{"id":26,"date":"2015-01-05T20:26:28","date_gmt":"2015-01-06T01:26:28","guid":{"rendered":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/?page_id=26"},"modified":"2015-01-05T21:41:47","modified_gmt":"2015-01-06T02:41:47","slug":"software","status":"publish","type":"page","link":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/software\/","title":{"rendered":"Software"},"content":{"rendered":"<p><span style=\"font-size: 16px\">Please note that you will need Jeff Fessler&#8217;s Medical Image Reconstruction Toolbox in your path, in order to run most of this software. This can be obtained from <\/span><a href=\"http:\/\/www.eecs.umich.edu\/~fessler\/\" target=\"_blank\">his website.<\/a><\/p>\n<ul>\n<li>Blipped Gradient Trajectories:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/blippedltades.zip\" target=\"_blank\">blippedltades.zip<\/a>: MATLAB scripts to jointly design large-tip-angle parallel RF pulses and blipped gradient trajectories. Algorithm described in\u00a0<a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/blippedltades.pdf\" target=\"_blank\">this manuscript<\/a> (pdf link).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Fast small- and large-tip-angle RF Pulse Design:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/ptx_test.tar.gz\">ptx_test.tar.gz<\/a>: MATLAB objects and examples of fast small- and large-tip-angle RF pulse design (parallel and single-channel). From\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16894579?ordinalpos=6&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum\">this paper<\/a> (Pubmed link) and\u00a0<a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/optcont_ismrm.pdf\">this abstract<\/a> (PDF link) and\u00a0<a href=\"http:\/\/ieeexplore.ieee.org\/stamp\/stamp.jsp?tp=&amp;arnumber=4915785&amp;isnumber=4359023\">this paper<\/a> (IEEE Xplore PDF link).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Hybrid Multibaseline and Referenceless PRF-shift thermometry:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/hybridthermo.zip\">hybridthermo.zip<\/a>: Hybrid multibaseline and referenceless PRF-shift temperature estimation. From\u00a0<a href=\"http:\/\/dx.doi.org\/10.1118\/1.3475943\">this paper<\/a> (doi link).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>K-space Hybrid Thermometry Demo:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/kspacedemo.zip\">kspacedemo.zip<\/a>: MATLAB scripts and data to demo reconstruction of temperature maps from undersampled k-space data using k-space hybrid thermometry. From\u00a0<a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/kspacehybrid.pdf\">this manuscript.<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Maximum linear-phase spectral-spatial RF pulse design:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/maxphase_spsp_test.tar.gz\">maxphase_spsp_test.tar.gz<\/a>: Example of maximum linear-phase spectral-spatial RF pulse design, developed to suppress fat in a long-TE\/short-TR GRE sequence for thermometry. This package will also require\u00a0<a href=\"http:\/\/rsl.stanford.edu\/research\/software.html\">John Pauly&#8217;s RF design tools<\/a> (rsl.stanford.edu). From\u00a0<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19780177\">this paper<\/a> (Pubmed link).<\/li>\n<\/ul>\n<\/li>\n<p>&nbsp;<\/p>\n<li>MultiDimensional Bloch Equation Simulatior:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/blochsim_cuda.zip\">blochsim_cuda.zip<\/a>: Crude mex+CUDA implementation of a multidimensional Bloch equation simulator for RF excitation. Hopefully some will find this useful as a starting point for a more robust MATLAB-callable CUDA-based Bloch simulator.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Nonuniform and multidimensional Shinnar-Le Roux RF pulse design:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/nuslr.zip\">nuslr.zip<\/a>, from\u00a0<a href=\"http:\/\/dx.doi.org\/10.1002\/mrm.23269\">this paper<\/a> (doi link). Two examples are included: a spiral in-out refocusing pulse and a fat-suppressing spectral-spatial refocusing pulse for 3T. MATLAB&#8217;s Parallel Computing Toolbox is used to implement two CUDA kernels, so you need both that toolbox and a CUDA-enabled NVIDIA GPU to use the software. The package will also require\u00a0<a href=\"http:\/\/rsl.stanford.edu\/research\/software.html\">John Pauly&#8217;s RF design tools<\/a> (rsl.stanford.edu).<\/li>\n<\/ul>\n<\/li>\n<p>&nbsp;<\/p>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/bsoptrf\/\">Optimized Bloch-Siegert Encoding Pulse Library<\/a>:\n<ul>\n<li>From\u00a0<a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/janki2012.pdf\">this abstract<\/a> (pdf link). These pulses are a dramatic improvement over conventional pulses (e.g. Fermi) used in Bloch-Siegert B1 mapping, due to their short duration (so you get a shorter TE and lower SAR for the same sensitivity), and have a much wider operating bandwidth. Two .zip files are in that directory, containing pulses sampled on 6.4us and 10us grids. We&#8217;ve also included phase difference-to-|B1+| lookup tables and example MATLAB scripts and data to do the lookup. This is the work of Marcin Jankiewicz.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Reweighted-l1 referenceless PRF-shift thermometry:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/rwtl1thermo.zip\">rwtl1thermo.zip<\/a>: Reweighted-l1 referenceless PRF-shift temperature estimation. From\u00a0<a href=\"http:\/\/dx.doi.org\/10.1002\/mrm.22502\">this paper<\/a> (doi link).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Root Flip Multiband RF and Matched-Phase Excitation:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/rootflipmultibandrf.zip\">rootflipmultibandrf.zip<\/a>: MATLAB scripts to design low-peak-power\/short duration multiband refocusing pulses, and matched-phase excitation pulses. Algorithm described in\u00a0<a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/r0submitted.pdf\">this manuscript<\/a> (pdf link) and\u00a0<a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/radF8CCC.pdf\">this submitted ISMRM 2015 abstract<\/a> (pdf link).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Selective B1+ Excitation Pulses:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/b1plusslr.zip\">b1plusslr.zip<\/a>: MATLAB scripts to design B1+-selective excitation pulses\u00a0using the Shinnar-Le Roux algorithm. The package will also require\u00a0<a href=\"http:\/\/rsl.stanford.edu\/research\/software.html\">John Pauly&#8217;s RF design tools<\/a>(rsl.stanford.edu).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>Spin-domain optimal control RF pulse design code:\n<ul>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/optimalcontrol.zip\">optimalcontrol.zip<\/a>: \u00a0Based on the hard pulse approximation. Included are multithreaded (pthreads) mex functions for bloch simulations and derivative calculations.<\/li>\n<\/ul>\n<\/li>\n<p>&nbsp;<\/p>\n<li><a href=\"http:\/\/www.vuiis.vanderbilt.edu\/~grissowa\/nacl_slrrf\/nacl_slr.html\">Native Client SLR Pulse Design Tool<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Please note that you will need Jeff Fessler&#8217;s Medical Image Reconstruction Toolbox in your path, in order to run most of this software. This can be obtained from his website. Blipped Gradient Trajectories: blippedltades.zip: MATLAB scripts to jointly design large-tip-angle parallel RF pulses and blipped gradient trajectories. Algorithm described in\u00a0this manuscript (pdf link). Fast small-&#8230;<\/p>\n","protected":false},"author":3438,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"tags":[],"class_list":["post-26","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/pages\/26","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/users\/3438"}],"replies":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/comments?post=26"}],"version-history":[{"count":16,"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/pages\/26\/revisions"}],"predecessor-version":[{"id":39,"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/pages\/26\/revisions\/39"}],"wp:attachment":[{"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/media?parent=26"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/grissomlab\/wp-json\/wp\/v2\/tags?post=26"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}