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ExploreASL · Jun 29, 2021 · 6df8b90 · 6df8b90
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diff --git a/docs/Tutorials-Advanced.md b/docs/Tutorials-Advanced.md
@@ -68,6 +68,47 @@ strRegEx = '^file.+$';
 filepaths = xASL_adm_GetFileList(strDirectory, strRegEx);
 ```
 
+----
+## Atlas Options
+
+The atlases of the **ExploreASL** population module can be defined in the `x.S` sub-structure. If you are interested in the `TotalGM`, `TotalWM`, `DeepWM`, `Hammers`, `HOcort_CONN`, `HOsub_CONN`, and `Mindboggle_OASIS_DKT31_CMA` atlases e.g., you can add the following lines to your `dataPar.json` file.
+
+
+```json
+{
+	"x": [{
+			"name": "Example",
+			"subject_regexp": "Example",
+			"S": {"Atlases": ["TotalGM","TotalWM","DeepWM","Hammers","HOcort_CONN","HOsub_CONN","Mindboggle_OASIS_DKT31_CMA"]}
+		}]
+}
+```
+
+Available atlases are:
+
+Free atlases: 
+
+- `TotalGM`: Mask of the entire GM
+- `TotalWM`: Mask of the entire WM
+- `DeepWM`: Mask of the deep WM
+- `WholeBrain`: Mask of the entire brain
+- `MNI_Structural`: MNI cortical atlas
+- `Tatu_ACA_MCA_PCA`: Original vascular territories by Tatu et al.
+- `Tatu_ICA_PCA`: Tatu (only ICA and PCA)
+- `Tatu_ICA_L_ICA_R_PCA`: Tatu (L ICA and R PCA)
+- `Tatu_ACA_MCA_PCA_Prox_Med_Dist`: Tatu separated to distal/medial/proximal of ACA/MCA/PCA
+- `Mindboggle_OASIS_DKT31_CMA`: Mindboggle-101 cortical atlas
+
+Free for non-commercial use only:
+
+- `HOcort_CONN`: Harvard-Oxford cortical atlas
+- `HOsub_CONN`: Harvard-Oxford subcortical atlas
+- `Hammers`: Alexander Hammers's brain atlas
+- `HammersCAT12`: Hammers atlas adapted to DARTEL template of IXI550 space
+- `Thalamus`: Harvad-Oxford thalamus atlas
+
+In a future **ExploreASL** version we want to add a custom atlases directory, where you can add your own atlas & metadata file including a description of how to do this.
+
 
 
 

diff --git a/docs/Tutorials-QC.md b/docs/Tutorials-QC.md
@@ -182,6 +182,8 @@ To create a nice visualization, open the T1w NIfTI, and then load the ASL CBF im
 | `(07-Mar-2019)`                     | The date of the analysis                                                                |
 | `PVC(0\|2)`                         | Partial volume correction (PVC) options: 0 (no PVC), 2 (two-compartment, classical PVC) |
 
+In the Stats folder's files, if the same `T1w` is used for multiple runs (`ASL_1`, `ASL_2` etc.), the values concerning the structural derivatives only (e.g. volumetrics and ratio) will be printed only for the first run.
+
 Start by opening ‘mean_qCBF_untreated_MNI_structural_n=1_07-Mar-2019_PVC2.tsv’. Notice that columns A to L are the ‘covariates’, whereas the remaining columns are the results of the ROI analysis. See the names of the MNI_structural atlas (Caudate, Cerebellum, Frontal, etc), and notice how from each of them, 3 columns are created, with the B (bilateral), L (left), or R (right) part of the ROI.
 
 **F) Run an ROI analysis with a custom atlas**

diff --git a/site/Tutorials-Advanced/index.html b/site/Tutorials-Advanced/index.html
@@ -411,6 +411,13 @@
     Basic File Operations
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#atlas-options" class="md-nav__link">
+    Atlas Options
+  </a>
+
 </li>
 
     </ul>
@@ -540,6 +547,13 @@
     Basic File Operations
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#atlas-options" class="md-nav__link">
+    Atlas Options
+  </a>
+
 </li>
 
     </ul>
@@ -606,6 +620,42 @@ <h2 id="basic-file-operations">Basic File Operations</h2>
 strRegEx = '^file.+$';
 filepaths = xASL_adm_GetFileList(strDirectory, strRegEx);
 </code></pre>
+
+<hr />
+<h2 id="atlas-options">Atlas Options</h2>
+<p>The atlases of the <strong>ExploreASL</strong> population module can be defined in the <code>x.S</code> sub-structure. If you are interested in the <code>TotalGM</code>, <code>TotalWM</code>, <code>DeepWM</code>, <code>Hammers</code>, <code>HOcort_CONN</code>, <code>HOsub_CONN</code>, and <code>Mindboggle_OASIS_DKT31_CMA</code> atlases e.g., you can add the following lines to your <code>dataPar.json</code> file.</p>
+<pre><code class="json">{
+    &quot;x&quot;: [{
+            &quot;name&quot;: &quot;Example&quot;,
+            &quot;subject_regexp&quot;: &quot;Example&quot;,
+            &quot;S&quot;: {&quot;Atlases&quot;: [&quot;TotalGM&quot;,&quot;TotalWM&quot;,&quot;DeepWM&quot;,&quot;Hammers&quot;,&quot;HOcort_CONN&quot;,&quot;HOsub_CONN&quot;,&quot;Mindboggle_OASIS_DKT31_CMA&quot;]}
+        }]
+}
+</code></pre>
+
+<p>Available atlases are:</p>
+<p>Free atlases: </p>
+<ul>
+<li><code>TotalGM</code>: Mask of the entire GM</li>
+<li><code>TotalWM</code>: Mask of the entire WM</li>
+<li><code>DeepWM</code>: Mask of the deep WM</li>
+<li><code>WholeBrain</code>: Mask of the entire brain</li>
+<li><code>MNI_Structural</code>: MNI cortical atlas</li>
+<li><code>Tatu_ACA_MCA_PCA</code>: Original vascular territories by Tatu et al.</li>
+<li><code>Tatu_ICA_PCA</code>: Tatu (only ICA and PCA)</li>
+<li><code>Tatu_ICA_L_ICA_R_PCA</code>: Tatu (L ICA and R PCA)</li>
+<li><code>Tatu_ACA_MCA_PCA_Prox_Med_Dist</code>: Tatu separated to distal/medial/proximal of ACA/MCA/PCA</li>
+<li><code>Mindboggle_OASIS_DKT31_CMA</code>: Mindboggle-101 cortical atlas</li>
+</ul>
+<p>Free for non-commercial use only:</p>
+<ul>
+<li><code>HOcort_CONN</code>: Harvard-Oxford cortical atlas</li>
+<li><code>HOsub_CONN</code>: Harvard-Oxford subcortical atlas</li>
+<li><code>Hammers</code>: Alexander Hammers's brain atlas</li>
+<li><code>HammersCAT12</code>: Hammers atlas adapted to DARTEL template of IXI550 space</li>
+<li><code>Thalamus</code>: Harvad-Oxford thalamus atlas</li>
+</ul>
+<p>In a future <strong>ExploreASL</strong> version we want to add a custom atlases directory, where you can add your own atlas &amp; metadata file including a description of how to do this.</p>
 
 
 

diff --git a/site/Tutorials-QC/index.html b/site/Tutorials-QC/index.html
@@ -796,6 +796,7 @@ <h2 id="62-quantitative-analysis-create-region-of-interest-roi-based-statistics"
 </tr>
 </tbody>
 </table>
+<p>In the Stats folder's files, if the same <code>T1w</code> is used for multiple runs (<code>ASL_1</code>, <code>ASL_2</code> etc.), the values concerning the structural derivatives only (e.g. volumetrics and ratio) will be printed only for the first run.</p>
 <p>Start by opening ‘mean_qCBF_untreated_MNI_structural_n=1_07-Mar-2019_PVC2.tsv’. Notice that columns A to L are the ‘covariates’, whereas the remaining columns are the results of the ROI analysis. See the names of the MNI_structural atlas (Caudate, Cerebellum, Frontal, etc), and notice how from each of them, 3 columns are created, with the B (bilateral), L (left), or R (right) part of the ROI.</p>
 <p><strong>F) Run an ROI analysis with a custom atlas</strong></p>
 <p><strong>1) Pick an atlas</strong></p>

diff --git a/site/search/search_index.json b/site/search/search_index.json
diff --git a/site/sitemap.xml b/site/sitemap.xml
@@ -1,71 +1,71 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"><url>
      <loc>https://github.com/ExploreASL/1.7.0/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Modules/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Import_Module/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Structural_Module/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/ASL_Module/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Population_Module/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Functions/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/SPMxASL/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Tutorials-ASL-BIDS/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Tutorials-Basics/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Tutorials-QC/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Tutorials-Advanced/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/FAQ/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Requirements/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/Changes/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/License/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url><url>
      <loc>https://github.com/ExploreASL/1.7.0/About/</loc>
-     <lastmod>2021-06-23</lastmod>
+     <lastmod>2021-06-29</lastmod>
      <changefreq>daily</changefreq>
     </url>
 </urlset>
diff --git a/site/sitemap.xml.gz b/site/sitemap.xml.gz
diff --git a/templates/TUTORIALS-ADVANCED.md b/templates/TUTORIALS-ADVANCED.md
@@ -68,6 +68,47 @@ strRegEx = '^file.+$';
 filepaths = xASL_adm_GetFileList(strDirectory, strRegEx);
 ```
 
+----
+## Atlas Options
+
+The atlases of the **ExploreASL** population module can be defined in the `x.S` sub-structure. If you are interested in the `TotalGM`, `TotalWM`, `DeepWM`, `Hammers`, `HOcort_CONN`, `HOsub_CONN`, and `Mindboggle_OASIS_DKT31_CMA` atlases e.g., you can add the following lines to your `dataPar.json` file.
+
+
+```json
+{
+	"x": [{
+			"name": "Example",
+			"subject_regexp": "Example",
+			"S": {"Atlases": ["TotalGM","TotalWM","DeepWM","Hammers","HOcort_CONN","HOsub_CONN","Mindboggle_OASIS_DKT31_CMA"]}
+		}]
+}
+```
+
+Available atlases are:
+
+Free atlases: 
+
+- `TotalGM`: Mask of the entire GM
+- `TotalWM`: Mask of the entire WM
+- `DeepWM`: Mask of the deep WM
+- `WholeBrain`: Mask of the entire brain
+- `MNI_Structural`: MNI cortical atlas
+- `Tatu_ACA_MCA_PCA`: Original vascular territories by Tatu et al.
+- `Tatu_ICA_PCA`: Tatu (only ICA and PCA)
+- `Tatu_ICA_L_ICA_R_PCA`: Tatu (L ICA and R PCA)
+- `Tatu_ACA_MCA_PCA_Prox_Med_Dist`: Tatu separated to distal/medial/proximal of ACA/MCA/PCA
+- `Mindboggle_OASIS_DKT31_CMA`: Mindboggle-101 cortical atlas
+
+Free for non-commercial use only:
+
+- `HOcort_CONN`: Harvard-Oxford cortical atlas
+- `HOsub_CONN`: Harvard-Oxford subcortical atlas
+- `Hammers`: Alexander Hammers's brain atlas
+- `HammersCAT12`: Hammers atlas adapted to DARTEL template of IXI550 space
+- `Thalamus`: Harvad-Oxford thalamus atlas
+
+In a future **ExploreASL** version we want to add a custom atlases directory, where you can add your own atlas & metadata file including a description of how to do this.
+
 
 
 

diff --git a/templates/TUTORIALS-QC.md b/templates/TUTORIALS-QC.md
@@ -182,6 +182,8 @@ To create a nice visualization, open the T1w NIfTI, and then load the ASL CBF im
 | `(07-Mar-2019)`                     | The date of the analysis                                                                |
 | `PVC(0\|2)`                         | Partial volume correction (PVC) options: 0 (no PVC), 2 (two-compartment, classical PVC) |
 
+In the Stats folder's files, if the same `T1w` is used for multiple runs (`ASL_1`, `ASL_2` etc.), the values concerning the structural derivatives only (e.g. volumetrics and ratio) will be printed only for the first run.
+
 Start by opening ‘mean_qCBF_untreated_MNI_structural_n=1_07-Mar-2019_PVC2.tsv’. Notice that columns A to L are the ‘covariates’, whereas the remaining columns are the results of the ROI analysis. See the names of the MNI_structural atlas (Caudate, Cerebellum, Frontal, etc), and notice how from each of them, 3 columns are created, with the B (bilateral), L (left), or R (right) part of the ROI.
 
 **F) Run an ROI analysis with a custom atlas**