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qMRLab · Feb 26, 2021 · 5bd5fe0 · 5bd5fe0
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diff --git a/source/b0_dem_batch.rst b/source/b0_dem_batch.rst
@@ -107,7 +107,7 @@ b0_dem map :  Dual Echo Method for B0 mapping
 	Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab: 
 	Quantitative MRI analysis, under one umbrella doi: 10.21105/joss.02343
 	
-	Documentation for b0_dem
+	Reference page in Doc Center
 	doc b0_dem
 	
 	
@@ -127,8 +127,8 @@ b0_dem map :  Dual Echo Method for B0 mapping
 	<div class="warning">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-info-circle" style="color:black;margin-left:5px;"></i></strong> See the <a href="#21">generic notes</a> section below for further information. </p>
 	</div>
-	</p><h2 id="11">2.b.2 Set <tt >protocol</tt> and <tt >options</tt> <i >the GUI way</i></h2><p >The following command opens a panel to set <tt >protocol</tt> and <tt >options</tt> (if <tt >GUI</tt> is available to the user):</p><pre class="codeinput">Model = Custom_OptionsGUI(Model);
-	</pre><img vspace="5" hspace="5" src="_static/b0_dem_batch_01.png" alt=""> <p ><i >You need to close this window for the remaining of the script to proceed.</i></p><p >
+	</p><h2 id="11">2.b.2 Set <tt >protocol</tt> and <tt >options</tt> <i >the GUI way</i></h2><p >The following command opens a panel to set <tt >protocol</tt> and <tt >options</tt> (if <tt >GUI</tt> is available to the user):</p><pre class="language-matlab">Model = Custom_OptionsGUI(Model);
+	</pre><p ><img vspace="5" hspace="5" src="https://github.com/qMRLab/doc_images/blob/main/usr/protPanels/b0_dem.png?raw=true" alt=""> </p><p ><i >If available, you need to close this panel for the remaining of the script to proceed.</i></p><p >
 	<div class="warning">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-info-circle" style="color:black;margin-left:5px;"></i></strong> Using this panel, you can save qMRLab protocol files that can be used in both interfaces. See the <a href="#21">generic notes</a> section below for details. </p>
 	</div>
@@ -154,7 +154,7 @@ b0_dem map :  Dual Echo Method for B0 mapping
 	</pre><p ><i >A representative fit curve will be plotted if available.</i></p><p >To render images in this page, we will load the fit results that had been saved before. You can skip the following code block;</p><pre class="codeinput"><span class="comment">% Load FitResults that comes with the example dataset.</span>
 	FitResults_old = load(<span class="string">'FitResults/FitResults.mat'</span>);
 	qMRshowOutput(FitResults_old,data,Model);
-	</pre><img vspace="5" hspace="5" src="_static/b0_dem_batch_02.png" alt=""> <h2 id="22">3.d. Save fit results</h2><p >Outputs can be saved as <tt >*.nii.(gz)</tt> if <tt >NIfTI</tt> inputs are available:</p><pre class="language-matlab"><span class="comment">% Generic function call to save nifti outputs</span>
+	</pre><img vspace="5" hspace="5" src="_static/b0_dem_batch_01.png" alt=""> <h2 id="22">3.d. Save fit results</h2><p >Outputs can be saved as <tt >*.nii.(gz)</tt> if <tt >NIfTI</tt> inputs are available:</p><pre class="language-matlab"><span class="comment">% Generic function call to save nifti outputs</span>
 	FitResultsSave_nii(FitResults, <span class="string">'reference/nifti/file.nii.(gz)'</span>);
 	</pre><p >If not, <tt >FitResults.mat</tt> file can be saved. This file contains all the outputs as workspace variables:</p><pre class="language-matlab"><span class="comment">% Generic function call to save FitResults.mat</span>
 	FitResultsSave_mat(FitResults);
@@ -163,7 +163,6 @@ b0_dem map :  Dual Echo Method for B0 mapping
 	<p style="margin:0px!important;"><strong > <i class="fa fa-clone" style="color:navy;margin-left:5px;"></i></strong> <code >FitResults.mat</code> files can be loaded to qMRLab <code >GUI</code> for <a href="l#data-viewer" target="_blank">visualization and ROI <br >        analyses</a>. </p>
 	</div>
 	</p><p >The section below will be dynamically generated in accordance with the example data format (<tt >mat</tt> or <tt >nii</tt>). You can substitute <tt >FitResults_old</tt> with <tt >FitResults</tt> if you executed the fitting using example dataset for this model in section <b >3.b.</b>.</p><pre class="codeinput">FitResultsSave_nii(FitResults_old, <span class="string">'b0_dem_data/Phase.nii.gz'</span>);
-	</pre><pre class="codeoutput">Warning: Directory already exists. 
