Documentation

Release:1.1.1 Date:July 30, 2018, 17:10 PDT

Previous versions: 1.1.0 1.0.4

Michael Notter’s Nipype guide

Be sure to read Michael’s excellent tutorials.

Guides

User User Guide Download and install Neurodocker tutorial Interface caching Nipype tutorials Porcupine graphical interface Using Nipype Plugins Configuration File Debugging Nipype Workflows Nipype Command Line Interface DataGrabber and DataSink explained The SelectFiles Interfaces The Function Interface MapNode, iterfield, and iterables explained JoinNode, synchronize and itersource Model Specification for First Level fMRI Analysis Saving Workflows and Nodes to a file (experimental) Using SPM with MATLAB Common Runtime Using MIPAV, JIST, and CBS Tools Running Nipype Interfaces from the command line (nipype_cmd) Using Nipype with Amazon Web Services (AWS) Resource Scheduling and Profiling with Nipype Sphinx extensions Changes in Nipype

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

Interfaces, Workflows and Examples

Workflows workflows.data workflows.dmri workflows.fmri workflows.misc workflows.rsfmri workflows.smri 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