Interfaces and Workflows




June 16, 2021, 13:18 PDT

Previous versions: 1.6.0 1.5.1



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.


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.

  • CAT12 (Computational Anatomy Toolbox) extends SPM12 to provide computational anatomy.

  • 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.

Index of Interfaces