doc/fsl.data.cifti.rst

+``fsl.data.cifti``
+==================
+
+.. automodule:: fsl.data.cifti
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.data.rst

@@ -5,6 +5,8 @@
    :hidden:
 
    fsl.data.atlases
+   fsl.data.bitmap
+   fsl.data.cifti
    fsl.data.constants
    fsl.data.dicom
    fsl.data.dtifit
@@ -20,6 +22,7 @@
    fsl.data.melodicimage
    fsl.data.mesh
    fsl.data.mghimage
+   fsl.data.utils
    fsl.data.vest
    fsl.data.volumelabels
    fsl.data.vtk

doc/fsl.data.utils.rst

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

doc/fsl.scripts.Text2Vest.rst

+``fsl.scripts.Text2Vest``
+=========================
+
+.. automodule:: fsl.scripts.Text2Vest
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.Vest2Text.rst

+``fsl.scripts.Vest2Text``
+=========================
+
+.. automodule:: fsl.scripts.Vest2Text
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.fsl_abspath.rst

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

doc/fsl.scripts.fsl_apply_x5.rst

+``fsl.scripts.fsl_apply_x5``
+============================
+
+.. automodule:: fsl.scripts.fsl_apply_x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.fsl_convert_x5.rst

+``fsl.scripts.fsl_convert_x5``
+==============================
+
+.. automodule:: fsl.scripts.fsl_convert_x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.imln.rst

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

doc/fsl.scripts.imrm.rst

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

doc/fsl.scripts.imtest.rst

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

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

@@ -5,12 +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: