tractometry · 36000 · Jun 4, 2025 · Jun 3, 2025 · Jun 4, 2025 · Jun 4, 2025
diff --git a/source/_static/001-pyafq.html b/source/_static/001-pyafq.html
diff --git a/source/_static/002-viz.html b/source/_static/002-viz.html
diff --git a/source/_static/003-BabyAFQ.html b/source/_static/003-BabyAFQ.html
diff --git a/source/_static/004-RecoBundles.html b/source/_static/004-RecoBundles.html
diff --git a/source/_static/005-Optic-Radiations.html b/source/_static/005-Optic-Radiations.html
diff --git a/source/_static/006-Acoustic-Radiations.html b/source/_static/006-Acoustic-Radiations.html
diff --git a/source/_static/007-SLF-Subdivisions.html b/source/_static/007-SLF-Subdivisions.html
diff --git a/source/_static/008-GPU-Tractography.html b/source/_static/008-GPU-Tractography.html
diff --git a/source/_static/009-Ray-MSMT.html b/source/_static/009-Ray-MSMT.html
diff --git a/source/_static/010-afqinsight-mass-univariate.html b/source/_static/010-afqinsight-mass-univariate.html
diff --git a/source/_static/011-afqinsight-regression.html b/source/_static/011-afqinsight-regression.html
diff --git a/source/_static/012-afqinsight-classification.html b/source/_static/012-afqinsight-classification.html
diff --git a/source/_static/013-tractable.html b/source/_static/013-tractable.html
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
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+# 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
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+# 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
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+# 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
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+# 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
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+# 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
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+# 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 +1,21 @@
+# Examples
+
+```{eval-rst}
+
+.. toctree::
+   :maxdepth: 1
+
+   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
@@ -1,21 +1,89 @@
 # Tractometry
+Tractometry uses diffusion-weighted MRI (dMRI) to extract microstructural tissue properties of major white matter pathways. Here, we maintain a suite of integrated, open-source software that performs all analysis stages:
 
-## Projects
+[**pyAFQ**](https://tractometry.org/pyAFQ): Automated Fiber Quantification in Python:  
+&emsp;• post-processing of dMRI data  
+&emsp;• delineation of major white matter pathways  
+&emsp;• modeling of the tissue properties within them  
+&emsp;• expects pre-processed data. Data can be pre-processed with [*QSIprep*](https://qsiprep.readthedocs.io/en/latest/)  
 
-[*pyAFQ*](https://tractometry.org/pyAFQ): Automated Fiber Quantification in Python
+[**AFQ-Insight**](https://tractometry.org/AFQ-Insight): Machine learning and statistics for tractomtery:  
+&emsp;• novel machine learning models such as convolutional neural networks (CNNs) and recurrent neural network (RNNs)  
+&emsp;• more standard approaches, such as ordinary least squares (OLS) and principal component analysis (PCA)  
+&emsp;• integrated with [*scikit-learn*](https://scikit-learn.org/stable/) and adapted for tract data, bridging these two worlds  
 
-[*AFQ-Insight*](https://tractometry.org/AFQ-Insight): Machine learning and statistics for tractomtery.
+[**Tractable**](https://tractometry.org/tractable): R-based statistical analysis of tractometry:  
+&emsp;• focuses on generalized additive models (GAMs)  
 
-[*Tractable*](https://tractometry.org/tractable): R-based statistical analysis of tractometry.
+[**AFQ-Browser**](https://tractometry.org/AFQ-Browser): Interactive exploratory visualization and sharing of tractometry studies:  
+&emsp;• allows researchers to interactively query the data to explore patterns  
 
-[*AFQ-Browser*](https://tractometry.org/AFQ-Browser): Interactive exploratory visualization and sharing of tractometry studies.
+[**Tractoscope**](https://nrdg.github.io/tractoscope): Visualization of large openly-available tractometry studies.
+
+## [Examples](examples/index.md)
+
+**pyAFQ**
+
+- *Basics*  
+
+  • [Introduction](examples/001.md)  
+  • [Visualizing AFQ derivatives](examples/002.md)
+
+- *Extensions* 
+
+  • [BabyAFQ: tractometry for infant dMRI data](examples/003.md)  
+  • [RecoBundles for tract delineation](examples/004.md)
+
+- *Adding New Bundles* 
+
+  • [Optic Radiations](examples/005.md)  
+  • [Acoustic Radiations](examples/006.md)  
+  • [SLF 1/2/3 Subdivisions](examples/007.md)
+
+- *Acceleration*
+
+  • [GPU Tractography](examples/008.md)  
+  • [Multiprocessing for Model Fitting (Ray)](examples/009.md)
+
+**AFQ-Insight**
+
+- [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)](examples/013.md)
+
+## How to get help
+
+We encourage you to seek help and share your questions with the community. Here's how to get support for Tractometry-related projects:
+
+1. **Check [NeuroStars](https://neurostars.org/)**  
+   NeuroStars is a community forum for neuroimaging questions. Search for existing answers or post your question using the `pyafq`, `afq-insight`, or other relevant tags.
+
+2. **Browse or open issues on the respective GitHub repositories**  
+   Many questions may already be answered in the project's issue tracker. If not, you can open a new issue:
+
+   - [**pyAFQ**](https://github.com/tractometry/pyAFQ/issues)
+   - [**AFQ-Insight**](https://github.com/tractometry/AFQ-Insight/issues)
+   - [**Tractable**](https://github.com/tractometry/tractable/issues)
+   - [**AFQ-Browser**](https://github.com/tractometry/AFQ-Browser/issues)
+   - [**Tractoscope**](https://github.com/tractometry/tractoscope/issues)
+
+3. **Include details when asking for help**  
+   When posting, please include:
+   - The software version you're using
+   - Relevant code or command-line calls
+   - Error messages (if any)
+   - Expected vs. actual behavior
 
-[*Tractoscope*](https://tractometry.org/tractoscope): Visualization of large openly-available tractometry studies.
 
 ```{eval-rst}
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+   :maxdepth: 1
+   :hidden:
 
+   examples/index.md
 ```