diff --git a/doc/conf.py b/doc/conf.py
index ff39e3029272a455f440c137aba81b4ac60c7857..81d9fbe5c05dc9aba96931a84c7753ce915a4915 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -52,7 +52,7 @@ source_suffix = '.rst'
 #source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = 'fsl'
 
 # General information about the project.
 project = u'fslpy'
diff --git a/doc/fsl.data.rst b/doc/fsl.data.rst
index 31516eabd18e39eb4b806392dfa45b01150e166c..b1d9ab5290a9f59f80f6921d1c316af7b5771d3c 100644
--- a/doc/fsl.data.rst
+++ b/doc/fsl.data.rst
@@ -1,6 +1,19 @@
 fsl.data package
 ================
 
+.. toctree::
+   :hidden:
+
+   fsl.data.atlases
+   fsl.data.constants
+   fsl.data.featimage
+   fsl.data.featresults
+   fsl.data.image
+   fsl.data.melodicimage
+   fsl.data.melodicresults
+   fsl.data.model
+   fsl.data.tensorimage
+
 .. automodule:: fsl.data
     :members:
     :undoc-members:
diff --git a/doc/fsl.rst b/doc/fsl.rst
index 378faff43e99542ddb72385ada3ace232bf32525..cb3575e0be33dd74a26d54d25368020da4ce592a 100644
--- a/doc/fsl.rst
+++ b/doc/fsl.rst
@@ -1,6 +1,13 @@
 fsl package
 ===========
 
+.. toctree::
+   :hidden:
+
+   fsl.version
+   fsl.utils
+   fsl.data
+
 .. automodule:: fsl
     :members:
     :undoc-members:
diff --git a/doc/fsl.utils.rst b/doc/fsl.utils.rst
index df2c72c5977421ae90a9548565f68ad535103faf..a8d95ca9ac4f992daa89aedb3e0eae22d19b02ce 100644
--- a/doc/fsl.utils.rst
+++ b/doc/fsl.utils.rst
@@ -1,6 +1,26 @@
 fsl.utils package
 =================
 
+.. toctree::
+   :hidden:
+
+   fsl.utils.async
+   fsl.utils.colourbarbitmap
+   fsl.utils.dialog
+   fsl.utils.imagepanel
+   fsl.utils.layout
+   fsl.utils.memoize
+   fsl.utils.notifier
+   fsl.utils.path
+   fsl.utils.platform
+   fsl.utils.runwindow
+   fsl.utils.settings
+   fsl.utils.status
+   fsl.utils.textbitmap
+   fsl.utils.transform
+   fsl.utils.typedict
+   fsl.utils.webpage
+
 .. automodule:: fsl.utils
     :members:
     :undoc-members:
diff --git a/doc/index.rst b/doc/index.rst
deleted file mode 100644
index 96904a8482a4428d07325bd0dd357df088251c61..0000000000000000000000000000000000000000
--- a/doc/index.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-``fslpy``
-=========
-
-
-.. toctree::
-   :hidden:
-   :maxdepth: 2
-
-   fsl
-   fsl.data
-   fsl.utils
-
-   
-This is the ``fslpy`` API documentation.
-
-
-Building the documentation
---------------------------
-
-These pages have been built with the following commands (assuming that we
-are starting in the ``fslpy`` root directory)::
-
-    cd apidoc
-    rm -rf html
-    sphinx-build . html
diff --git a/fsl/data/__init__.py b/fsl/data/__init__.py
index bce706e83d85a52dc5d3601c541a3a53fbcb09b2..29f4c34355ce275bc1d45413fd09be382c398ddf 100644
--- a/fsl/data/__init__.py
+++ b/fsl/data/__init__.py
@@ -6,19 +6,4 @@
 #
 """This module contains various data types and associated I/O routines,
 models, constants, and other data-like things used throughout ``fslpy``.
-
-
- .. autosummary::
-    :nosignatures:
-
-    ~fsl.data.image.Nifti1
-    ~fsl.data.image.Image
-    ~fsl.data.featimage.FEATImage
-    ~fsl.data.melodicimage.MelodicImage
-    ~fsl.data.tensorimage.TensorImage
-    ~fsl.data.model.Model
-    ~fsl.data.featresults
-    ~fsl.data.melodicresults
-    ~fsl.data.atlases
-    ~fsl.data.constants
 """
diff --git a/fsl/utils/__init__.py b/fsl/utils/__init__.py
index 1091be9be125a6cf162d5c49d7d1f9c876269b2c..12e2d002ca9223ba86ff0f9e1eaa40a8ef9b4d00 100644
--- a/fsl/utils/__init__.py
+++ b/fsl/utils/__init__.py
@@ -6,22 +6,4 @@
 #
 """This module contains a collection of small utility modules for doing random
 things.
-
- .. autosummary::
-    :nosignatures:
-
-    ~fsl.utils.settings
-    ~fsl.utils.transform
-    ~fsl.utils.typedict
-    ~fsl.utils.layout
-    ~fsl.utils.colourbarbitmap
-    ~fsl.utils.textbitmap
-    ~fsl.utils.dialog
-    ~fsl.utils.runwindow
-    ~fsl.utils.webpage
-    ~fsl.utils.status
-    ~fsl.utils.memoize
-    ~fsl.utils.path
-    ~fsl.utils.async
-    ~fsl.utils.notifier
 """