 	</pre><h2 id="24">3.e. Re-use or share fit configuration files</h2><p >qMRLab's fit configuration files (<tt >b0_dem_Demo.qmrlab.mat</tt>) store all the <tt >options</tt> and <tt >protocol</tt> in relation to the used model and the release version.</p><p >
 	<div class="info">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-retweet" style="color:navy;margin-left:5px;"></i></strong> <code >*.qmrlab.mat</code> files can be easily shared with collaborators to allow them fit their own <br >       data or run simulations using identical <code >option</code> and <code >protocol</code> configurations. </p>
@@ -222,4 +221,4 @@ b0_dem map :  Dual Echo Method for B0 mapping
 	<center >| <a href="https://github.com/qmrlab/pulse_sequences" target="_blank">qMRPullseq</a> | <a href="https://github.com/qmrlab/qmrflow" target="_blank">qMRFlow</a> | <a href="https://qmrlab.org/blog.html" target="_blank">Interactive Tutorials</a> | </p></center>
 	<center ><p ><a href="https://www.neuro.polymtl.ca/doku.php" target="_blank">NeuroPoly Lab</a>, Montreal, Canada</p></center>
 	<hr >
-	</p><p class="footer"><br ><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB® R2019b</a><br ></p></div>
+	</p><p class="footer"><br ><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB® R2018b</a><br ></p></div>
diff --git a/source/b1_afi_batch.rst b/source/b1_afi_batch.rst
@@ -81,7 +81,7 @@ b1_afi map:  Actual Flip-Angle Imaging for B1+ mapping
 	B1map_filtered     Smoothed B1+ field map using Gaussian, Median, Spline or polynomial filter (see FilterClass.m for more info)
 	Spurious           Map of datapoints that were set to 1 prior to smoothing
 	
-	Documentation for b1_afi
+	Reference page in Doc Center
 	doc b1_afi
 	
 	
@@ -102,8 +102,8 @@ b1_afi map:  Actual Flip-Angle Imaging for B1+ mapping
 	<div class="warning">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-info-circle" style="color:black;margin-left:5px;"></i></strong> See the <a href="#21">generic notes</a> section below for further information. </p>
 	</div>
-	</p><h2 id="11">2.b.2 Set <tt >protocol</tt> and <tt >options</tt> <i >the GUI way</i></h2><p >The following command opens a panel to set <tt >protocol</tt> and <tt >options</tt> (if <tt >GUI</tt> is available to the user):</p><pre class="codeinput">Model = Custom_OptionsGUI(Model);
-	</pre><img vspace="5" hspace="5" src="_static/b1_afi_batch_01.png" alt=""> <p ><i >You need to close this window for the remaining of the script to proceed.</i></p><p >
+	</p><h2 id="11">2.b.2 Set <tt >protocol</tt> and <tt >options</tt> <i >the GUI way</i></h2><p >The following command opens a panel to set <tt >protocol</tt> and <tt >options</tt> (if <tt >GUI</tt> is available to the user):</p><pre class="language-matlab">Model = Custom_OptionsGUI(Model);
+	</pre><p ><img vspace="5" hspace="5" src="https://github.com/qMRLab/doc_images/blob/main/usr/protPanels/b1_afi.png?raw=true" alt=""> </p><p ><i >If available, you need to close this panel for the remaining of the script to proceed.</i></p><p >
 	<div class="warning">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-info-circle" style="color:black;margin-left:5px;"></i></strong> Using this panel, you can save qMRLab protocol files that can be used in both interfaces. See the <a href="#21">generic notes</a> section below for details. </p>
 	</div>
@@ -130,7 +130,7 @@ b1_afi map:  Actual Flip-Angle Imaging for B1+ mapping
 	</pre><p ><i >A representative fit curve will be plotted if available.</i></p><p >To render images in this page, we will load the fit results that had been saved before. You can skip the following code block;</p><pre class="codeinput"><span class="comment">% Load FitResults that comes with the example dataset.</span>
 	FitResults_old = load(<span class="string">'FitResults/FitResults.mat'</span>);
 	qMRshowOutput(FitResults_old,data,Model);
-	</pre><img vspace="5" hspace="5" src="_static/b1_afi_batch_02.png" alt=""> <h2 id="22">3.d. Save fit results</h2><p >Outputs can be saved as <tt >*.nii.(gz)</tt> if <tt >NIfTI</tt> inputs are available:</p><pre class="language-matlab"><span class="comment">% Generic function call to save nifti outputs</span>
+	</pre><img vspace="5" hspace="5" src="_static/b1_afi_batch_01.png" alt=""> <h2 id="22">3.d. Save fit results</h2><p >Outputs can be saved as <tt >*.nii.(gz)</tt> if <tt >NIfTI</tt> inputs are available:</p><pre class="language-matlab"><span class="comment">% Generic function call to save nifti outputs</span>
 	FitResultsSave_nii(FitResults, <span class="string">'reference/nifti/file.nii.(gz)'</span>);
 	</pre><p >If not, <tt >FitResults.mat</tt> file can be saved. This file contains all the outputs as workspace variables:</p><pre class="language-matlab"><span class="comment">% Generic function call to save FitResults.mat</span>
 	FitResultsSave_mat(FitResults);
@@ -139,7 +139,6 @@ b1_afi map:  Actual Flip-Angle Imaging for B1+ mapping
 	<p style="margin:0px!important;"><strong > <i class="fa fa-clone" style="color:navy;margin-left:5px;"></i></strong> <code >FitResults.mat</code> files can be loaded to qMRLab <code >GUI</code> for <a href="l#data-viewer" target="_blank">visualization and ROI <br >        analyses</a>. </p>
 	</div>
 	</p><p >The section below will be dynamically generated in accordance with the example data format (<tt >mat</tt> or <tt >nii</tt>). You can substitute <tt >FitResults_old</tt> with <tt >FitResults</tt> if you executed the fitting using example dataset for this model in section <b >3.b.</b>.</p><pre class="codeinput">FitResultsSave_nii(FitResults_old, <span class="string">'b1_afi_data/AFIData1.nii.gz'</span>);
-	</pre><pre class="codeoutput">Warning: Directory already exists. 
 	</pre><h2 id="24">3.e. Re-use or share fit configuration files</h2><p >qMRLab's fit configuration files (<tt >b1_afi_Demo.qmrlab.mat</tt>) store all the <tt >options</tt> and <tt >protocol</tt> in relation to the used model and the release version.</p><p >
 	<div class="info">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-retweet" style="color:navy;margin-left:5px;"></i></strong> <code >*.qmrlab.mat</code> files can be easily shared with collaborators to allow them fit their own <br >       data or run simulations using identical <code >option</code> and <code >protocol</code> configurations. </p>
@@ -198,4 +197,4 @@ b1_afi map:  Actual Flip-Angle Imaging for B1+ mapping
 	<center >| <a href="https://github.com/qmrlab/pulse_sequences" target="_blank">qMRPullseq</a> | <a href="https://github.com/qmrlab/qmrflow" target="_blank">qMRFlow</a> | <a href="https://qmrlab.org/blog.html" target="_blank">Interactive Tutorials</a> | </p></center>
 	<center ><p ><a href="https://www.neuro.polymtl.ca/doku.php" target="_blank">NeuroPoly Lab</a>, Montreal, Canada</p></center>
 	<hr >
-	</p><p class="footer"><br ><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB® R2019b</a><br ></p></div>
+	</p><p class="footer"><br ><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB® R2018b</a><br ></p></div>
diff --git a/source/b1_dam_batch.rst b/source/b1_dam_batch.rst
@@ -112,7 +112,7 @@ b1_dam map:  Double-Angle Method for B1+ mapping
 	Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab: 
 	Quantitative MRI analysis, under one umbrella doi: 10.21105/joss.02343
 	
-	Documentation for b1_dam
+	Reference page in Doc Center
 	doc b1_dam
 	
 	
@@ -132,8 +132,8 @@ b1_dam map:  Double-Angle Method for B1+ mapping
 	<div class="warning">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-info-circle" style="color:black;margin-left:5px;"></i></strong> See the <a href="#21">generic notes</a> section below for further information. </p>
 	</div>
-	</p><h2 id="11">2.b.2 Set <tt >protocol</tt> and <tt >options</tt> <i >the GUI way</i></h2><p >The following command opens a panel to set <tt >protocol</tt> and <tt >options</tt> (if <tt >GUI</tt> is available to the user):</p><pre class="codeinput">Model = Custom_OptionsGUI(Model);
-	</pre><img vspace="5" hspace="5" src="_static/b1_dam_batch_01.png" alt=""> <p ><i >You need to close this window for the remaining of the script to proceed.</i></p><p >
+	</p><h2 id="11">2.b.2 Set <tt >protocol</tt> and <tt >options</tt> <i >the GUI way</i></h2><p >The following command opens a panel to set <tt >protocol</tt> and <tt >options</tt> (if <tt >GUI</tt> is available to the user):</p><pre class="language-matlab">Model = Custom_OptionsGUI(Model);
+	</pre><p ><img vspace="5" hspace="5" src="https://github.com/qMRLab/doc_images/blob/main/usr/protPanels/b1_dam.png?raw=true" alt=""> </p><p ><i >If available, you need to close this panel for the remaining of the script to proceed.</i></p><p >
 	<div class="warning">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-info-circle" style="color:black;margin-left:5px;"></i></strong> Using this panel, you can save qMRLab protocol files that can be used in both interfaces. See the <a href="#21">generic notes</a> section below for details. </p>
 	</div>
@@ -160,7 +160,7 @@ b1_dam map:  Double-Angle Method for B1+ mapping
 	</pre><p ><i >A representative fit curve will be plotted if available.</i></p><p >To render images in this page, we will load the fit results that had been saved before. You can skip the following code block;</p><pre class="codeinput"><span class="comment">% Load FitResults that comes with the example dataset.</span>
 	FitResults_old = load(<span class="string">'FitResults/FitResults.mat'</span>);
 	qMRshowOutput(FitResults_old,data,Model);
-	</pre><img vspace="5" hspace="5" src="_static/b1_dam_batch_02.png" alt=""> <h2 id="22">3.d. Save fit results</h2><p >Outputs can be saved as <tt >*.nii.(gz)</tt> if <tt >NIfTI</tt> inputs are available:</p><pre class="language-matlab"><span class="comment">% Generic function call to save nifti outputs</span>
+	</pre><img vspace="5" hspace="5" src="_static/b1_dam_batch_01.png" alt=""> <h2 id="22">3.d. Save fit results</h2><p >Outputs can be saved as <tt >*.nii.(gz)</tt> if <tt >NIfTI</tt> inputs are available:</p><pre class="language-matlab"><span class="comment">% Generic function call to save nifti outputs</span>
 	FitResultsSave_nii(FitResults, <span class="string">'reference/nifti/file.nii.(gz)'</span>);
 	</pre><p >If not, <tt >FitResults.mat</tt> file can be saved. This file contains all the outputs as workspace variables:</p><pre class="language-matlab"><span class="comment">% Generic function call to save FitResults.mat</span>
 	FitResultsSave_mat(FitResults);
@@ -169,7 +169,6 @@ b1_dam map:  Double-Angle Method for B1+ mapping
 	<p style="margin:0px!important;"><strong > <i class="fa fa-clone" style="color:navy;margin-left:5px;"></i></strong> <code >FitResults.mat</code> files can be loaded to qMRLab <code >GUI</code> for <a href="l#data-viewer" target="_blank">visualization and ROI <br >        analyses</a>. </p>
 	</div>
 	</p><p >The section below will be dynamically generated in accordance with the example data format (<tt >mat</tt> or <tt >nii</tt>). You can substitute <tt >FitResults_old</tt> with <tt >FitResults</tt> if you executed the fitting using example dataset for this model in section <b >3.b.</b>.</p><pre class="codeinput">FitResultsSave_nii(FitResults_old, <span class="string">'b1_dam_data/SFalpha.nii.gz'</span>);
-	</pre><pre class="codeoutput">Warning: Directory already exists. 
 	</pre><h2 id="24">3.e. Re-use or share fit configuration files</h2><p >qMRLab's fit configuration files (<tt >b1_dam_Demo.qmrlab.mat</tt>) store all the <tt >options</tt> and <tt >protocol</tt> in relation to the used model and the release version.</p><p >
 	<div class="info">
 	<p style="margin:0px!important;"><strong > <i class="fa fa-retweet" style="color:navy;margin-left:5px;"></i></strong> <code >*.qmrlab.mat</code> files can be easily shared with collaborators to allow them fit their own <br >       data or run simulations using identical <code >option</code> and <code >protocol</code> configurations. </p>
@@ -228,4 +227,4 @@ b1_dam map:  Double-Angle Method for B1+ mapping
 	<center >| <a href="https://github.com/qmrlab/pulse_sequences" target="_blank">qMRPullseq</a> | <a href="https://github.com/qmrlab/qmrflow" target="_blank">qMRFlow</a> | <a href="https://qmrlab.org/blog.html" target="_blank">Interactive Tutorials</a> | </p></center>
 	<center ><p ><a href="https://www.neuro.polymtl.ca/doku.php" target="_blank">NeuroPoly Lab</a>, Montreal, Canada</p></center>
 	<hr >
-	</p><p class="footer"><br ><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB® R2019b</a><br ></p></div>
+	</p><p class="footer"><br ><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB® R2018b</a><br ></p></div>