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DOC: Fix typos found by copdespell
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‎doc/changelog/1.X.X-changelog.rst

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@@ -47,8 +47,8 @@ graph nodes might conflict with pydot parsing.
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Bug-fix release in the 1.8.x series.
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The previous release vendored ``distutils.version.LooseVersion``, and the vendored objects did not
50-
preserve compatiblity with the ``distutils`` objects. This release switches to the
51-
``looseversion`` package that ensures compatiblity.
50+
preserve compatibility with the ``distutils`` objects. This release switches to the
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``looseversion`` package that ensures compatibility.
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1.8.0 (May 10, 2022)

‎doc/devel/cmd_interface_devel.rst

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@@ -65,7 +65,7 @@ extra inputs: environ (a dictionary of environmental variables), and args (a
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string defining extra flags). In addition input spec can define the relation
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between the inputs and the generated command line. To achieve this we have
6767
added two metadata: ``argstr`` (string defining how the argument should be
68-
formated) and ``position`` (number defining the order of the arguments).
68+
formatted) and ``position`` (number defining the order of the arguments).
6969
For example
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.. testcode::
@@ -204,7 +204,7 @@ keep_extension (optional)
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205205
In addition one can add functionality to your class or base class, to allow
206206
changing extensions specific to package or interface. This overload function is
207-
trigerred only if keep_extension is not defined.
207+
triggered only if keep_extension is not defined.
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.. testcode::
210210

‎doc/devel/filename_generation.rst

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@@ -148,8 +148,8 @@ case?
148148
Out[115]: 'bet foo.nii /Users/cburns/tmp/junk/not_bar.nii'
149149

150150

151-
In this case we provide ``outfile`` but not as an absolue path, so the
152-
absolue path is generated and used for the ``cmdline`` when run, but
151+
In this case we provide ``outfile`` but not as an absolute path, so the
152+
absolute path is generated and used for the ``cmdline`` when run, but
153153
``mybet.inputs.outfile`` is not updated with the absolute path.
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.. sourcecode:: ipython

‎doc/devel/interface_specs.rst

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@@ -437,7 +437,7 @@ SPM
437437
^^^
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439439
``field``
440-
name of the structure refered by the SPM job manager
440+
name of the structure referred by the SPM job manager
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**Required:** This metadata is required by all SPM-mediated
443443
interface classes.

‎doc/devel/matlab_interface_devel.rst

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@@ -9,7 +9,7 @@ Example 1
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+++++++++
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This is a minimal script for wrapping MATLAB code. You should replace the MATLAB
12-
code template, and define approriate inputs and outputs.
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code template, and define appropriate inputs and outputs.
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.. literalinclude:: matlab_example1.py
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‎nipype/algorithms/__init__.py

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@@ -4,7 +4,7 @@
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"""
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Package contains pure python neuroimaging algorithms
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7-
Exaples: artifactdetect
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Examples: artifactdetect
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"""
1010
__docformat__ = "restructuredtext"

‎nipype/algorithms/confounds.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1152,7 +1152,7 @@ def is_outlier(points, thresh=3.5):
11521152
a modified z-score (based on the median absolute deviation) greater
11531153
than this value will be classified as outliers.
11541154
1155-
:return: A bolean mask, of size numobservations-length array.
1155+
:return: A boolean mask, of size numobservations-length array.
11561156
11571157
.. note:: References
11581158

‎nipype/algorithms/metrics.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -42,13 +42,13 @@ class DistanceInputSpec(BaseInterfaceInputSpec):
4242
"eucl_wmean",
4343
"eucl_max",
4444
desc='""eucl_min": Euclidean distance between two closest points\
45-
"eucl_cog": mean Euclidian distance between the Center of Gravity\
45+
"eucl_cog": mean Euclidean distance between the Center of Gravity\
4646
of volume1 and CoGs of volume2\
47-
"eucl_mean": mean Euclidian minimum distance of all volume2 voxels\
47+
"eucl_mean": mean Euclidean minimum distance of all volume2 voxels\
4848
to volume1\
49-
"eucl_wmean": mean Euclidian minimum distance of all volume2 voxels\
49+
"eucl_wmean": mean Euclidean minimum distance of all volume2 voxels\
5050
to volume1 weighted by their values\
51-
"eucl_max": maximum over minimum Euclidian distances of all volume2\
51+
"eucl_max": maximum over minimum Euclidean distances of all volume2\
5252
voxels to volume1 (also known as the Hausdorff distance)',
5353
usedefault=True,
5454
)

