{"version":1,"kind":"Article","sha256":"","slug":"640","location":"","dependencies":[],"doi":"10.54294/jculxw","thumbnail":"https://pub.desci.com/ipfs/bafkreigjlfkqxaehfqficitugc7fkygmenuindbkcb4o5s4wa7uludleai","frontmatter":{"title":"N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction","abstract":"Several algorithms exist for correcting the nonuniform intensity in magnetic resonance images caused by field inhomogeneities. These algorithms constitute important preprocessing steps for subsequent image analysis tasks. One such algorithm, known as parametric bias field correction (PABIC), has already been implemented in ITK. Another popular algorithm is the nonuniform intensity normalization (N3) approach. A particularly salient advantage of this algorithm is that it does not require a prior tissue model for its application. In addition, the source code for N3 is publicly available at the McConnell Brain Imaging Centre (Montreal Neurological Institute, McGill University) which includes source code and the coordinating set of perl scripts. This submission describes an implementation of the N3 algorithm for the Insight Toolkit given as a single class, viz.\titk::N3MRIBiasFieldCorrectionImageFilter. We tried to maintain minimal difference between the publicly available MNI N3 implementation and our ITK im- plementation. The only intentional variation is the substitution of an earlier contribution, i.e. the class itk::BSplineScatteredDataPointSetToImageFilter, for the originally proposed least-squares approach for B-spline fitting used to model the bias field. In addition, we include a more extensive modification to the original N3 algorithm found in the class itk::N4MRIBiasFieldCorrectionImageFilter. The latter algorithm employs a multi-resolution approach, similar to FFD image registration strategies, and has a slightly modified iterative update scheme.","license":"You are licensing your work to Kitware Inc. under the\nCreative Commons Attribution License Version 3.0.\n\nKitware Inc. agrees to the following:\n\nKitware is free\n * to copy, distribute, display, and perform the work\n * to make derivative works\n * to make commercial use of the work\n\nUnder the following conditions:\n\\\"by Attribution\\\" - Kitware must attribute the work in the manner specified by the author or licensor.\n\n * For any reuse or distribution, they must make clear to others the license terms of this work.\n * Any of these conditions can be waived if they get permission from the copyright holder.\n\nYour fair use and other rights are in no way affected by the above.\n\nThis is a human-readable summary of the Legal Code (the full license) available at\nhttp://creativecommons.org/licenses/by/3.0/legalcode","keywords":["inhomogeneity","MRI","bias field","ninjas"],"authors":[{"name":"Tustison, Nicholas","email":"ntustison@gmail.com","affiliations":[],"corresponding":true},{"name":"Gee, James","email":"gee@mail.med.upenn.edu","affiliations":[]}],"date_submitted":"2010-12-07 20:13:48","external_publication_id":640,"revision_cids":["bafkreic7rj2wvbdhixc7dpetbed2ouk6vcrzk52aogehdnfcmnom4vdvwq"],"github":"https://github.com/midas-journal/midas-journal-640.git","thumbnail":"https://pub.desci.com/ipfs/bafkreigjlfkqxaehfqficitugc7fkygmenuindbkcb4o5s4wa7uludleai"},"mdast":{"type":"root"},"downloads":[{"url":"https://ipfs.desci.com/ipfs/bafkreie3zlpyiksxyhilgz2ta3fc6rvbw47iwapkdw7r7qoea2rqgspj7i","title":"root/comments.md","filename":"comments.md","extra":{"size_bytes":541,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidpxxf4ydb5tjhjx3t6qqgeigmuoszlwqtvy7tx5c4ygnpnfrv3ri","title":"root/code/Source/.DS_Store","filename":".DS_Store","extra":{"size_bytes":6148,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidazi7gwj3u42lrjtvsecbivth7svwunlugjardnyrdrj5iq5p6vi","title":"root/code/Source/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":2874,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiatekj56hyg737rvw5gkabmhk7ye6xg7bmajgtz5nqzoienkeah7y","title":"root/code/Source/IJMacros.txt","filename":"IJMacros.txt","extra":{"size_bytes":3973,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibkmvwafbdnl5eu3wo3mbsngdakpjngxd44bxtbpeovnvaktafvcu","title":"root/code/Source/ImageCompare.cxx","filename":"ImageCompare.cxx","extra":{"size_bytes":8164,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreia7nl5ivnnoupm32pklr3kr4lowo3ffhqierj4j3p7geomgj4xrre","title":"root/code/Source/N4.cxx","filename":"N4.cxx","extra":{"size_bytes":28213,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihgw5iqgirscqof7um72hakaomhdaa2ogdg2wr4h37bszewgqvliq","title":"root/code/Source/antsCommandLineOption.cxx","filename":"antsCommandLineOption.cxx","extra":{"size_bytes":2526,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidjmbpdybm6pqae3ibis7f64eeu3jia4ljygoidfgh2eb7barccda","title":"root/code/Source/antsCommandLineOption.h","filename":"antsCommandLineOption.h","extra":{"size_bytes":5109,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiatekwg33p64kaz32yr33kxzfyobfdqa3ztrezmhkwkvvv5v3v7c4","title":"root/code/Source/antsCommandLineParser.cxx","filename":"antsCommandLineParser.cxx","extra":{"size_bytes":14922,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreify3ofnzg47lltkcjxmkx565xgm52clvgdtcf377mnkdjkgttves4","title":"root/code/Source/antsCommandLineParser.h","filename":"antsCommandLineParser.h","extra":{"size_bytes":5077,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidw4lmcajx23i3gsznhlxkuw6j2omxdfbyqdtqjngobxqpndvsnpu","title":"root/code/Source/itkBSplineControlPointImageFilter.h","filename":"itkBSplineControlPointImageFilter.h","extra":{"size_bytes":15036,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigfvejx266zqtyradfmf2bslcgz2tj4bsedbbwczetqh5t7ckngtq","title":"root/code/Source/itkBSplineControlPointImageFilter.txx","filename":"itkBSplineControlPointImageFilter.txx","extra":{"size_bytes":32771,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiam6a5sam4rdeoudvu6g6ho4de4hg7da6ympjaroex3qvxnjezfj4","title":"root/code/Source/itkN3MRIBiasFieldCorrectionImageFilter.h","filename":"itkN3MRIBiasFieldCorrectionImageFilter.h","extra":{"size_bytes":12259,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicgukja7bmbmiuwjhsj5n6uroqpb3jlorrdpkpffc6p2bk23irpia","title":"root/code/Source/itkN3MRIBiasFieldCorrectionImageFilter.txx","filename":"itkN3MRIBiasFieldCorrectionImageFilter.txx","extra":{"size_bytes":27049,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigqwsvgmzmzkprl4smiwvlag74knvpfx4tqikaiu5alwnj2hakx2u","title":"root/code/Source/itkN3MRIBiasFieldCorrectionImageFilterTest.cxx","filename":"itkN3MRIBiasFieldCorrectionImageFilterTest.cxx","extra":{"size_bytes":7222,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidgobfw2sh2ecb3hf3ufs7wseilw2ycqgbnnivjciiashhm3ptbwq","title":"root/code/Source/itkN4MRIBiasFieldCorrectionImageFilter.h","filename":"itkN4MRIBiasFieldCorrectionImageFilter.h","extra":{"size_bytes":9810,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigghji5kcjyhm75fs2zzw3ycqhw4dqo4soqvo5775l5x5dhsawphy","title":"root/code/Source/itkN4MRIBiasFieldCorrectionImageFilter.txx","filename":"itkN4MRIBiasFieldCorrectionImageFilter.txx","extra":{"size_bytes":25170,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigwkfsspeifzjtxggafabui35f5y2ncy63xc5jpbjdo6eqlp7moym","title":"root/code/Source/Output/.DS_Store","filename":".DS_Store","extra":{"size_bytes":6148,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibengbjpnji7iwxcwnd2bfwjuvjwfmpvnanhfzymksv4lohyxdkdy","title":"root/code/Source/Output/he3biasfield.mha","filename":"he3biasfield.mha","extra":{"size_bytes":952678,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafybeig3iufyg2fhxfu5jx26wvvldj2gjofpf4ggp7a4kxcm4abxhje44i","title":"root/code/Source/Output/he3biasfield.nii.gz","filename":"he3biasfield.nii.gz","extra":{"size_bytes":1057493,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiciapucauiig4yujcqizl6qbfk54n7dj5oltjdkfzb5c7to4uesga","title":"root/code/Source/Output/he3corrected.nii.gz","filename":"he3corrected.nii.gz","extra":{"size_bytes":1005803,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreifxotxbwga3ywtfimssjt3qpwvxvkm72qwahelv34bzrlifgtcqwy","title":"root/code/Source/Output/t81biasfield.mha","filename":"t81biasfield.mha","extra":{"size_bytes":147789,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreih7wbd6x3kxa4co7basqyycie66ipobpwfsclynpg6m7wzjo3p56a","title":"root/code/Source/Output/t81biasfield.nii.gz","filename":"t81biasfield.nii.gz","extra":{"size_bytes":156836,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreign6jxkmkxrjwvuphslmkdgve346a5fzcqe6a7ftxiyavjzynlidq","title":"root/code/Source/Output/t81corrected.nii.gz","filename":"t81corrected.nii.gz","extra":{"size_bytes":175819,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreib2n5rvf7yx5nveum4ipvghof622y26apal4psheud4pb2yujmyge","title":"root/code/Source/Input/.DS_Store","filename":".DS_Store","extra":{"size_bytes":6148,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreif6qgqxt57jzftkb4bj3lm2kolkqumxtp47nxkysamu5capuey4mq","title":"root/code/Source/Input/he3mask.nii.gz","filename":"he3mask.nii.gz","extra":{"size_bytes":4764,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigr2d3jkr5a3wa5mu677cbg5rckdfmenxdx2lht4bdzwbjqh26kju","title":"root/code/Source/Input/he3volume.nii.gz","filename":"he3volume.nii.gz","extra":{"size_bytes":307737,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibqm3qh5mjycmu4apkh3bcv3nypbzflz3ae7l2r4gjyfk3jmwrnry","title":"root/code/Source/Input/t81mask.nii.gz","filename":"t81mask.nii.gz","extra":{"size_bytes":1130,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihblb7sqk3ztblwi6myovbqwpckrqqj4w62h3alt5esifgh2jaffm","title":"root/code/Source/Input/t81slice.nii.gz","filename":"t81slice.nii.gz","extra":{"size_bytes":174988,"type":"file"}},{"url":"https://ipfs.desci.com/ipfs/bafkreibqla5miucv2lthyom4mq5spzl2rnuqwssgmwsd7gpo5jvgkobwye","title":"root/insight-journal-metadata.json","filename":"insight-journal-metadata.json","extra":{"size_bytes":7606,"type":"file"}},{"url":"https://dweb.link/ipfs/bafkreia7zqwbiynrlparyrbi2old54dcpzc6n722ojutrqdh26suy67mxm","title":"root/article.pdf","filename":"article.pdf","extra":{"size_bytes":580182,"type":"file"}}],"references":{"cite":{"order":["ref1","ref2","ref3","ref4","ref5","ref6","ref7","ref8","ref9","ref10"]},"data":{"ref1":{"label":"ref1","enumerator":"1","url":"https://doi.org/10.1016/j.neuroimage.2007.10.026","html":"Intensity non-uniformity correction using n3 on 3-t scanners with multichannel phased array coils+Neuroimage+39+4+1+1762+Feb 2008+G Boyes Richard+Derek L G Hill+Paul M Thompson+Michael W Weiner+A. D. N. I. Study."},"ref2":{"label":"ref2","enumerator":"2","url":"https://doi.org/10.1137/0916069","html":"A limited memory algorithm for bound constrained optimization+SIAM Journal on Scientific and Statistical Computing+2+2+1208+1995+R. H. Byrd+P. Lu+J. Nocedal"},"ref3":{"label":"ref3","enumerator":"3","url":"https://doi.org/10.1155/ijbi/2006/49515","html":"A review on mr image intensity inhomogeneity correction+Internation Journal of Biomedical Imaging+2006+1+11+Zujun Hou"},"ref4":{"label":"ref4","enumerator":"4","url":"https://doi.org/10.1109/42.668698","html":"(document+IEEE Trans Med Imaging+1+2+3+97+Feb 1998+J. G. Sled+A. P. Zijdenbos+A. C. Evans"},"ref5":{"label":"ref5","enumerator":"5","url":"https://doi.org/10.1109/42.845174","html":"(document)+IEEE Transactions on Medical Imaging+19+3+153+165+March 2000+M. Styner+C. Brechbuhler+G. Gerig"},"ref6":{"label":"ref6","enumerator":"6","html":"-spline scattered data approximation+The Insight Journal+2005+2+3+N. J. Tustison+J. C. Gee. N-d Ck"},"ref7":{"label":"ref7","enumerator":"7","url":"https://doi.org/10.1007/11812715_10","html":"-spline scattered data approximation with confidence values+In Proc. Third International Workshop Medical Imaging and Augmented Reality+3+83+2006+2+N. J. Tustison+J. C. Gee. Generalized+Ck"},"ref8":{"label":"ref8","enumerator":"8","html":"Run-length matrices for texture analysis+Insight Journal, page published online+2008+N. J. Tustison+J. C. Gee"},"ref9":{"label":"ref9","enumerator":"9","url":"https://doi.org/10.1109/tip.2008.2010072","html":"Directly manipulated free-form deformation image registration+IEEE Trans Image Process+18+3+3+635+Mar 2009+J Tustison Nicholas"},"ref10":{"label":"ref10","enumerator":"10","url":"https://doi.org/10.1109/tmi.2006.891486","html":"A review of methods for correction of intensity inhomogeneity in mri+IEEE Transactions on Medical Imaging+26+3+405+421+March 2007+U. Vovk+F. Pernus+B. Likar"}}}}