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# Interfaces and Workflows

Release:

  1.9.2

Date:

  May 18, 2025, 16:39 PDT

Previous versions: 1.9.1 1.9.0

## 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:

> - Algorithms

> - Image manipulation

> - I/O Operations

> - Self-reporting interfaces

> - Utilities

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

- nipype.algorithms package
  - Submodules
    - nipype.algorithms.confounds module
    - nipype.algorithms.icc module
    - nipype.algorithms.mesh module
    - nipype.algorithms.metrics module
    - nipype.algorithms.misc module
    - nipype.algorithms.modelgen module
    - nipype.algorithms.rapidart module
    - nipype.algorithms.stats module
- nipype.interfaces package
  - Subpackages
    - nipype.interfaces.afni package
    - nipype.interfaces.ants package
    - nipype.interfaces.base package
    - nipype.interfaces.brainsuite package
    - nipype.interfaces.camino package
    - nipype.interfaces.camino2trackvis package
    - nipype.interfaces.cat12 package
    - nipype.interfaces.cmtk package
    - nipype.interfaces.diffusion_toolkit package
    - nipype.interfaces.dipy package
    - nipype.interfaces.dtitk package
    - nipype.interfaces.elastix package
    - nipype.interfaces.freesurfer package
    - nipype.interfaces.fsl package
    - nipype.interfaces.minc package
    - nipype.interfaces.mipav package
    - nipype.interfaces.mixins package
    - nipype.interfaces.mne package
    - nipype.interfaces.mrtrix package
    - nipype.interfaces.mrtrix3 package
    - nipype.interfaces.niftyfit package
    - nipype.interfaces.niftyreg package
    - nipype.interfaces.niftyseg package
    - nipype.interfaces.nipy package
    - nipype.interfaces.nitime package
    - nipype.interfaces.robex package
    - nipype.interfaces.semtools package
    - nipype.interfaces.slicer package
    - nipype.interfaces.spm package
    - nipype.interfaces.utility package
    - nipype.interfaces.vista package
    - nipype.interfaces.workbench package
  - Submodules
    - nipype.interfaces.bru2nii module
    - nipype.interfaces.c3 module
    - nipype.interfaces.dcm2nii module
    - nipype.interfaces.dcmstack module
    - nipype.interfaces.dynamic_slicer module
    - nipype.interfaces.image module
    - nipype.interfaces.io module
    - nipype.interfaces.matlab module
    - nipype.interfaces.meshfix module
    - nipype.interfaces.nilearn module
    - nipype.interfaces.petpvc module
    - nipype.interfaces.quickshear module
    - nipype.interfaces.r module
    - nipype.interfaces.vtkbase module