build based on 87bc689

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-12-02T13:00:15","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-12-02T16:14:59","documenter_version":"1.8.0"}}

dev/generated/examples/advanced_reco/index.html

@@ -13,17 +13,17 @@
   "LUT"            => Float32[93.0 0.5; 94.0 0.5; … ; 5287.0 -0.5; 5288.0 -0.5]
   "params_reco"    => Dict{Symbol, Any}(:iterations=>30, :solver=>FISTA, :reg=>…
   "params_MP2RAGE" => ParamsMP2RAGE(800.0, 2284.1, 7.0, 5000.0, 128, 7.0, 7.0)
-  "im_reco"        => ComplexF32[20.8242+0.387125im 10.105+14.7264im … 68.1592-…
-  "T1map"          => Float32[2702.0 2283.0 … 1309.0 1517.0; 2302.0 1177.0 … 10…
+  "im_reco"        => ComplexF32[20.6719+0.527998im 10.2103+14.8792im … 68.1409…
+  "T1map"          => Float32[2686.0 2301.0 … 1311.0 1511.0; 2327.0 1187.0 … 10…
   "params_prot"    => BrukerFile: /home/runner/.julia/artifacts/04cd4c29bb9e2ae…
-  &quot;MP2RAGE&quot;        =&gt; Float32[-0.377357 -0.291027 … 0.0974735 -0.00846032; -0.2…</code></pre><p>for comparison purposes let&#39;s perform the undersampled reconstruction (without the paramCS keyword)</p><pre><code class="language-julia hljs">d_under = reconstruction_MP2RAGE(path_bruker; mean_NR=true)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Dict{Any, Any} with 7 entries:
+  &quot;MP2RAGE&quot;        =&gt; Float32[-0.374886 -0.295793 … 0.0963395 -0.00548892; -0.3…</code></pre><p>for comparison purposes let&#39;s perform the undersampled reconstruction (without the paramCS keyword)</p><pre><code class="language-julia hljs">d_under = reconstruction_MP2RAGE(path_bruker; mean_NR=true)</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Dict{Any, Any} with 7 entries:
   &quot;LUT&quot;            =&gt; Float32[93.0 0.5; 94.0 0.5; … ; 5287.0 -0.5; 5288.0 -0.5]
   &quot;params_reco&quot;    =&gt; Dict{Any, Any}(:iterations=&gt;1, :reconSize=&gt;(128, 128, 96)…
   &quot;params_MP2RAGE&quot; =&gt; ParamsMP2RAGE(800.0, 2284.1, 7.0, 5000.0, 128, 7.0, 7.0)
-  &quot;im_reco&quot;        =&gt; ComplexF32[61.3559+125.33im 14.4777+115.613im … 53.6951-5…
-  &quot;T1map&quot;          =&gt; Float32[2458.0 2484.0 … 1006.0 1792.0; 1926.0 1697.0 … 12…
+  &quot;im_reco&quot;        =&gt; ComplexF32[61.5519+126.668im 14.7966+115.13im … 53.1283-5…
+  &quot;T1map&quot;          =&gt; Float32[2463.0 2481.0 … 1006.0 1777.0; 1924.0 1701.0 … 12…
   &quot;params_prot&quot;    =&gt; BrukerFile: /home/runner/.julia/artifacts/04cd4c29bb9e2ae…
-  &quot;MP2RAGE&quot;        =&gt; Float32[-0.331966 -0.337323 … 0.2601 -0.131011; -0.181981…</code></pre><p>We can check the results</p><pre><code class="language-julia hljs">begin
+  &quot;MP2RAGE&quot;        =&gt; Float32[-0.333003 -0.336819 … 0.260251 -0.124936; -0.1811…</code></pre><p>We can check the results</p><pre><code class="language-julia hljs">begin
   f = Figure(size=(500,400))
   ax=Axis(f[1,1],title=&quot;TI₁ undersampled&quot;)
   h=heatmap!(ax,abs.(d_under[&quot;im_reco&quot;][:,:,60,1,1]),colormap=:grays)
@@ -44,6 +44,6 @@
 
   Colorbar(f[2,3],h,label = &quot;T₁ [ms]&quot;, flip_vertical_label=true)
   f
-end</code></pre><img src="eca99084.png" alt="Example block output"/><h2 id="Write-results-in-BIDS-format"><a class="docs-heading-anchor" href="#Write-results-in-BIDS-format">Write results in BIDS format</a><a id="Write-results-in-BIDS-format-1"></a><a class="docs-heading-anchor-permalink" href="#Write-results-in-BIDS-format" title="Permalink"></a></h2><p>Results can be written following most of the <a href="https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html">qBIDS format recommandation</a></p><pre><code class="language-julia hljs">subject_name = &quot;sub_01_cs&quot;
+end</code></pre><img src="72f1c151.png" alt="Example block output"/><h2 id="Write-results-in-BIDS-format"><a class="docs-heading-anchor" href="#Write-results-in-BIDS-format">Write results in BIDS format</a><a id="Write-results-in-BIDS-format-1"></a><a class="docs-heading-anchor-permalink" href="#Write-results-in-BIDS-format" title="Permalink"></a></h2><p>Results can be written following most of the <a href="https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html">qBIDS format recommandation</a></p><pre><code class="language-julia hljs">subject_name = &quot;sub_01_cs&quot;
 dir_path = &quot;&quot; # directory path where the files will be create
-write_bids_MP2RAGE(d,subject_name,dir_path)</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../simple_reco/">« Simple reconstruction</a><a class="docs-footer-nextpage" href="../../../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></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 1.8.0 on <span class="colophon-date" title="Monday 2 December 2024 13:00">Monday 2 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+write_bids_MP2RAGE(d,subject_name,dir_path)</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../simple_reco/">« Simple reconstruction</a><a class="docs-footer-nextpage" href="../../../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></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 1.8.0 on <span class="colophon-date" title="Monday 2 December 2024 16:14">Monday 2 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/generated/examples/simple_reco/index.html

