Fix documentation build errors in index.rst

- Remove references to non-existent files in toctree
- Consolidate API reference into main toctree
- Add missing imports to FreeSurfer example
- Ensures Surface Visualization section displays properly

Author: yasseraleman

docs/source/index.rst

@@ -10,14 +10,24 @@ A comprehensive Python toolkit for neuroimaging data processing and analysis, sp
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :caption: API Reference:
 
-   installation
-   quickstart
-   api
-   examples
-   contributing
-   changelog
+   modules/bidstools
+   modules/connectivitytools
+   modules/dicomtools
+   modules/dwitools
+   modules/freesurfertools
+   modules/imagetools
+   modules/misctools
+   modules/morphometrytools
+   modules/networktools
+   modules/parcellationtools
+   modules/pipelinetools
+   modules/plottools
+   modules/qcqatools
+   modules/segmentationtools
+   modules/surfacetools
+   modules/visualizationtools
 
 Installation
 ============
@@ -39,7 +49,6 @@ Quick Start
 
 Surface Visualization
 =====================
-
 .. code-block:: python
     import clabtoolkit.surfacetools as cltsurf
 
@@ -58,7 +67,9 @@ Working with FreeSurfer
 =======================
 .. code-block:: python
 
+    import os
     import clabtoolkit.freesurfertools as cltfree
+    import clabtoolkit.misctools as cltmisc
 
     # Get the FREESURFER_HOME environment variable
     freesurfer_home = os.environ.get('FREESURFER_HOME')
@@ -76,28 +87,6 @@ Working with FreeSurfer
     print(f"Subject Directory: ")
     cltmisc.print_dict_tree(subject.fs_files)
 
-API Reference
-=============
-
-.. toctree::
-   :maxdepth: 2
-   
-   modules/bidstools
-   modules/connectivitytools
-   modules/dicomtools
-   modules/dwitools
-   modules/freesurfertools
-   modules/imagetools
-   modules/misctools
-   modules/morphometrytools
-   modules/networktools
-   modules/parcellationtools
-   modules/pipelinetools
-   modules/plottools
-   modules/qcqatools
-   modules/segmentationtools
-   modules/surfacetools
-   modules/visualizationtools
 
 Indices and tables
 ==================