [Accessed August 25, 2012]."},{"key":"9296_CR22","doi-asserted-by":"crossref","unstructured":"Maes, F., Vandermeulen, D. & Suetens, P. (2003). Medical image registration using mutual information. Proceedings of the IEEE, 91(10), pp.1699\u20131722. Available at: http:\/\/ieeexplore.ieee.org\/xpl\/articleDetails.jsp?arnumber=1232201 [Accessed October 18, 2012].","DOI":"10.1109\/JPROC.2003.817864"},{"key":"9296_CR23","doi-asserted-by":"crossref","unstructured":"Marcus, D.S. et al. (2007). The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics, 5(1), pp.11\u201334. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17426351 [Accessed August 17, 2012].","DOI":"10.1385\/NI:5:1:11"},{"key":"9296_CR24","unstructured":"Milchenko, M. V. et al. (2014). Comparison of perfusion- and diffusion-weighted imaging parameters in brain tumor studies processed using different software platforms. Academic radiology. Available at: http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1076633214002219 [Accessed August 1, 2014]."},{"key":"9296_CR25","doi-asserted-by":"crossref","unstructured":"Orsingher, L., Piccinini, S. & Crisi, G. (2014). Differences in dynamic susceptibility contrast MR perfusion maps generated by different methods implemented in commercial software. Journal of Computer Assisted Tomography, 38(5), pp.647\u2013654. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24879459 [Accessed November 3, 2014].","DOI":"10.1097\/RCT.0000000000000115"},{"key":"9296_CR26","doi-asserted-by":"crossref","unstructured":"Prior, F.W. et al., (2013). Predicting a multi-parametric probability map of active tumor extent using random forests. Conference proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 2013, pp.6478\u20136481. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24111225 [Accessed October 14, 2013].","DOI":"10.1109\/EMBC.2013.6611038"},{"key":"9296_CR27","unstructured":"Rex, D.E., Ma, J.Q. & Toga, A.W. (2003). The LONI pipeline processing environment. NeuroImage, 19(3), pp.1033\u20131048. Available at: http:\/\/dx.doi.org\/10.1016\/S1053-8119 (03)00185-X [Accessed May 29, 2013]."},{"key":"9296_CR28","doi-asserted-by":"crossref","unstructured":"Rorden, C., Karnath, H.-O. & Bonilha, L. (2007). Improving lesion-symptom mapping. Journal of Cognitive Neuroscience, 19(7), pp.1081\u20131088. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17583985 [Accessed August 5, 2014].","DOI":"10.1162\/jocn.2007.19.7.1081"},{"key":"9296_CR29","doi-asserted-by":"crossref","unstructured":"Rowland, D.J. et al. (2005). Registration of [18F]FDG microPET and small-animal MRI. Nuclear Medicine and Biology, 32(6), pp.567\u2013572. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16026703 [Accessed April 18, 2012].","DOI":"10.1016\/j.nucmedbio.2005.05.002"},{"key":"9296_CR30","doi-asserted-by":"crossref","unstructured":"Vrooman, H.A. et al., 2007. Multi-spectral brain tissue segmentation using automatically trained k-Nearest-Neighbor classification. NeuroImage, 37(1), pp.71\u201381. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17572111 [Accessed June 18, 2013].","DOI":"10.1016\/j.neuroimage.2007.05.018"},{"key":"9296_CR31","doi-asserted-by":"crossref","unstructured":"Zonari, P., Baraldi, P. & Crisi, G. (2007). Multimodal MRI in the characterization of glial neoplasms: the combined role of single-voxel MR spectroscopy, diffusion imaging and echo-planar perfusion imaging. Neuroradiology, 49(10), pp.795\u2013803. Available at: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17619871 [Accessed August 12, 2013].","DOI":"10.1007\/s00234-007-0253-x"}],"container-title":["Neuroinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s12021-016-9296-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s12021-016-9296-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s12021-016-9296-7","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,1]],"date-time":"2019-06-01T21:57:26Z","timestamp":1559426246000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s12021-016-9296-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,2,24]]},"references-count":31,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,7]]}},"alternative-id":["9296"],"URL":"https:\/\/doi.org\/10.1007\/s12021-016-9296-7","relation":{},"ISSN":["1539-2791","1559-0089"],"issn-type":[{"type":"print","value":"1539-2791"},{"type":"electronic","value":"1559-0089"}],"subject":[],"published":{"date-parts":[[2016,2,24]]}}}