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12 changes: 6 additions & 6 deletions doc/devel/testing_nipype.rst
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ environment variable is not set, some FreeSurfer related tests will fail.
If any of the tests failed, please report them on our `bug tracker
<http://github.com/nipy/nipype/issues>`_.

On Debian systems with a local copy of MATLAB installed, set the following
On Debian systems with a local copy of MATLAB installed, set the following
environment variable before running tests::

export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB
Expand All @@ -74,8 +74,8 @@ A few tests in Nipype make use of some images distributed within the `FSL course
<http://fsl.fmrib.ox.ac.uk/fslcourse/>`_. This reduced version of the package can be downloaded `here
<https://files.osf.io/v1/resources/nefdp/providers/osfstorage/57f472cf9ad5a101f977ecfe>`_.
To enable the tests depending on these data, just unpack the targz file and set the :code:`FSL_COURSE_DATA` environment
variable to point to that folder.
Note, that the test execution time can increase significantly with these additional tests.
variable to point to that folder.
Note, that the test execution time can increase significantly with these additional tests.


Xfailed tests
Expand All @@ -87,14 +87,14 @@ Some tests are expect to fail until the code will be changed or for other reason
Testing Nipype using Docker
---------------------------

Nipype is tested inside Docker containers and users can use nipype images to test local versions.
Nipype is tested inside Docker containers and users can use nipype images to test local versions.
First, install the `Docker Engine <https://docs.docker.com/engine/installation/>`_.
Nipype has one base docker image called nipype/nipype:base, that contains several useful tools
(FreeSurfer, AFNI, FSL, ANTs, etc.), and additional test images
for specific Python versions: py27 for Python 2.7 and py36 for Python 3.6.

Users can pull the nipype image for Python 3.6 as follows::

docker pull nipype/nipype:py36

In order to test a local version of nipype you can run test within container as follows::
Expand All @@ -105,5 +105,5 @@ In order to test a local version of nipype you can run test within container as
Additional comments
-------------------

If the project is tested both on your local OS and within a Docker container, you might have to remove all
If the project is tested both on your local OS and within a Docker container, you might have to remove all
``__pycache__`` directories before switching between your OS and a container.
24 changes: 12 additions & 12 deletions nipype/interfaces/afni/preprocess.py
Original file line number Diff line number Diff line change
Expand Up @@ -2423,19 +2423,19 @@ class TProjectInputSpec(AFNICommandInputSpec):
exists=True)
censortr = traits.List(
traits.Str(),
desc="""list of strings that specify time indexes
desc="""list of strings that specify time indexes
to be removed from the analysis. Each string is
of one of the following forms:
37 => remove global time index #37
2:37 => remove time index #37 in run #2
37..47 => remove global time indexes #37-47
37-47 => same as above
2:37..47 => remove time indexes #37-47 in run #2
*:0-2 => remove time indexes #0-2 in all runs
+Time indexes within each run start at 0.
+Run indexes start at 1 (just be to confusing).
+N.B.: 2:37,47 means index #37 in run #2 and
global time index 47; it does NOT mean
of one of the following forms:
37 => remove global time index #37
2:37 => remove time index #37 in run #2
37..47 => remove global time indexes #37-47
37-47 => same as above
2:37..47 => remove time indexes #37-47 in run #2
*:0-2 => remove time indexes #0-2 in all runs
+Time indexes within each run start at 0.
+Run indexes start at 1 (just be to confusing).
+N.B.: 2:37,47 means index #37 in run #2 and
global time index 47; it does NOT mean
index #37 in run #2 AND index #47 in run #2.""",
argstr="-CENSORTR %s")
cenmode = traits.Enum(
Expand Down