build based on 232eca24

4be0ee7f · Documenter.jl · f1743c16 · 4be0ee7f · 4be0ee7f · 4be0ee7f
Commit 4be0ee7f authored 5 months ago by Documenter.jl
--- a/dev/.documenter-siteinfo.json
+++ b/dev/.documenter-siteinfo.json
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-18T14:27:28","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-18T15:04:00","documenter_version":"1.7.0"}}
\ No newline at end of file
--- a/dev/adjust_sequences/index.html
+++ b/dev/adjust_sequences/index.html
--- a/dev/api/index.html
+++ b/dev/api/index.html
--- a/dev/defining_sequence/index.html
+++ b/dev/defining_sequence/index.html
--- a/dev/dwi_1_80_min_2_15.png
+++ b/dev/dwi_1_80_min_2_15.png
--- a/dev/dwi_1_80_min_2_15_epi.png
+++ b/dev/dwi_1_80_min_2_15_epi.png
--- a/dev/implemented_sequences/index.html
+++ b/dev/implemented_sequences/index.html
--- a/dev/index.html
+++ b/dev/index.html
 <!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · MRIBuilder.jl</title><meta name="title" content="Home · MRIBuilder.jl"/><meta property="og:title" content="Home · MRIBuilder.jl"/><meta property="twitter:title" content="Home · MRIBuilder.jl"/><meta name="description" content="Documentation for MRIBuilder.jl: an MRI sequence builder in Julia"/><meta property="og:description" content="Documentation for MRIBuilder.jl: an MRI sequence builder in Julia"/><meta property="twitter:description" content="Documentation for MRIBuilder.jl: an MRI sequence builder in Julia"/><meta property="og:url" content="https://open.win.ox.ac.uk/pages/ndcn0236/mribuilder.jl/stable/"/><meta property="twitter:url" content="https://open.win.ox.ac.uk/pages/ndcn0236/mribuilder.jl/stable/"/><link rel="canonical" href="https://open.win.ox.ac.uk/pages/ndcn0236/mribuilder.jl/stable/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>MRIBuilder.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li></ul></li><li><a class="tocitem" href="sequence_optimisation/">Optimisation</a></li><li><a class="tocitem" href="implemented_sequences/">Implemented sequences</a></li><li><a class="tocitem" href="defining_sequence/">Defining sequences</a></li><li><a class="tocitem" href="adjust_sequences/">Post-hoc adjustments</a></li><li><a class="tocitem" href="scanners/">Scanners</a></li><li><a class="tocitem" href="api/">Internal API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://git.fmrib.ox.ac.uk/ndcn0236/MRIBuilder.jl" title="View the repository"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">Repository</span></a><a class="docs-navbar-link" href="https://git.fmrib.ox.ac.uk/ndcn0236/MRIBuilder.jl/-/tree/main/docs/src/index.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="MRIBuilder"><a class="docs-heading-anchor" href="#MRIBuilder">MRIBuilder</a><a id="MRIBuilder-1"></a><a class="docs-heading-anchor-permalink" href="#MRIBuilder" title="Permalink"></a></h1><p><a href="https://git.fmrib.ox.ac.uk/ndcn0236/mribuilder.jl">MRIBuilder</a> allows for the creation and optimisation of MRI sequences within <a href="https://julialang.org">Julia</a>.</p><p>Depending on your application, there are several levels at which you can interact with MRIBuilder. The ones lower down require more expertise with Julia and the internals of MRIBuilder:</p><ol><li>Many sequences have already been implemented and can be obtained through a simple function call (see <a href="implemented_sequences/#implemented_sequences">Using implemented sequences</a>).</li><li>New sequences can be created out of pre-defined sequence components and by defining sequence-specific metrics (see <a href="defining_sequence/#defining_sequences">Defining new sequences</a>).</li><li>Finally, one can actually define new sequence components (not documented yet).</li></ol><p>Typically, the resulting sequence will only cover a single repetition time (TR). MRIBuilder enables the concatenation of single-TR sequences into a multi-TR sequence. During these repeats minor adjustments can be made to the single-TR sequence. This can be used to allow different repeats to image different lines in k-space or excite different slices (see <a href="adjust_sequences/#adjust_sequences">Post-hoc adjustment of sequences</a>).</p><p>The signal formation for the resulting sequence can be predicted using <a href="https://open.win.ox.ac.uk/pages/ndcn0236/mcmrsimulator.jl/stable">MCMRSimulator</a> given some representation of the imaged tissue. MRIBuilder can be used to read/write to the <a href="https://pulseq.github.io">pulseq</a> MR sequence file format. This can be used to run the sequence on MRI scanners as described in the <a href="https://pulseq.github.io">pulseq homepage</a>. Rather than just directly running the sequences from this library on the scanner, we strongly recommend to load it using the <a href="https://github.com/pulseq/pulseq">MATLAB pulseq</a> or <a href="https://github.com/imr-framework/pypulseq">python pypulseq</a> first as these libraries run additional checks!</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>It can be run from the command line using the Julia REPL, from a Julia script, or in a <a href="https://jupyter.org">Jupyter notebook</a>. Like any Julia package, Julia can be installed using the built-in <a href="https://pkgdocs.julialang.org/v1/">Julia package manager</a>:</p><pre><code class="nohighlight hljs">pkg&gt; add https://git.fmrib.ox.ac.uk/ndcn0236/mribuilder.jl.git</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="sequence_optimisation/">Optimisation »</a><div class="flexbox-break"></div></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Friday 18 October 2024 14:27">Friday 18 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · MRIBuilder.jl</title><meta name="title" content="Home · MRIBuilder.jl"/><meta property="og:title" content="Home · MRIBuilder.jl"/><meta property="twitter:title" content="Home · MRIBuilder.jl"/><meta name="description" content="Documentation for MRIBuilder.jl: an MRI sequence builder in Julia"/><meta property="og:description" content="Documentation for MRIBuilder.jl: an MRI sequence builder in Julia"/><meta property="twitter:description" content="Documentation for MRIBuilder.jl: an MRI sequence builder in Julia"/><meta property="og:url" content="https://open.win.ox.ac.uk/pages/ndcn0236/mribuilder.jl/stable/"/><meta property="twitter:url" content="https://open.win.ox.ac.uk/pages/ndcn0236/mribuilder.jl/stable/"/><link rel="canonical" href="https://open.win.ox.ac.uk/pages/ndcn0236/mribuilder.jl/stable/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>MRIBuilder.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li></ul></li><li><a class="tocitem" href="sequence_optimisation/">Optimisation</a></li><li><a class="tocitem" href="implemented_sequences/">Implemented sequences</a></li><li><a class="tocitem" href="defining_sequence/">Defining sequences</a></li><li><a class="tocitem" href="adjust_sequences/">Post-hoc adjustments</a></li><li><a class="tocitem" href="scanners/">Scanners</a></li><li><a class="tocitem" href="api/">Internal API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://git.fmrib.ox.ac.uk/ndcn0236/MRIBuilder.jl" title="View the repository"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">Repository</span></a><a class="docs-navbar-link" href="https://git.fmrib.ox.ac.uk/ndcn0236/MRIBuilder.jl/-/tree/main/docs/src/index.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="MRIBuilder"><a class="docs-heading-anchor" href="#MRIBuilder">MRIBuilder</a><a id="MRIBuilder-1"></a><a class="docs-heading-anchor-permalink" href="#MRIBuilder" title="Permalink"></a></h1><p><a href="https://git.fmrib.ox.ac.uk/ndcn0236/mribuilder.jl">MRIBuilder</a> allows for the creation and optimisation of MRI sequences within <a href="https://julialang.org">Julia</a>.</p><p>Depending on your application, there are several levels at which you can interact with MRIBuilder. The ones lower down require more expertise with Julia and the internals of MRIBuilder:</p><ol><li>Many sequences have already been implemented and can be obtained through a simple function call (see <a href="implemented_sequences/#implemented_sequences">Using implemented sequences</a>).</li><li>New sequences can be created out of pre-defined sequence components and by defining sequence-specific metrics (see <a href="defining_sequence/#defining_sequences">Defining new sequences</a>).</li><li>Finally, one can actually define new sequence components (not documented yet).</li></ol><p>Typically, the resulting sequence will only cover a single repetition time (TR). MRIBuilder enables the concatenation of single-TR sequences into a multi-TR sequence. During these repeats minor adjustments can be made to the single-TR sequence. This can be used to allow different repeats to image different lines in k-space or excite different slices (see <a href="adjust_sequences/#adjust_sequences">Post-hoc adjustment of sequences</a>).</p><p>The signal formation for the resulting sequence can be predicted using <a href="https://open.win.ox.ac.uk/pages/ndcn0236/mcmrsimulator.jl/stable">MCMRSimulator</a> given some representation of the imaged tissue. MRIBuilder can be used to read/write to the <a href="https://pulseq.github.io">pulseq</a> MR sequence file format. This can be used to run the sequence on MRI scanners as described in the <a href="https://pulseq.github.io">pulseq homepage</a>. Rather than just directly running the sequences from this library on the scanner, we strongly recommend to load it using the <a href="https://github.com/pulseq/pulseq">MATLAB pulseq</a> or <a href="https://github.com/imr-framework/pypulseq">python pypulseq</a> first as these libraries run additional checks!</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>It can be run from the command line using the Julia REPL, from a Julia script, or in a <a href="https://jupyter.org">Jupyter notebook</a>. Like any Julia package, Julia can be installed using the built-in <a href="https://pkgdocs.julialang.org/v1/">Julia package manager</a>:</p><pre><code class="nohighlight hljs">pkg&gt; add https://git.fmrib.ox.ac.uk/ndcn0236/mribuilder.jl.git</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="sequence_optimisation/">Optimisation »</a><div class="flexbox-break"></div></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Friday 18 October 2024 15:04">Friday 18 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
--- a/dev/objects.inv
+++ b/dev/objects.inv
--- a/dev/scanners/index.html
+++ b/dev/scanners/index.html
--- a/dev/sequence_optimisation/index.html
+++ b/dev/sequence_optimisation/index.html