@@ -6,7 +6,7 @@
   "LUT"            => Float32[93.0 0.5; 94.0 0.5; … ; 5287.0 -0.5; 5288.0 -0.5]
   "params_reco"    => Dict{Any, Any}(:iterations=>1, :reconSize=>(128, 128, 96)…
   "params_MP2RAGE" => ParamsMP2RAGE(800.0, 2284.1, 7.0, 5000.0, 128, 7.0, 7.0)
-  "im_reco"        => ComplexF32[113.687-120.06im -6.3911+141.334im … 35.198+49…
+  "im_reco"        => ComplexF32[113.687-120.06im -6.39107+141.334im … 35.198+4…
   "T1map"          => Float32[4376.0 3452.0 … 2116.0 2853.0; 3571.0 377.0 … 238…
   "params_prot"    => BrukerFile: /home/runner/.julia/artifacts/04cd4c29bb9e2ae…
   &quot;MP2RAGE&quot;        =&gt; Float32[-0.493312 -0.458414 … -0.244732 -0.399954; -0.465…</code></pre><p>the result is a dictionnary with the following fields :</p><ul><li>&quot;im_reco&quot; : (x,y,z, Number of Repetition,TI) Complex</li><li>&quot;MP2RAGE&quot; : (x,y,z , Number of Repetition) Float</li><li>&quot;T1map&quot; : (x,y,z , Number of Repetition) Float</li><li>&quot;params_prot&quot;</li><li>&quot;params_reco&quot;</li><li>&quot;params_MP2RAGE&quot;</li></ul><p>im_reco corresponds to the TI₁ and TI₂ images in the complex format with 5 dimensions : (x,y,z , Number of Repetition,TI). Channels are combined during the reconstruction</p><p>We can check the results</p><pre><code class="language-julia hljs">begin
@@ -29,7 +29,7 @@
 
   Colorbar(f[2,3],h,label = &quot;T₁ [ms]&quot;, flip_vertical_label=true)
   f
-end</code></pre><img src="64c3e95e.png" alt="Example block output"/><p>The Lookup table used for the reconstruction is stored in the dictionnary (LUT). First dimension is the range of T1 and the 2nd is the expected value of the MP2RAGE signal between -0.5 to 0.5.</p><pre><code class="language-julia hljs">f=Figure()
+end</code></pre><img src="227a88df.png" alt="Example block output"/><p>The Lookup table used for the reconstruction is stored in the dictionnary (LUT). First dimension is the range of T1 and the 2nd is the expected value of the MP2RAGE signal between -0.5 to 0.5.</p><pre><code class="language-julia hljs">f=Figure()
 ax = Axis(f[1,1],xlabel=&quot;T₁ [ms]&quot;)
 lines!(ax,d[&quot;LUT&quot;])
 f</code></pre><img src="679134f9.png" alt="Example block output"/><h2 id="Write-results-in-BIDS-format"><a class="docs-heading-anchor" href="#Write-results-in-BIDS-format">Write results in BIDS format</a><a id="Write-results-in-BIDS-format-1"></a><a class="docs-heading-anchor-permalink" href="#Write-results-in-BIDS-format" title="Permalink"></a></h2><p>Results can be written following most of the <a href="https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html">qBIDS format recommandation</a></p><pre><code class="language-julia hljs">subject_name = &quot;sub_01&quot;
@@ -44,4 +44,4 @@
    ├─ sub_01_inv-1-phase_MP2RAGE.nii.gz
    ├─ sub_01_inv-2-complex_MP2RAGE.nii.gz
    ├─ sub_01_inv-2-mag_MP2RAGE.nii.gz
-   └─ sub_01_inv-2-phase_MP2RAGE.nii.gz</code></pre><p>For simplicity the T₁ map is stored in the anat/ folder like the ones created by Siemens.</p><p>If you want to generate the T1 map with another tool like qMRLab the required MP2RAGE parameters are stored in the <strong>MP2RAGE.json</strong> file. In that case the data are supposed to be stored in a derivatives folder (see<a href="https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html">qBIDS format recommandation</a>)</p><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../../reconstruction/">« Installation and usage</a><a class="docs-footer-nextpage" href="../advanced_reco/">Compressed-sensing reconstruction »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></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 1.8.0 on <span class="colophon-date" title="Monday 2 December 2024 13:00">Monday 2 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+   └─ sub_01_inv-2-phase_MP2RAGE.nii.gz</code></pre><p>For simplicity the T₁ map is stored in the anat/ folder like the ones created by Siemens.</p><p>If you want to generate the T1 map with another tool like qMRLab the required MP2RAGE parameters are stored in the <strong>MP2RAGE.json</strong> file. In that case the data are supposed to be stored in a derivatives folder (see<a href="https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html">qBIDS format recommandation</a>)</p><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../../reconstruction/">« Installation and usage</a><a class="docs-footer-nextpage" href="../advanced_reco/">Compressed-sensing reconstruction »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></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 1.8.0 on <span class="colophon-date" title="Monday 2 December 2024 16:14">Monday 2 December 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>