doc/fsl.transform.rst

+``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:

doc/fsl.transform.x5.rst

+``fsl.transform.x5``
+====================
+
+.. automodule:: fsl.transform.x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.bids.rst

+``fsl.utils.bids``
+==================
+
+.. automodule:: fsl.utils.bids
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.deprecated.rst

+``fsl.utils.deprecated``
+========================
+
+.. automodule:: fsl.utils.deprecated
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.filetree.filetree.rst

+``fsl.utils.filetree.filetree``
+===============================
+
+.. automodule:: fsl.utils.filetree.filetree
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.filetree.parse.rst

+``fsl.utils.filetree.parse``
+============================
+
+.. automodule:: fsl.utils.filetree.parse
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.filetree.query.rst

+``fsl.utils.filetree.query``
+============================
+
+.. automodule:: fsl.utils.filetree.query
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.filetree.rst

+``fsl.utils.filetree``
+======================
+
+.. toctree::
+   :hidden:
+
+   fsl.utils.filetree.filetree
+   fsl.utils.filetree.parse
+   fsl.utils.filetree.query
+   fsl.utils.filetree.utils
+
+.. automodule:: fsl.utils.filetree
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.filetree.utils.rst

+``fsl.utils.filetree.utils``
+============================
+
+.. automodule:: fsl.utils.filetree.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.image.resample.rst

+``fsl.utils.image.resample``
+============================
+
+.. automodule:: fsl.utils.image.resample
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.image.roi.rst

+``fsl.utils.image.roi``
+=======================
+
+.. automodule:: fsl.utils.image.roi
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.rst → doc/fsl.utils.image.rst

-``fsl``
-=======
+``fsl.utils.image``
+===================
 
 .. toctree::
    :hidden:
 
-   fsl.data
-   fsl.scripts
-   fsl.utils
-   fsl.version
-   fsl.wrappers
+   fsl.utils.image.resample
+   fsl.utils.image.roi
 
-.. automodule:: fsl
+.. automodule:: fsl.utils.image
     :members:
     :undoc-members:
     :show-inheritance:

doc/fsl.utils.parse_data.rst

+``fsl.utils.parse_data``
+========================
+
+.. automodule:: fsl.utils.parse_data
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.rst

@@ -5,21 +5,25 @@
    :hidden:
 
    fsl.utils.assertions
+   fsl.utils.bids
    fsl.utils.cache
+   fsl.utils.deprecated
    fsl.utils.ensure
+   fsl.utils.filetree
    fsl.utils.fslsub
    fsl.utils.idle
    fsl.utils.imcp
+   fsl.utils.image
    fsl.utils.memoize
    fsl.utils.meta
    fsl.utils.naninfrange
    fsl.utils.notifier
    fsl.utils.path
+   fsl.utils.parse_data
    fsl.utils.platform
    fsl.utils.run
    fsl.utils.settings
    fsl.utils.tempdir
-   fsl.utils.transform
    fsl.utils.weakfuncref
 
 .. automodule:: fsl.utils

doc/fsl.utils.tempdir.rst

-``fsl.utils.temdir``
-====================
+``fsl.utils.tempdir``
+=====================
 
 .. automodule:: fsl.utils.tempdir
     :members:

doc/fsl.wrappers.avwutils.rst

+``fsl.wrappers.avwutils``
+=========================
+
+.. automodule:: fsl.wrappers.avwutils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.bedpostx.rst

+``fsl.wrappers.bedpostx``
+=========================
+
+.. automodule:: fsl.wrappers.bedpostx
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.bianca.rst

+``fsl.wrappers.bianca``
+=======================
+
+.. automodule:: fsl.wrappers.bianca
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.cluster_commands.rst

+``fsl.wrappers.cluster_commands``
+=================================
+
+.. automodule:: fsl.wrappers.cluster_commands
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.wrappers.dtifit.rst

+``fsl.wrappers.dtifit``
+=======================
+
+.. automodule:: fsl.wrappers.dtifit
+    :members:
+    :undoc-members:
+    :show-inheritance: