diff --git a/doc/fsl.rst b/doc/fsl.rst
index fb702bca8580962ba9fd1da2a06c2e895efa767a..c92138a86ddb95c109a747fa3a4624d6d74613d5 100644
--- a/doc/fsl.rst
+++ b/doc/fsl.rst
@@ -7,6 +7,7 @@
    fsl.data
    fsl.scripts
    fsl.utils
+   fsl.transform
    fsl.version
    fsl.wrappers
 
diff --git a/doc/fsl.transform.affine.rst b/doc/fsl.transform.affine.rst
new file mode 100644
index 0000000000000000000000000000000000000000..93792be10f033d6b36801012d2a223dd05d75409
--- /dev/null
+++ b/doc/fsl.transform.affine.rst
@@ -0,0 +1,7 @@
+``fsl.transform.affine``
+========================
+
+.. automodule:: fsl.transform.affine
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/fsl.utils.transform.rst b/doc/fsl.transform.flirt.rst
similarity index 57%
rename from doc/fsl.utils.transform.rst
rename to doc/fsl.transform.flirt.rst
index b21d270e979bf113d60e5966879b1586d4292d65..836a82f49332eecf65e5ce70ca1778619a1f20d0 100644
--- a/doc/fsl.utils.transform.rst
+++ b/doc/fsl.transform.flirt.rst
@@ -1,7 +1,7 @@
-``fsl.utils.transform``
+``fsl.transform.flirt``
 =======================
 
-.. automodule:: fsl.utils.transform
+.. automodule:: fsl.transform.flirt
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/doc/fsl.transform.fnirt.rst b/doc/fsl.transform.fnirt.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4a1efe50fc5ed17c2844bf49a8838bd467dc245e
--- /dev/null
+++ b/doc/fsl.transform.fnirt.rst
@@ -0,0 +1,7 @@
+``fsl.transform.fnirt``
+=======================
+
+.. automodule:: fsl.transform.fnirt
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/fsl.transform.nonlinear.rst b/doc/fsl.transform.nonlinear.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d137a81f30c54cb5e436047307feca854353cea6
--- /dev/null
+++ b/doc/fsl.transform.nonlinear.rst
@@ -0,0 +1,7 @@
+``fsl.transform.nonlinear``
+===========================
+
+.. automodule:: fsl.transform.nonlinear
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/fsl.transform.rst b/doc/fsl.transform.rst
new file mode 100644
index 0000000000000000000000000000000000000000..fdbd859adaa5828574327c49463d3084d0cd9769
--- /dev/null
+++ b/doc/fsl.transform.rst
@@ -0,0 +1,16 @@
+``fsl.transform``
+=================
+
+.. toctree::
+   :hidden:
+
+   fsl.transform.affine
+   fsl.transform.flirt
+   fsl.transform.fnirt
+   fsl.transform.nonlinear
+   fsl.transform.x5
+
+.. automodule:: fsl.transform
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/fsl.transform.x5.rst b/doc/fsl.transform.x5.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9b6978cf742e613b850e3157aa78cc489661066e
--- /dev/null
+++ b/doc/fsl.transform.x5.rst
@@ -0,0 +1,7 @@
+``fsl.transform.x5``
+====================
+
+.. automodule:: fsl.transform.x5
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/fsl.utils.rst b/doc/fsl.utils.rst
index 5722c7eb4f726f3b17c1ce32f7edee2f85779e4a..f253bac7e11914f3d5ccebcd152a576cd326ce66 100644
--- a/doc/fsl.utils.rst
+++ b/doc/fsl.utils.rst
@@ -23,7 +23,6 @@
    fsl.utils.run
    fsl.utils.settings
    fsl.utils.tempdir
-   fsl.utils.transform
    fsl.utils.weakfuncref
 
 .. automodule:: fsl.utils
diff --git a/doc/mock_modules.txt b/doc/mock_modules.txt
index 8bb6c230a3289007c59d160f6b6ec1cb7572b809..07e5f8d09209425941f9f5bd273d05ce39ad51fe 100644
--- a/doc/mock_modules.txt
+++ b/doc/mock_modules.txt
@@ -1,4 +1,5 @@
 deprecation
+h5py
 nibabel
 nibabel.fileslice
 nibabel.freesurfer