# Interfaces and Workflows¶

Release

1.6.0

Date

December 08, 2020, 17:20 PDT

Previous versions: 1.5.1 1.5.0

## Workflows¶

Important

The workflows that used to live as a module under nipype.workflows have been migrated to the new project NiFlows. These may be installed with the niflow-nipype1-examples package, but their continued use is discouraged.

## Interfaces¶

An index of all nipype interfaces is found below. Nipype provides some in-house interfaces to help with workflow management tasks, basic image manipulations, and filesystem/storage interfaces:

Nipype provides interfaces for the following third-party tools:

• AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (fMRI) data.

• ANTs (Advanced Normalization ToolS) computes high-dimensional mappings to capture the statistics of brain structure and function.

• BrainSuite is a collection of open source software tools that enable largely automated processing of magnetic resonance images (MRI) of the human brain.

• BRU2NII is a simple tool for converting Bruker ParaVision MRI data to NIfTI.

• Convert3D is a command-line tool for converting 3D images between common file formats.

• Camino is an open-source software toolkit for diffusion MRI processing.

• Camino-TrackVis allows interoperability between Camino and TrackVis.

• Connectome Mapper (CMP) implements a full processing pipeline for creating multi-variate and multi-resolution connectomes with dMRI data.

• dcm2nii converts images from the proprietary scanner DICOM format to NIfTI

• DCMStack allows series of DICOM images to be stacked into multi-dimensional arrays.

• Diffusion Toolkit is a set of command-line tools with a GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images.

• DIPY is a free and open source software project for computational neuroanatomy, focusing mainly on diffusion magnetic resonance imaging (dMRI) analysis.

• DTITK is a spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data.

• Elastix is a toolbox for rigid and nonrigid registration of images.

• FreeSurfer is an open source software suite for processing and analyzing (human) brain MRI images.

• FSL is a comprehensive library of analysis tools for fMRI, MRI and DTI brain imaging data.

• Matlab script wrapper provides interfaces to integrate matlab scripts within workflows.

• MeshFix converts a raw digitized polygon mesh to a clean mesh where all the occurrences of a specific set of “defects” are corrected.

• MINC Toolkit contains the most commonly used tools developed at the McConnell Brain Imaging Centre, Montreal Neurological Institute.

• MIPAV (Medical Image Processing, Analysis, and Visualization) enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy.

• MNE is a software for exploring, visualizing, and analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, and more.

• MRTrix is a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses (MRTrix3, and the deprecated MRTrix version 2).

• Nifty Tools: NiftyFit is a software package for multi-parametric model-fitting of 4D MRI; NiftyReg is an open-source software for efficient medical image registration; and NiftySeg contains programs to perform EM based segmentation of images in NIfTI or Analyze format.

• NiLearn is a Python library for fast and easy statistical learning on NeuroImaging data.

• NiPy is a Python project for analysis of structural and functional neuroimaging data.

• Nitime is a library for time-series analysis of data from neuroscience experiments.

• PETPVC is toolbox for PVC of PET imaging.

• QuickShear uses a skull-stripped version of an anatomical images as a reference to deface the unaltered anatomical image.

• SEM Tools are useful tools for Structural Equation Modeling.

• SPM (Statistical Parametric Mapping) is a software package for the analysis of brain imaging data sequences.

• VistaSoft contains Matlab code to perform a variety of analysis on MRI data, including functional MRI and diffusion MRI.

• Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

• 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization.