Nipype

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Nipype

What is Nipype?

Nipype (Neuroimaging in Python Pipelines and Interfaces) is a flexible, lightweight and extensible neuroimaging data processing framework in Python. It is a community-developed initiative under the umbrella of Nipy. It addresses the heterogeneous collection of specialized applications in neuroimaging: SPM in MATLAB, FSL in shell, and Nipy in Python. A uniform interface is proposed to facilitate interaction between these different packages within a single workflow. The source code, issues and pull requests can be found here. The fundamental parts of Nipype are Interfaces, the Workflow Engine and the Execution Plugins, as you can see in the figure at the left: Interface: wraps a program or function (Map)Node: wraps an Interface for use in a Workflow Workflow: a graph or a forest of graphs whose edges represent data flow Plugin: a component which describes how a Workflow should be executed Among the execution plugins, you can find an OAR plugin here. an Slurm plugin here.

Installation

pip can be used to install the stable release of Nipype:

fontend.site:

pip install --user nipype

It is recommended to install python dependencies within a virtual environment. To do so, execute the following commands before running the pip command:

frontend.site:

python3 -m venv nipype

frontend.site:

source nipype/bin/activate

frontend.site:

pip install nipype

Basic usage

Let's assume that you have previously installed Nipype's dependencies and you have installed fsl to process the Rhyme judgment dataset available on OpenNeuro.

Here, we present an basic example of performing pre-processing using Nipype:

import nipype.interfaces.fsl as fsl
from nipype import Node, Workflow

preprocessing = Workflow(name='preprocessing')

mcflirt = Node(fsl.MCFLIRT(), name='mcflirt')

mean = Node(fsl.MeanImage(), name='mean')

preprocessing.connect(mcflirt, 'out_file', mean, 'in_file')

mcflirt.inputs.in_file = '/home/ychi/nipype/ds000003/sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz'

preprocessing.run()

Pydra

Pydra is a part of the second generation of the Nipype ecosystem, which is meant to provide additional flexibility and reproducibility. Pydra rewrites Nipype engine with mapping and joining as first-class operations. However, Pydra does not have OAR Support. Examples and details of Pydra's OAR extension can be found here.