organize examples

36000 · 36000 · commit 552b2ac3690d · 2025-06-03T20:00:55.000-07:00
diff --git a/source/examples/001.md b/source/examples/001.md
@@ -0,0 +1,5 @@
+# Introduction
+
+<div>
+    <iframe src="../_static/001-pyafq.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/002.md b/source/examples/002.md
@@ -0,0 +1,5 @@
+# Visualizing AFQ derivatives
+
+<div>
+    <iframe src="../_static/002-viz.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/003.md b/source/examples/003.md
@@ -0,0 +1,5 @@
+# BabyAFQ
+
+<div>
+    <iframe src="../_static/003-BabyAFQ.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/004.md b/source/examples/004.md
@@ -0,0 +1,5 @@
+# RecoBundles
+
+<div>
+    <iframe src="../_static/004-RecoBundles.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/005.md b/source/examples/005.md
@@ -0,0 +1,5 @@
+# Optic Radiations
+
+<div>
+    <iframe src="../_static/005-Optic-Radiations.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/006.md b/source/examples/006.md
@@ -0,0 +1,5 @@
+# Acoustic Radiations
+
+<div>
+    <iframe src="../_static/006-Acoustic-Radiations.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/007.md b/source/examples/007.md
@@ -0,0 +1,5 @@
+# SLF Subdivisions
+
+<div>
+    <iframe src="../_static/007-SLF-Subdivisions.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/008.md b/source/examples/008.md
@@ -0,0 +1,5 @@
+# GPU Tractography
+
+<div>
+    <iframe src="../_static/008-GPU-Tractography.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/009.md b/source/examples/009.md
@@ -0,0 +1,5 @@
+# Ray MSMT
+
+<div>
+    <iframe src="../_static/009-Ray-MSMT.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/010.md b/source/examples/010.md
@@ -0,0 +1,5 @@
+# Parametric Statistics for Group Comparison
+
+<div>
+    <iframe src="../_static/010-afqinsight-mass-univariate.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/011.md b/source/examples/011.md
@@ -0,0 +1,5 @@
+# Regression: Predict Age from White Matter
+
+<div>
+    <iframe src="../_static/011-afqinsight-regression.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/012.md b/source/examples/012.md
@@ -0,0 +1,5 @@
+# Classification: ALS Diagnosis
+
+<div>
+    <iframe src="../_static/012-afqinsight-classification.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/013.md b/source/examples/013.md
@@ -0,0 +1,5 @@
+# Fitting GAMs
+
+<div>
+    <iframe src="../_static/013-tractable.html" width="100%" height="500px"></iframe>
+</div>
diff --git a/source/examples/index.md b/source/examples/index.md
@@ -0,0 +1,22 @@
+# Examples
+
+```{eval-rst}
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Examples
+
+   001.md
+   002.md
+   003.md
+   004.md
+   005.md
+   006.md
+   007.md
+   008.md
+   009.md
+   010.md
+   011.md
+   012.md
+   013.md
+```
diff --git a/source/index.md b/source/index.md
@@ -20,40 +20,40 @@ Tractometry uses diffusion-weighted MRI (dMRI) to extract microstructural tissue
 
 [**Tractoscope**](https://nrdg.github.io/tractoscope): Visualization of large openly-available tractometry studies.
 
-## Examples
+## [Examples](examples/index.md)
 
 **pyAFQ**
 
 - *Basics*  
 
-  • [Introduction](_static/001-pyafq.html)  
-  • [Visualizing AFQ derivatives](_static/002-viz.html)
+  • [Introduction](examples/001.md)  
+  • [Visualizing AFQ derivatives](examples/002.md)
 
 - *Extensions* 
 
-  • [BabyAFQ: tractometry for infant dMRI data](_static/003-BabyAFQ.html)  
-  • [RecoBundles for tract delineation](_static/004-RecoBundles.html)
+  • [BabyAFQ: tractometry for infant dMRI data](examples/003.md)  
+  • [RecoBundles for tract delineation](examples/004.md)
 
 - *Adding New Bundles* 
 
-  • [Optic Radiations](_static/005-Optic-Radiations.html)  
-  • [Acoustic Radiations](_static/006-Acoustic-Radiations.html)  
-  • [SLF 1/2/3 Subdivisions](_static/007-SLF-Subdivisions.html)
+  • [Optic Radiations](examples/005.md)  
+  • [Acoustic Radiations](examples/006.md)  
+  • [SLF 1/2/3 Subdivisions](examples/007.md)
 
 - *Acceleration*
 
-  • [GPU Tractography](_static/008-GPU-Tractography.html)  
-  • [Multiprocessing for Model Fitting (Ray)](_static/009-Ray-MSMT.html)
+  • [GPU Tractography](examples/008.md)  
+  • [Multiprocessing for Model Fitting (Ray)](examples/009.md)
 
 **AFQ-Insight**
 
-- [Parametric Statistics for Group Comparison](_static/010-afqinsight-mass-univariate.html)  
-- [Regression: Predict Age from White Matter](_static/011-afqinsight-regression.html)  
-- [Classification: ALS Diagnosis](_static/012-afqinsight-classification.html)
+- [Parametric Statistics for Group Comparison](examples/010.md)  
+- [Regression: Predict Age from White Matter](examples/011.md)  
+- [Classification: ALS Diagnosis](examples/012.md)
 
 **Tractable**
 
-- [Fitting Generalized Additive Models (GAMs)](_static/013-tractable.html)
+- [Fitting Generalized Additive Models (GAMs)](examples/013.md)
 
 ## How to get help
 
@@ -82,7 +82,9 @@ We encourage you to seek help and share your questions with the community. Here'
 ```{eval-rst}
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+   :maxdepth: 1
+   :caption: Examples
+   :hidden:
 
+   examples/index.md
 ```

-Original file line number
+Diff line change
@@ @@ -0,0 +1,5 @@ @@
 +# Introduction
++
 +<div>
 +    <iframe src="../_static/001-pyafq.html" width="100%" height="500px"></iframe>
 +</div>