Interfaces and Workflows¶
September 11, 2023, 12:32 PDT
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¶
- nipype.algorithms package
- nipype.interfaces package
- 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
- 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