Documentation

Release:0.9.2 Date:February 04, 2014, 13:51 PDT

Previous versions: 0.8 0.7

Guides

User User Guide Download and install Running Nipype in a VM Tutorial : Interfaces Interface caching Tutorial : Workflows Using Nipype Plugins Configuration File Debugging Nipype Workflows 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 Changes in Nipype

Developer API caching.memory interfaces.base interfaces.matlab pipeline.engine 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

Interfaces, Workflows and Examples

Workflows workflows.dmri.camino.connectivity_mapping workflows.dmri.camino.diffusion workflows.dmri.camino.group_connectivity workflows.dmri.connectivity.group_connectivity workflows.dmri.connectivity.nx workflows.dmri.fsl.dti workflows.dmri.fsl.epi workflows.dmri.fsl.tbss workflows.dmri.mrtrix.connectivity_mapping workflows.dmri.mrtrix.diffusion workflows.dmri.mrtrix.group_connectivity workflows.fmri.fsl.estimate workflows.fmri.fsl.preprocess workflows.fmri.spm.preprocess workflows.misc.utils workflows.rsfmri.fsl.resting workflows.smri.ants.ANTSBuildTemplate workflows.smri.ants.antsRegistrationBuildTemplate workflows.smri.freesurfer.bem workflows.smri.freesurfer.utils 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: TBSS on NKI RS data fMRI: surface smooth - FreeSurfer, SPM fMRI: FSL fMRI: FEEDS - FSL fMRI: FSL reuse workflows fMRI: NiPy GLM, SPM fMRI: OpenfMRI.org data, FSL 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: FSL - CSF regressed rsfMRI: FSL, Nipype, tCompCorr rsfMRI: AFNI, ANTS, DicomStack, FreeSurfer, FSL, Nipy, aCompCorr 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: FreeSurfer sMRI: Regional Tessellation and Surface Smoothing Workflow from scratch Workshop: Dartmouth College 2010

Interfaces algorithms.icc algorithms.mesh algorithms.misc algorithms.modelgen algorithms.rapidart interfaces.afni.preprocess interfaces.ants.legacy interfaces.ants.registration interfaces.ants.resampling interfaces.ants.segmentation interfaces.ants.utils interfaces.c3 interfaces.camino.calib interfaces.camino.connectivity interfaces.camino.convert interfaces.camino.dti interfaces.camino.odf interfaces.camino2trackvis.convert interfaces.cmtk.cmtk interfaces.cmtk.convert interfaces.cmtk.nbs interfaces.cmtk.nx interfaces.cmtk.parcellation interfaces.dcm2nii interfaces.dcmstack interfaces.diffusion_toolkit.dti interfaces.diffusion_toolkit.odf interfaces.diffusion_toolkit.postproc interfaces.dipy.tensors interfaces.dipy.tracks interfaces.dynamic_slicer interfaces.freesurfer.model interfaces.freesurfer.preprocess interfaces.freesurfer.utils interfaces.fsl.dti interfaces.fsl.epi interfaces.fsl.maths interfaces.fsl.model interfaces.fsl.preprocess interfaces.fsl.utils interfaces.io interfaces.meshfix interfaces.mne.base interfaces.mrtrix.convert interfaces.mrtrix.preprocess interfaces.mrtrix.tensors interfaces.mrtrix.tracking interfaces.nipy.model interfaces.nipy.preprocess interfaces.nipy.utils interfaces.nitime.analysis interfaces.slicer.base interfaces.slicer.converters interfaces.slicer.diffusion.diffusion interfaces.slicer.filtering.arithmetic interfaces.slicer.filtering.checkerboardfilter interfaces.slicer.filtering.denoising interfaces.slicer.filtering.extractskeleton interfaces.slicer.filtering.histogrammatching interfaces.slicer.filtering.imagelabelcombine interfaces.slicer.filtering.morphology interfaces.slicer.filtering.n4itkbiasfieldcorrection interfaces.slicer.filtering.resamplescalarvectordwivolume interfaces.slicer.filtering.thresholdscalarvolume interfaces.slicer.filtering.votingbinaryholefillingimagefilter interfaces.slicer.legacy.converters interfaces.slicer.legacy.diffusion.denoising interfaces.slicer.legacy.filtering interfaces.slicer.legacy.registration interfaces.slicer.legacy.segmentation interfaces.slicer.quantification.changequantification interfaces.slicer.quantification.petstandarduptakevaluecomputation interfaces.slicer.registration.brainsfit interfaces.slicer.registration.brainsresample interfaces.slicer.registration.specialized interfaces.slicer.segmentation.simpleregiongrowingsegmentation interfaces.slicer.segmentation.specialized interfaces.slicer.surface interfaces.slicer.utilities interfaces.spm.model interfaces.spm.preprocess interfaces.spm.utils interfaces.utility interfaces.vista.vista