doc/fsl.scripts.remove_ext.rst

+``fsl.scripts.remove_ext``
+==========================
+
+.. automodule:: fsl.scripts.remove_ext
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.resample_image.rst

+``fsl.scripts.resample_image``
+==============================
+
+.. automodule:: fsl.scripts.resample_image
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.rst

@@ -5,11 +5,26 @@
    :hidden:
 
    fsl.scripts.atlasq
+   fsl.scripts.fsl_abspath
+   fsl.scripts.fsl_apply_x5
+   fsl.scripts.fsl_convert_x5
+   fsl.scripts.fsl_ents
    fsl.scripts.imcp
    fsl.scripts.imglob
+   fsl.scripts.imln
    fsl.scripts.immv
+   fsl.scripts.imrm
+   fsl.scripts.imtest
+   fsl.scripts.remove_ext
+   fsl.scripts.resample_image
+   fsl.scripts.Text2Vest
+   fsl.scripts.Vest2Text
 
-.. automodule:: fsl.scripts
-    :members:
-    :undoc-members:
-    :show-inheritance:
+
+The ``fsl.scripts`` package contains all of the executable scripts provided by
+``fslpy``, and other python-based FSL packages.
+
+
+The ``fsl.scripts`` package is a `native namespace package
+<https://packaging.python.org/guides/packaging-namespace-packages/>`_, which
+means that it can be used by other Python libraries.

doc/fsl.transform.affine.rst

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

doc/fsl.utils.transform.rst → doc/fsl.transform.flirt.rst

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

doc/fsl.transform.fnirt.rst

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

doc/fsl.transform.nonlinear.rst

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

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: