{"id":217,"date":"2016-06-09T08:16:00","date_gmt":"2016-06-09T08:16:00","guid":{"rendered":"https:\/\/mri.sbollmann.net\/?p=217"},"modified":"2020-06-14T08:23:10","modified_gmt":"2020-06-14T08:23:10","slug":"gre-and-qsm-average-7t-model","status":"publish","type":"post","link":"https:\/\/mri.sbollmann.net\/index.php\/2016\/06\/09\/gre-and-qsm-average-7t-model\/","title":{"rendered":"GRE and QSM average 7T model"},"content":{"rendered":"\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1385\" height=\"516\" src=\"https:\/\/i1.wp.com\/mri.sbollmann.net\/wp-content\/uploads\/2020\/06\/qsm.png?fit=750%2C280&amp;ssl=1\" alt=\"\" class=\"wp-image-218\" srcset=\"https:\/\/mri.sbollmann.net\/wp-content\/uploads\/2020\/06\/qsm.png 1385w, https:\/\/mri.sbollmann.net\/wp-content\/uploads\/2020\/06\/qsm-300x112.png 300w, https:\/\/mri.sbollmann.net\/wp-content\/uploads\/2020\/06\/qsm-1024x382.png 1024w, https:\/\/mri.sbollmann.net\/wp-content\/uploads\/2020\/06\/qsm-768x286.png 768w\" sizes=\"auto, (max-width: 1385px) 100vw, 1385px\" \/><\/figure>\n\n\n\n<p>For the ISMRM 2016 we build a minimum deformation average (MDA) from a population of subjects based upon high resolution 7T MR imaging.<\/p>\n\n\n\n<p>View online and download the model in MINC or NiFTI format here:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>GRE model<ul><li><a rel=\"noreferrer noopener\" href=\"http:\/\/tissuestack.org\/desktop.html?ds=30&amp;plane=z&amp;x=20.917&amp;y=18.87&amp;z=-18.45&amp;zoom=4\" target=\"_blank\">View model online<\/a> via tissuestack.org<\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/imaging.org.au\/uploads\/Human7T\/greModel_L14_gre-7T-weightedMeanOfAllEchoes-asym-mincanon_v0.8.mnc\" target=\"_blank\">Download mnc (517 MB)<\/a> <\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/imaging.org.au\/uploads\/Human7T\/greModel_L14_gre-7T-weightedMeanOfAllEchoes-asym-mincanon_v0.8.nii\" target=\"_blank\">Download nii (647 MB)<\/a><\/li><\/ul><\/li><li>QSM model<ul><li><a rel=\"noreferrer noopener\" href=\"http:\/\/tissuestack.org\/desktop.html?ds=34&amp;plane=z&amp;x=24.939&amp;y=1.35&amp;z=-12.45&amp;zoom=6\" target=\"_blank\">View model online<\/a> via tissuestack.org<\/li><li><a href=\"https:\/\/imaging.org.au\/uploads\/Human7T\/qsmModel_L14_gre-7T-weightedMeanOfAllEchoes-asym-mincanon_v0.8.mnc\" target=\"_blank\" rel=\"noreferrer noopener\">Download mnc (168 MB)<\/a><\/li><li><a href=\"https:\/\/imaging.org.au\/uploads\/Human7T\/qsmModel_L14_gre-7T-weightedMeanOfAllEchoes-asym-mincanon_v0.8.nii\" target=\"_blank\" rel=\"noreferrer noopener\">Download nii (647 MB)<\/a><\/li><\/ul><\/li><li>code: <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/CAISR\/volgenmodel-nipype\" target=\"_blank\">https:\/\/github.com\/CAISR\/volgenmodel-nipype<\/a><\/li><\/ul>\n\n\n\n<figure class=\"wp-block-embed-youtube wp-block-embed is-type-video is-provider-youtube wp-embed-aspect-4-3 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"qsmAtlasFullPremiere\" width=\"750\" height=\"563\" src=\"https:\/\/www.youtube.com\/embed\/hsFcm0UIJKI?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<p>Citing this model: Bollmann, Steffen, Andrew Janke, Lars Marstaller, David Reutens, Kieran O\u2019Brien, and Markus Barth. \u201cGRE and QSM Average 7T Model\u201d January 1, 2017.\u00a0<a rel=\"noreferrer noopener\" target=\"_blank\" href=\"http:\/\/dx.doi.org\/10.14264\/uql.2017.178\">doi:10.14264\/uql.2017.178.<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Acquisition details<\/h2>\n\n\n\n<p>QSM: 29 (14 female, 26.6\u00b13.8yr) individuals were imaged using a multiple echo gradient recalled echo 3D whole brain dataset. TR=25ms, TE=4.4,7.25,10.2,13.25,16.4, 19.65,23ms flip angle=13, FOV 210&#215;181.5x120mm, matrix=280x242x160, GRAPPA=2. The phase data was combined using COMPOSER [8] and susceptibility processing was performed using total generalized variation (TGV) [9], which incorporates phase unwrapping, background field removal and dipole inversion in a single step.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">References<\/h2>\n\n\n\n<p>8. Robinson SD, Wolfgang Bogner, Barbara Dymerska, Pedro Cardoso, G\u00fcnther Grabner, Xeni Deligianni, et al. COMbining Phased array data using Offsets from a Short Echo-time Reference scan (COMPOSER). ISMRM 23rd Annual Meeting &amp; Exhibition. 2015<br>9. Langkammer, C., Bredies, K., Poser, B.A., Barth, M., Reishofer, G., Fan, A.P., Bilgic, B., Fazekas, F., Mainero, C., Ropele, S., 2015. Fast quantitative susceptibility mapping using 3D EPI and total generalized variation. NeuroImage 111, 622\u2013630. doi:10.1016\/j.neuroimage.2015.02.041<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">References describing this model:<\/h2>\n\n\n\n<p>Bollmann, Steffen, Simon Daniel Robinson, Kieran O\u2019Brien, Viktor Vegh, Andrew Janke, Lars Marstaller, David Reutens, and Markus Barth. \u201c<a href=\"https:\/\/mri.sbollmann.net\/index.php\/2018\/01\/09\/the-challenge-of-bias-free-coil-combination-for-quantitative-susceptibility-mapping-at-ultra-high-field-bias-free-coil-combination-for-qsm-at-ultra-high-field\/\" target=\"_blank\" rel=\"noreferrer noopener\">The Challenge of Bias-Free Coil Combination for Quantitative Susceptibility Mapping at Ultra-High Field.<\/a>\u201d Magnetic Resonance in Medicine, March 1, 2017, n\/a-n\/a. doi:10.1002\/mrm.26644.<\/p>\n\n\n\n<p>Janke AL, O&#8217;Brien K, Bollmann S, Kober T, Marstaller L, Barth M. A 7T Human Brain Microstructure Atlas by Minimum Deformation Averaging at 300um. In 24th Annual ISMRM Scientific Meeting and Exhibition, Singapore. <a rel=\"noreferrer noopener\" href=\"http:\/\/indexsmart.mirasmart.com\/ISMRM2016\/PDFfiles\/1165.html\" target=\"_blank\">http:\/\/indexsmart.mirasmart.com\/ISMRM2016\/PDFfiles\/1165.html<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>For the ISMRM 2016 we build a minimum deformation average (MDA) from a population of subjects based upon high resolution 7T MR imaging. View online and download the model in MINC or NiFTI format here: GRE model View model online via tissuestack.org Download mnc (517 MB) Download nii (647 MB) [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":218,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[20,21,14,15],"tags":[],"class_list":["post-217","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-conferences","category-minimum-deformation-averaging","category-quantitative-susceptibility-mapping","category-ultra-high-field"],"jetpack_featured_media_url":"https:\/\/mri.sbollmann.net\/wp-content\/uploads\/2020\/06\/qsm.png","_links":{"self":[{"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/posts\/217","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/comments?post=217"}],"version-history":[{"count":2,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/posts\/217\/revisions"}],"predecessor-version":[{"id":221,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/posts\/217\/revisions\/221"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/media\/218"}],"wp:attachment":[{"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/media?parent=217"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/categories?post=217"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mri.sbollmann.net\/index.php\/wp-json\/wp\/v2\/tags?post=217"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}