build based on 03b0744

Author: Documenter.jl

dev/API/index.html

@@ -30,4 +30,4 @@
 
 # do reconstruction
 Ireco = reconstruction(acqData, params)
-</code></pre><p>Below one can see the orignal phantom on the left and the reconstruction on the right:</p><p><img src="../assets/phantom.png" alt="Phantom"/> <img src="../assets/senseReco.png" alt="Reconstruction"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../offresonance/">« Offresonance</a><a class="docs-footer-nextpage" href="../compressedSensing/">Compressed Sensing »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:36">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>Below one can see the orignal phantom on the left and the reconstruction on the right:</p><p><img src="../assets/phantom.png" alt="Phantom"/> <img src="../assets/senseReco.png" alt="Reconstruction"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../offresonance/">« Offresonance</a><a class="docs-footer-nextpage" href="../compressedSensing/">Compressed Sensing »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:40">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/SENSE/index.html

@@ -67,4 +67,4 @@
 "ACQ_IS_PHASECORR_DATA", 
 "ACQ_IS_DUMMYSCAN_DATA", 
 &quot;ACQ_IS_PHASE_STABILIZATION_REFERENCE&quot;, &quot;ACQ_IS_PHASE_STABILIZATION&quot;</code></pre><h2 id="Pre-processing-tools"><a class="docs-heading-anchor" href="#Pre-processing-tools">Pre-processing tools</a><a id="Pre-processing-tools-1"></a><a class="docs-heading-anchor-permalink" href="#Pre-processing-tools" title="Permalink"></a></h2><h3 id="Remove-readout-oversampling"><a class="docs-heading-anchor" href="#Remove-readout-oversampling">Remove readout oversampling</a><a id="Remove-readout-oversampling-1"></a><a class="docs-heading-anchor-permalink" href="#Remove-readout-oversampling" title="Permalink"></a></h3><p>On clinical MR scanners, the raw data are often oversampled in the readout direction. This oversampling is not necessary for image reconstruction and can be removed to save memory and computation time. This step is generally applied right after the acquisition of each line. The current implementation is performed on the <code>RawAcquisitionData</code> (before conversion to <code>AcquisitionData</code>) and is based on the following parameters:</p><ul><li><code>rawData.params[&quot;encodedFOV&quot;][1]</code></li><li><code>rawData.params[&quot;reconFOV&quot;][1]</code></li></ul><p>If an oversampling factor of 2 is applied during acquisition, the <code>encodedFOV</code> will be 2 times larger than <code>reconFOV</code> along the readout dimension.</p><pre><code class="language-none">!!! note
-    Be careful to remove all the profiles from a `RawAcquisitionData` that are not supposed to be of the same size; like noise acquisition or navigators. You can use the function `raw = remove_raw_by_flags(raw)`.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../overview/">« Overview</a><a class="docs-footer-nextpage" href="../filehandling/">File Handling »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:36">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    Be careful to remove all the profiles from a `RawAcquisitionData` that are not supposed to be of the same size; like noise acquisition or navigators. You can use the function `raw = remove_raw_by_flags(raw)`.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../overview/">« Overview</a><a class="docs-footer-nextpage" href="../filehandling/">File Handling »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:40">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/acquisitionData/index.html

@@ -34,4 +34,4 @@
 params[:tolInner] = 1.e-2
 params[:normalizeReg] = MeasurementBasedNormalization()
 
-img_tv = reconstruction(acqDataSub, params)</code></pre><p>Lets compare the results, left the regular SENSE reconstruction and right the TV reglarized solution:</p><p><img src="../assets/kneeCG.png" alt="SENSE"/> <img src="../assets/kneeTV.png" alt="TV"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../SENSE/">« Parallel Imaging</a><a class="docs-footer-nextpage" href="../custom/">Customize »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:36">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+img_tv = reconstruction(acqDataSub, params)</code></pre><p>Lets compare the results, left the regular SENSE reconstruction and right the TV reglarized solution:</p><p><img src="../assets/kneeCG.png" alt="SENSE"/> <img src="../assets/kneeTV.png" alt="TV"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../SENSE/">« Parallel Imaging</a><a class="docs-footer-nextpage" href="../custom/">Customize »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:40">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/compressedSensing/index.html

@@ -63,4 +63,4 @@
 img_d = reconstruction(acqData,params)</code></pre><p>For comparison, let us perform the same reconstruction as above but with a Wavelet transform</p><pre><code class="language-julia">delete!(params, :sparseTrafo)
 params[:sparseTrafoName] = &quot;Wavelet&quot;
 
-img_w = reconstruction(acqData,params)</code></pre><p>The following pictures shows the wavelet based CS reconstruction on the left and the dictionary based CS reconstruction on the right:</p><p><img src="../assets/brainWavelet.png" alt="BrainWavelet"/> <img src="../assets/brainDict.png" alt="BrainDict"/></p><p>For reference, the original data is shown here:</p><p><img src="../assets/brainOrig.png" alt="BrainOrig"/></p><p>One can clearly see that the dictionary approach performs better than a simple Wavelet L1 prior.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../compressedSensing/">« Compressed Sensing</a><a class="docs-footer-nextpage" href="../generated/examples/01-binning/">Binning »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:36">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+img_w = reconstruction(acqData,params)</code></pre><p>The following pictures shows the wavelet based CS reconstruction on the left and the dictionary based CS reconstruction on the right:</p><p><img src="../assets/brainWavelet.png" alt="BrainWavelet"/> <img src="../assets/brainDict.png" alt="BrainDict"/></p><p>For reference, the original data is shown here:</p><p><img src="../assets/brainOrig.png" alt="BrainOrig"/></p><p>One can clearly see that the dictionary approach performs better than a simple Wavelet L1 prior.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../compressedSensing/">« Compressed Sensing</a><a class="docs-footer-nextpage" href="../generated/examples/01-binning/">Binning »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:40">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/custom/index.html

@@ -9,4 +9,4 @@
 save(fout, raw)</code></pre><p>which will generate an ISMRMRD file containing the data.</p><h2 id="Conversion"><a class="docs-heading-anchor" href="#Conversion">Conversion</a><a id="Conversion-1"></a><a class="docs-heading-anchor-permalink" href="#Conversion" title="Permalink"></a></h2><p>It should now be no surprise that MRIReco.jl does also allow for file conversion:</p><pre><code class="language-julia">f = BrukerFile(&quot;brukerfileCart&quot;)
 raw = RawAcquisitionData(f)
 fout = ISMRMRDFile(&quot;outputfile.h5&quot;)
-save(fout, raw)</code></pre><p>Currently, this is only limited to converting Bruker files into ISMRMRD files but the infrastructure is not limited to that.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../acquisitionData/">« Acquisition Data</a><a class="docs-footer-nextpage" href="../image/">Images »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:36">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+save(fout, raw)</code></pre><p>Currently, this is only limited to converting Bruker files into ISMRMRD files but the infrastructure is not limited to that.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../acquisitionData/">« Acquisition Data</a><a class="docs-footer-nextpage" href="../image/">Images »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 August 2025 18:40">Friday 1 August 2025</span>. Using Julia version 1.11.6.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>