‎nipype/algorithms/misc.py

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Original file line numberDiff line numberDiff line change
@@ -1178,7 +1178,7 @@ def _list_outputs(self):
11781178

11791179

11801180
class SplitROIsInputSpec(TraitedSpec):
1181-
in_file = File(exists=True, mandatory=True, desc="file to be splitted")
1181+
in_file = File(exists=True, mandatory=True, desc="file to be split")
11821182
in_mask = File(exists=True, desc="only process files inside mask")
11831183
roi_size = traits.Tuple(traits.Int, traits.Int, traits.Int, desc="desired ROI size")
11841184

‎nipype/algorithms/rapidart.py

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Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@
3838
def _get_affine_matrix(params, source):
3939
"""Return affine matrix given a set of translation and rotation parameters
4040
41-
params : np.array (upto 12 long) in native package format
41+
params : np.array (up to 12 long) in native package format
4242
source : the package that generated the parameters
4343
supports SPM, AFNI, FSFAST, FSL, NIPY
4444
"""

‎nipype/interfaces/ants/base.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
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1212
iflogger = logging.getLogger("nipype.interface")
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14-
# -Using -1 gives primary responsibilty to ITKv4 to do the correct
14+
# -Using -1 gives primary responsibility to ITKv4 to do the correct
1515
# thread limitings.
1616
# -Using 1 takes a very conservative approach to avoid overloading
1717
# the computer (when running MultiProc) by forcing everything to
@@ -20,7 +20,7 @@
2020
LOCAL_DEFAULT_NUMBER_OF_THREADS = 1
2121
# -Using NSLOTS has the same behavior as ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
2222
# as long as ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS is not set. Otherwise
23-
# ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS takes precidence.
23+
# ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS takes precedence.
2424
# This behavior states that you the user explicitly specifies
2525
# num_threads, then respect that no matter what SGE tries to limit.
2626
PREFERED_ITKv4_THREAD_LIMIT_VARIABLE = "NSLOTS"

‎nipype/interfaces/ants/legacy.py

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Original file line numberDiff line numberDiff line change
@@ -58,7 +58,7 @@ class antsIntroductionInputSpec(ANTSCommandInputSpec):
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"maximum number of iterations (must be "
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"list of integers in the form [J,K,L...]: "
6060
"J = coarsest resolution iterations, K = "
61-
"middle resolution interations, L = fine "
61+
"middle resolution iterations, L = fine "
6262
"resolution iterations"
6363
),
6464
)
@@ -231,7 +231,7 @@ class buildtemplateparallelInputSpec(ANTSCommandInputSpec):
231231
"maximum number of iterations (must be "
232232
"list of integers in the form [J,K,L...]: "
233233
"J = coarsest resolution iterations, K = "
234-
"middle resolution interations, L = fine "
234+
"middle resolution iterations, L = fine "
235235
"resolution iterations"
236236
),
237237
)

‎nipype/interfaces/ants/registration.py

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Original file line numberDiff line numberDiff line change
@@ -453,7 +453,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
453453
usedefault=True, # This should be true for explicit completeness
454454
desc=(
455455
"Initialize linear transforms from the previous stage. By enabling this option, "
456-
"the current linear stage transform is directly intialized from the previous "
456+
"the current linear stage transform is directly initialized from the previous "
457457
"stages linear transform; this allows multiple linear stages to be run where "
458458
"each stage directly updates the estimated linear transform from the previous "
459459
"stage. (e.g. Translation -> Rigid -> Affine). "
@@ -641,7 +641,7 @@ class Registration(ANTSCommand):
641641
*stages*. For example first an Affine, then a Rigid, and ultimately a non-linear
642642
(Syn)-transformation.
643643
644-
antsRegistration can be initialized using one ore more transforms from moving_image
644+
antsRegistration can be initialized using one or more transforms from moving_image
645645
to fixed_image with the ``initial_moving_transform``-input. For example, when you
646646
already have a warpfield that corrects for geometrical distortions in an EPI (functional) image,
647647
that you want to apply before an Affine registration to a structural image.

