Documentation

Previous versions: 1.2.3 1.2.2

Michael Notter’s Nipype guide

Be sure to read Michael’s excellent tutorials.

Interfaces, Workflows and Examples

Workflows Examples dMRI: Camino, DTI dMRI: Connectivity - Camino, CMTK, FreeSurfer dMRI: Connectivity - MRtrix, CMTK, FreeSurfer dMRI: DTI - Diffusion Toolkit, FSL dMRI: HARDI - Diffusion Toolkit, FSL dMRI: DTI, FSL dMRI: Group connectivity - Camino, FSL, FreeSurfer dMRI: Group connectivity - MRtrix, FSL, FreeSurfer dMRI: DTI - MRtrix, FSL dMRI: Preprocessing dMRI: TBSS on NKI RS data fMRI: OpenfMRI.org data, FSL, ANTS, c3daffine fMRI: surface smooth - FreeSurfer, SPM fMRI: FSL fMRI: FEEDS - FSL fMRI: FSL reuse workflows fMRI: NiPy GLM, SPM fMRI: Coregistration - Slicer, BRAINS fMRI: SPM, FSL fMRI: SPM Auditory dataset fMRI: DARTEL, SPM fMRI: Famous vs non-famous faces, SPM fMRI: SPM nested workflows HOWTO: Using caching without using Workflow rsfMRI: ANTS, FS, FSL, SPM, aCompCor rsfMRI: ANTS, FS, FSL, NiPy, aCompCor Paper: Smoothing comparison sMRI: Using new ANTS for creating a T1 template sMRI: Using ANTS for registration sMRI: Using new ANTS for creating a T1 template (ITK4) sMRI: USing CBS Tools for skullstripping sMRI: FreeSurfer sMRI: FSReconAll sMRI: Regional Tessellation and Surface Smoothing Workflow from scratch Workshop: Dartmouth College 2010

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

Developer Guides

API API caching.memory conftest interfaces.matlab pipeline.engine.base pipeline.engine.nodes pipeline.engine.utils pipeline.engine.workflows sphinxext.plot_workflow

Developer Guide Developer Guide Interface Specifications How to wrap a command line tool How to wrap a MATLAB script How to wrap a Python script Working with nipype source code Architecture (discussions from 2009) W3C PROV support Software using Nipype Testing nipype