build based on bb95ebc

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-02T19:35:00","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-03T09:31:45","documenter_version":"1.3.0"}}

dev/building_basis/index.html

@@ -8,7 +8,7 @@
 ETL = 50
 NUM_BASIS = 6
 
-basis_exp,exp_dict = MESE_basis_exp(NUM_BASIS,TE,ETL,T2_vec)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/CRMSB/PAPER_subspace_MESE/blob/fbf99f23e26bedb7df7ca02b2a983f4961995d52/src/build_basis.jl#L53-L82">source</a></section></article><p>In the publication, the subspace is extracted from a dictionary generated with a range of <span>$T_2$</span> from 1 ms to 2000 ms with a step of 1 ms.</p><p>Other approachs can be used :</p><ul><li>a logarithmic repartition of <span>$T_2$</span> </li><li>extracting from a fully acquisition the distribution of <span>$T_2$</span> and then generate from that distribution the dictionary (Tamir et al, MRM,2017)</li></ul><p>Let&#39;s take a look at the first 6 subspace vectors from a linear repartition :</p><pre><code class="language-julia hljs">using Subspace_MESE
+basis_exp,exp_dict = MESE_basis_exp(NUM_BASIS,TE,ETL,T2_vec)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/CRMSB/PAPER_subspace_MESE/blob/bb95ebc54a1f9ef84a7cfe2e5d092f0397d379ca/src/build_basis.jl#L53-L82">source</a></section></article><p>In the publication, the subspace is extracted from a dictionary generated with a range of <span>$T_2$</span> from 1 ms to 2000 ms with a step of 1 ms.</p><p>Other approachs can be used :</p><ul><li>a logarithmic repartition of <span>$T_2$</span> </li><li>extracting from a fully acquisition the distribution of <span>$T_2$</span> and then generate from that distribution the dictionary (Tamir et al, MRM,2017)</li></ul><p>Let&#39;s take a look at the first 6 subspace vectors from a linear repartition :</p><pre><code class="language-julia hljs">using Subspace_MESE
 
 T2_vec = 1.0:1.0:2000.0
 TE = 7.0
@@ -44,7 +44,7 @@
 ETL = 50
 NUM_BASIS = 6
 
-basis_epg, epg_dict =MESE_basis_EPG(NUM_BASIS,TE,ETL,T2_vec,B1_vec,T1_vec;TR=TR,dummy=dummy)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/CRMSB/PAPER_subspace_MESE/blob/fbf99f23e26bedb7df7ca02b2a983f4961995d52/src/build_basis.jl#L103-L138">source</a></section></article><p>In order to generate the EPG subspace, more parameters need to be defined. Specifically, the range of <span>$B_1$</span> to be expected in the acquisition might be larger for surfacic transmit coil than for volumic coils that have a homogeneous <span>$B_1^+$</span> field.</p><p>Of note, B1<em>vec, T2</em>vec, T1<em>vec can also be passed as float values rather than vectors. In the publication, the T1</em>vec was fixed to 1000 ms.</p><pre><code class="language-julia hljs">using Subspace_MESE
+basis_epg, epg_dict =MESE_basis_EPG(NUM_BASIS,TE,ETL,T2_vec,B1_vec,T1_vec;TR=TR,dummy=dummy)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/CRMSB/PAPER_subspace_MESE/blob/bb95ebc54a1f9ef84a7cfe2e5d092f0397d379ca/src/build_basis.jl#L103-L138">source</a></section></article><p>In order to generate the EPG subspace, more parameters need to be defined. Specifically, the range of <span>$B_1$</span> to be expected in the acquisition might be larger for surfacic transmit coil than for volumic coils that have a homogeneous <span>$B_1^+$</span> field.</p><p>Of note, B1<em>vec, T2</em>vec, T1<em>vec can also be passed as float values rather than vectors. In the publication, the T1</em>vec was fixed to 1000 ms.</p><pre><code class="language-julia hljs">using Subspace_MESE
 B1_vec = 0.8:0.01:1.0
 T2_vec = 1.0:1.0:2000.0
 T1_vec = 1000.0 #can also be a vector of float
@@ -73,9 +73,9 @@
 raw = RawAcquisitionData_MESE(b)
 acq = AcquisitionData(raw,OffsetBruker = true);
 
-basis, calib_dict = MESE_basis_calibration(acq,(15,15,15),6)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/CRMSB/PAPER_subspace_MESE/blob/fbf99f23e26bedb7df7ca02b2a983f4961995d52/src/build_basis.jl#L8-L33">source</a></section></article><p>The calibration subspace reconstructs low-resolution images from a fully sampled area of the k-space. </p><p>You can generate the subspace from the acquired accelerated acquisition with the parameter <code>crop_size</code> equal to the size of the fully sampled area of the k-space.</p><p>But you can also generate the subspace from a different fully acquisition (for example on a control acquisition)</p><pre><code class="language-julia hljs">b = BrukerFile(&quot;path/to/dataset&quot;)
+basis, calib_dict = MESE_basis_calibration(acq,(15,15,15),6)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/CRMSB/PAPER_subspace_MESE/blob/bb95ebc54a1f9ef84a7cfe2e5d092f0397d379ca/src/build_basis.jl#L8-L33">source</a></section></article><p>The calibration subspace reconstructs low-resolution images from a fully sampled area of the k-space. </p><p>You can generate the subspace from the acquired accelerated acquisition with the parameter <code>crop_size</code> equal to the size of the fully sampled area of the k-space.</p><p>But you can also generate the subspace from a different fully acquisition (for example on a control acquisition)</p><pre><code class="language-julia hljs">b = BrukerFile(&quot;path/to/dataset&quot;)
 
 raw = RawAcquisitionData_MESE(b)
 acq = AcquisitionData(raw,OffsetBruker = true);
 
-basis,_ = MESE_basis_calibration(acq,(15,15,15),6)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../convert/">« Convert data</a><a class="docs-footer-nextpage" href="../reconstruction_subspace/">Subspace 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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Monday 2 December 2024 19:34">Monday 2 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+basis,_ = MESE_basis_calibration(acq,(15,15,15),6)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../convert/">« Convert data</a><a class="docs-footer-nextpage" href="../reconstruction_subspace/">Subspace 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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Tuesday 3 December 2024 09:31">Tuesday 3 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/convert/index.html

@@ -9,4 +9,4 @@
 params[:reco] = "direct"
 
 im_u = reconstruction(acq, params);</code></pre><p>This returns images which can be artifacted in the case of an undersampled acquisitioncan.</p><p>We can combine the different coil elements with a sum of squares :</p><pre><code class="language-julia hljs">using Subspace_MESE.MRICoilSensitivities
-im_u_sos = mergeChannels(im_u)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« Installation</a><a class="docs-footer-nextpage" href="../building_basis/">Subspace generation »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Monday 2 December 2024 19:34">Monday 2 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+im_u_sos = mergeChannels(im_u)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« Installation</a><a class="docs-footer-nextpage" href="../building_basis/">Subspace generation »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Tuesday 3 December 2024 09:31">Tuesday 3 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>