‎nipype/interfaces/ants/resampling.py

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Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ class WarpTimeSeriesImageMultiTransformInputSpec(ANTSCommandInputSpec):
3434
tightest_box = traits.Bool(
3535
argstr="--tightest-bounding-box",
3636
desc=(
37-
"computes tightest bounding box (overrided by " "reference_image if given)"
37+
"computes tightest bounding box (overridden by " "reference_image if given)"
3838
),
3939
xor=["reference_image"],
4040
)
@@ -186,7 +186,7 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
186186
tightest_box = traits.Bool(
187187
argstr="--tightest-bounding-box",
188188
desc=(
189-
"computes tightest bounding box (overrided by " "reference_image if given)"
189+
"computes tightest bounding box (overridden by " "reference_image if given)"
190190
),
191191
xor=["reference_image"],
192192
)

‎nipype/interfaces/ants/segmentation.py

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Original file line numberDiff line numberDiff line change
@@ -698,7 +698,7 @@ class CorticalThicknessInputSpec(ANTSCommandInputSpec):
698698
class CorticalThicknessOutputSpec(TraitedSpec):
699699
BrainExtractionMask = File(exists=True, desc="brain extraction mask")
700700
ExtractedBrainN4 = File(exists=True, desc="extracted brain from N4 image")
701-
BrainSegmentation = File(exists=True, desc="brain segmentaion image")
701+
BrainSegmentation = File(exists=True, desc="brain segmentation image")
702702
BrainSegmentationN4 = File(exists=True, desc="N4 corrected image")
703703
BrainSegmentationPosteriors = OutputMultiPath(
704704
File(exists=True), desc="Posterior probability images"
@@ -1009,10 +1009,10 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
10091009
runtime = super(BrainExtraction, self)._run_interface(runtime)
10101010

10111011
# Still, double-check if it didn't found N4
1012-
if "we cant find" in runtime.stdout:
1012+
if "we can't find" in runtime.stdout:
10131013
for line in runtime.stdout.split("\n"):
1014-
if line.strip().startswith("we cant find"):
1015-
tool = line.strip().replace("we cant find the", "").split(" ")[0]
1014+
if line.strip().startswith("we can't find"):
1015+
tool = line.strip().replace("we can't find the", "").split(" ")[0]
10161016
break
10171017

10181018
errmsg = (

‎nipype/interfaces/base/core.py

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@@ -987,7 +987,7 @@ class MpiCommandLine(CommandLine):
987987

988988
@property
989989
def cmdline(self):
990-
"""Adds 'mpiexec' to begining of command"""
990+
"""Adds 'mpiexec' to beginning of command"""
991991
result = []
992992
if self.inputs.use_mpi:
993993
result.append("mpiexec")

‎nipype/interfaces/base/tests/test_resource_monitor.py

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@@ -79,7 +79,7 @@ def test_cmdline_profiling(tmpdir, mem_gb, n_procs, use_resource_monitor):
7979

8080

8181
@pytest.mark.skipif(
82-
True, reason="test disabled temporarily, until funcion profiling works"
82+
True, reason="test disabled temporarily, until function profiling works"
8383
)
8484
@pytest.mark.parametrize("mem_gb,n_procs", [(0.5, 3), (2.2, 8), (0.8, 4), (1.5, 1)])
8585
def test_function_profiling(tmpdir, mem_gb, n_procs, use_resource_monitor):

‎nipype/interfaces/brainsuite/brainsuite.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1492,7 +1492,7 @@ class BDPInputSpec(CommandLineInputSpec):
14921492
)
14931493
ignoreFieldmapFOV = traits.Bool(
14941494
argstr="--ignore-fieldmap-fov",
1495-
desc="Supresses the error generated by an insufficient field of view of the "
1495+
desc="Suppresses the error generated by an insufficient field of view of the "
14961496
"input fieldmap and continues with the processing. It is useful only when "
14971497
"used with fieldmap-based distortion correction. See "
14981498
"fieldmap-correction for a detailed explanation. ",
@@ -1677,7 +1677,7 @@ class BDPInputSpec(CommandLineInputSpec):
16771677
desc="Enables estimation of diffusion tensors and/or ODFs (and statistics if "
16781678
"applicable) in the native diffusion coordinate in addition to the "
16791679
"default T1-coordinate. All native diffusion coordinate files are saved "
1680-
'in a seperate folder named "diffusion_coord_outputs". In case statistics '
1680+
'in a separate folder named "diffusion_coord_outputs". In case statistics '
16811681
"computation is required, it will also transform/save all label/mask "
16821682
"files required to diffusion coordinate (see generateStats for "
16831683
"details). ",

‎nipype/interfaces/camino/connectivity.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -133,7 +133,7 @@ class Conmat(CommandLine):
133133
Such fibers will add to the diagonal elements of the matrix. To remove
134134
these entries, run procstreamlines with -endpointfile before running conmat.
135135
136-
If the seed point is inside a labled region, it counts as one end of the
136+
If the seed point is inside a labeled region, it counts as one end of the
137137
connection. So ::
138138
139139
----[SEED inside A]---------B

‎nipype/interfaces/camino/convert.py

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Original file line numberDiff line numberDiff line change
@@ -780,7 +780,7 @@ class AnalyzeHeaderInputSpec(StdOutCommandLineInputSpec):
780780
position=3,
781781
desc=(
782782
"Reads header information from file and "
783-
"intializes a new header with the values read "
783+
"initializes a new header with the values read "
784784
"from the file. You may replace any "
785785
"combination of fields in the new header by "
786786
"specifying subsequent options."

‎nipype/interfaces/camino/dti.py

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@@ -621,7 +621,7 @@ class PicoPDFsInputSpec(StdOutCommandLineInputSpec):
621621
units="NA",
622622
desc="The maximum number of PDs in a voxel (default 3) for PD data."
623623
"This option determines the size of the input and output voxels."
624-
"This means that the data file may be large enough to accomodate three or more PDs,"
624+
"This means that the data file may be large enough to accommodate three or more PDs,"
625625
"but does not mean that any of the voxels are classified as containing three or more PDs.",
626626
)
627627

@@ -1251,7 +1251,7 @@ class TrackBootstrapInputSpec(TrackInputSpec):
12511251

12521252
class TrackBootstrap(Track):
12531253
"""
1254-
Performs bootstrap streamline tractography using mulitple scans of the same subject
1254+
Performs bootstrap streamline tractography using multiple scans of the same subject
12551255
12561256
Example
12571257
-------

‎nipype/interfaces/camino/odf.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -170,7 +170,7 @@ class LinRecon(StdOutCommandLine):
170170
Reads a linear transformation from the matrix file assuming the
171171
imaging scheme specified in the scheme file. Performs the linear
172172
transformation on the data in every voxel and outputs the result to
173-
the standard output. The ouput in every voxel is actually: ::
173+
the standard output. The output in every voxel is actually: ::
174174
175175
[exit code, ln(S(0)), p1, ..., pR]
176176

‎nipype/interfaces/cat12/preprocess.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -136,7 +136,7 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
136136
" method that refines the probability maps of the SPM approach by region-growing techniques of "
137137
"the gcut approach with a final surface-based optimization strategy. This is currently the method"
138138
" with the most accurate and reliable results. If you use already skull-stripped data you can "
139-
"turn off skull-stripping although this is automaticaly detected in most cases. Please note that "
139+
"turn off skull-stripping although this is automatically detected in most cases. Please note that "
140140
"the choice of the skull-stripping method will also influence the estimation of TIV, because the"
141141
" methods mainly differ in the handling of the outer CSF around the cortical surface. "
142142
"\nPossible Values:\n - none (already skull-stripped): -1;\n - SPM approach: 0; "
@@ -329,7 +329,7 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
329329
# Labels
330330
_help_label_desc = (
331331
"This is the option to save a labeled version of your segmentations in the %s space for fast visual "
332-
"comparision. Labels are saved as Partial Volume Estimation (PVE) values with different mix "
332+
"comparison. Labels are saved as Partial Volume Estimation (PVE) values with different mix "
333333
"classes for GM-WM (2.5) and GM-CSF (1.5). BG=0, CSF=1, GM=2, WM=3, WMH=4 (if WMHC=3), "
334334
"SL=1.5 (if SLC)"
335335
)

‎nipype/interfaces/cat12/surface.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@ class ExtractAdditionalSurfaceParametersInputSpec(SPMCommandInputSpec):
3333
False,
3434
field="SD",
3535
usedefault=True,
36-
desc="Extract sulcus depth based on euclidian distance between the central "
36+
desc="Extract sulcus depth based on euclidean distance between the central "
3737
"surface anf its convex hull.",
3838
)
3939
fractal_dimension = traits.Bool(
@@ -92,7 +92,7 @@ class ExtractAdditionalSurfaceParameters(SPMCommand):
9292
* Sulcus depth
9393
* Toro's gyrification index
9494
* Shaer's local gyrification index
95-
* Laplacian gyrification indeces
95+
* Laplacian gyrification indices
9696
* Addicional surfaces
9797
* Measure normalization
9898
* Lazy processing
@@ -153,7 +153,7 @@ def _list_outputs(self):
153153
)
154154

155155
# Add all hemisphere files into one list, this is important because only the left hemisphere
156-
# files are used as input in the Surface ROI Tools, fpr instance.
156+
# files are used as input in the Surface ROI Tools, for instance.
157157
outputs[all_files_hemisphere].append(
158158
os.path.join(pth, generated_filename)
159159
)

‎nipype/interfaces/cmtk/cmtk.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -282,7 +282,7 @@ def cmat(
282282
)
283283
except IndexError:
284284
iflogger.error(
285-
"AN INDEXERROR EXCEPTION OCCURED FOR FIBER %s. "
285+
"AN INDEXERROR EXCEPTION OCCURRED FOR FIBER %s. "
286286
"PLEASE CHECK ENDPOINT GENERATION",
287287
i,
288288
)

‎nipype/interfaces/diffusion_toolkit/dti.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -173,7 +173,7 @@ class DTITrackerInputSpec(CommandLineInputSpec):
173173
Input and output file type. Accepted values are:
174174
175175
* analyze -> analyze format 7.5
176-
* ni1 -> nifti format saved in seperate .hdr and .img file
176+
* ni1 -> nifti format saved in separate .hdr and .img file
177177
* nii -> nifti format with one .nii file
178178
* nii.gz -> nifti format with compression
179179

‎nipype/interfaces/dipy/base.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -265,7 +265,7 @@ def get_dipy_workflows(module):
265265
-------
266266
l_wkflw : list of tuple
267267
This a list of tuple containing 2 elements:
268-
Worflow name, Workflow class obj
268+
Workflow name, Workflow class obj
269269
270270
Examples
271271
--------

‎nipype/interfaces/dtitk/base.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -58,8 +58,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
5858
"""Generate a filename based on the given parameters.
5959
6060
The filename will take the form: cwd/basename<suffix><ext>.
61-
If change_ext is True, it will use the extentions specified in
62-
<instance>intputs.output_type.
61+
If change_ext is True, it will use the extensions specified in
62+
<instance>inputs.output_type.
6363
6464
Parameters
6565
----------

‎nipype/interfaces/freesurfer/longitudinal.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ class RobustTemplateInputSpec(FSTraitedSpecOpenMP):
7878
fixed_timepoint = traits.Bool(
7979
default_value=False,
8080
argstr="--fixtp",
81-
desc="map everthing to init TP# (init TP is not resampled)",
81+
desc="map everything to init TP# (init TP is not resampled)",
8282
)
8383
no_iteration = traits.Bool(
8484
default_value=False,

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