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.settings | ||
.pydevproject | ||
.idea/ | ||
/documentation.zip |
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- apt | ||
language: python | ||
python: | ||
- 2.6 | ||
- 2.7 | ||
env: | ||
- INSTALL_DEB_DEPENDECIES=true | ||
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#!/usr/bin/env python | ||
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- | ||
# vi: set ft=python sts=4 ts=4 sw=4 et: | ||
import sys | ||
from nipype.utils.nipype_cmd import main | ||
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if __name__ == '__main__': | ||
main(sys.argv) |
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saving_workflows | ||
spmmcr | ||
mipav | ||
nipypecmd | ||
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.. _nipypecmd: | ||
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============================================================ | ||
Running Nipype Interfaces from the command line (nipype_cmd) | ||
============================================================ | ||
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The primary use of Nipype_ is to build automated non-interactive pipelines. | ||
However, sometimes there is a need to run some interfaces quickly from the command line. | ||
This is especially useful when running Interfaces wrapping code that does not have | ||
command line equivalents (nipy or SPM). Being able to run Nipype interfaces opens new | ||
possibilities such as inclusion of SPM processing steps in bash scripts. | ||
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To run Nipype Interafces you need to use the nipype_cmd tool that should already be installed. | ||
The tool allows you to list Interfaces available in a certain package: | ||
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.. testcode:: | ||
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$nipype_cmd nipype.interfaces.nipy | ||
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Available Interfaces: | ||
SpaceTimeRealigner | ||
Similarity | ||
ComputeMask | ||
FitGLM | ||
EstimateContrast | ||
FmriRealign4d | ||
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After selecting a particular Interface you can learn what inputs it requires: | ||
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.. testcode:: | ||
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$nipype_cmd nipype.interfaces.nipy ComputeMask --help | ||
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usage:nipype_cmd nipype.interfaces.nipy ComputeMask [-h] [--M M] [--cc CC] | ||
[--ignore_exception IGNORE_EXCEPTION] | ||
[--m M] | ||
[--reference_volume REFERENCE_VOLUME] | ||
mean_volume | ||
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Run ComputeMask | ||
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positional arguments: | ||
mean_volume mean EPI image, used to compute the threshold for the | ||
mask | ||
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optional arguments: | ||
-h, --help show this help message and exit | ||
--M M upper fraction of the histogram to be discarded | ||
--cc CC Keep only the largest connected component | ||
--ignore_exception IGNORE_EXCEPTION | ||
Print an error message instead of throwing an | ||
exception in case the interface fails to run | ||
--m M lower fraction of the histogram to be discarded | ||
--reference_volume REFERENCE_VOLUME | ||
reference volume used to compute the mask. If none is | ||
give, the mean volume is used. | ||
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Finally you can run run the Interface: | ||
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.. testcode:: | ||
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$nipype_cmd nipype.interfaces.nipy ComputeMask mean.nii.gz | ||
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All that from the command line without having to start python interpreter manually. | ||
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.. include:: ../links_names.txt |
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