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.rst

@@ -5,13 +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.rst → doc/fsl.transform.rst

-``fsl``
-=======
+``fsl.transform``
+=================
 
 .. toctree::
    :hidden:
 
-   fsl.data
-   fsl.scripts
-   fsl.utils
-   fsl.version
-   fsl.wrappers
+   fsl.transform.affine
+   fsl.transform.flirt
+   fsl.transform.fnirt
+   fsl.transform.nonlinear
+   fsl.transform.x5
 
-.. automodule:: fsl
+.. 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.image.roi.rst

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

doc/fsl.utils.image.rst

@@ -5,6 +5,7 @@
    :hidden:
 
    fsl.utils.image.resample
+   fsl.utils.image.roi
 
 .. automodule:: fsl.utils.image
     :members:

doc/fsl.utils.rst

@@ -5,6 +5,7 @@
    :hidden:
 
    fsl.utils.assertions
+   fsl.utils.bids
    fsl.utils.cache
    fsl.utils.deprecated
    fsl.utils.ensure
@@ -23,7 +24,6 @@
    fsl.utils.run
    fsl.utils.settings
    fsl.utils.tempdir
-   fsl.utils.transform
    fsl.utils.weakfuncref
 
 .. automodule:: fsl.utils

doc/fsl.wrappers.avwutils.rst

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