MNT: fix typos found by codespell

Author: DimitriPapadopoulos

CONTRIBUTING.md

@@ -141,7 +141,7 @@ Pull requests titles should begin with a descriptive prefix:
 * ``DOC``: new or updated documentation
 * ``STY``: style changes
 * ``REF``: refactoring existing code
-* ``CI``: updates to continous integration infrastructure
+* ``CI``: updates to continuous integration infrastructure
 * ``MAINT``: general maintenance
 
 For example: `[ENH] Support for SB-reference in multi-band datasets`

NOTICE

@@ -11,7 +11,7 @@ This software redistributes the versioneer Python package, which is
 Public domain source code.
 
 This software is also distributed as a Docker container image.
-The bootstraping file for the image ("Dockerfile") is licensed
+The bootstrapping file for the image ("Dockerfile") is licensed
 under the MIT License.
 
 This software may be distributed through an add-on package called

README.rst

@@ -34,7 +34,7 @@ outputs that can be easily connected to subsequent tools such as
 
 .. image:: https://github.com/oesteban/smriprep/raw/033a6b4a54ecbd9051c45df979619cda69847cd1/docs/_resources/workflow.png
 
-The workflow is based on `Nipype <https://nipype.readthedocs.io>`__ and encompases
+The workflow is based on `Nipype <https://nipype.readthedocs.io>`__ and encompasses
 a combination of tools from well-known software packages, including
 `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`__,
 `ANTs <https://stnava.github.io/ANTs/>`__,

smriprep/cli/run.py

@@ -155,7 +155,7 @@ def get_parser():
         dest="verbose_count",
         action="count",
         default=0,
-        help="increases log verbosity for each occurence, debug level is -vvv",
+        help="increases log verbosity for each occurrence, debug level is -vvv",
     )
 
     g_conf = parser.add_argument_group("Workflow configuration")

smriprep/workflows/surfaces.py

@@ -88,7 +88,7 @@ def init_surface_recon_wf(*, omp_nthreads, hires, name="surface_recon_wf"):
     Second, the brain mask is grown, including pixels that have a high likelihood
     to the GM tissue distribution:
 
-      3. Dilate and substract the brain mask, defining the region to search for candidate
+      3. Dilate and subtract the brain mask, defining the region to search for candidate
          pixels that likely belong to cortical GM.
 
       4. Pixels found in the search region that are labeled as GM by ANTs
@@ -558,7 +558,7 @@ def init_gifti_surface_wf(*, name="gifti_surface_wf"):
     If midthickness (or graymid) surfaces do not exist, they are generated and
     saved to the subject directory as ``lh/rh.midthickness``.
     These, along with the gray/white matter boundary (``lh/rh.white``), pial
-    sufaces (``lh/rh.pial``) and inflated surfaces (``lh/rh.inflated``) are
+    surfaces (``lh/rh.pial``) and inflated surfaces (``lh/rh.inflated``) are
     converted to GIFTI files.
     Additionally, the vertex coordinates are :py:class:`recentered
     <smriprep.interfaces.NormalizeSurf>` to align with native T1w space.