Documentation

Release:0.13.0-rc1 Date:January 04, 2017, 22:33 PDT

Previous versions: 0.12.0 0.11.0

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 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) Changes in Nipype

Developer API caching.memory interfaces.base interfaces.matlab pipeline.engine.base pipeline.engine.nodes pipeline.engine.utils pipeline.engine.workflows 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.camino.connectivity_mapping workflows.dmri.camino.diffusion workflows.dmri.camino.group_connectivity workflows.dmri.connectivity.group_connectivity workflows.dmri.connectivity.nx workflows.dmri.dipy.denoise workflows.dmri.fsl.artifacts workflows.dmri.fsl.dti workflows.dmri.fsl.epi workflows.dmri.fsl.tbss workflows.dmri.fsl.utils 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.autorecon1 workflows.smri.freesurfer.autorecon2 workflows.smri.freesurfer.bem workflows.smri.freesurfer.recon 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: 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 interfaces.afni.preprocess interfaces.afni.svm interfaces.afni.utils interfaces.ants.legacy interfaces.ants.registration interfaces.ants.resampling interfaces.ants.segmentation interfaces.ants.utils interfaces.ants.visualization interfaces.brainsuite.brainsuite interfaces.bru2nii interfaces.c3 interfaces.camino.calib interfaces.camino.connectivity interfaces.camino.convert interfaces.camino.dti interfaces.camino.odf interfaces.camino.utils 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.base interfaces.dipy.preprocess interfaces.dipy.reconstruction interfaces.dipy.simulate interfaces.dipy.tensors interfaces.dipy.tracks interfaces.dynamic_slicer interfaces.elastix.registration interfaces.elastix.utils interfaces.freesurfer.longitudinal interfaces.freesurfer.model interfaces.freesurfer.preprocess interfaces.freesurfer.registration interfaces.freesurfer.utils interfaces.fsl.dti interfaces.fsl.epi interfaces.fsl.maths interfaces.fsl.model interfaces.fsl.possum interfaces.fsl.preprocess interfaces.fsl.utils interfaces.io interfaces.meshfix interfaces.minc.base interfaces.minc.minc interfaces.minc.testdata interfaces.mipav.developer interfaces.mne.base interfaces.mrtrix.convert interfaces.mrtrix.preprocess interfaces.mrtrix.tensors interfaces.mrtrix.tracking interfaces.mrtrix3.base interfaces.mrtrix3.connectivity interfaces.mrtrix3.preprocess interfaces.mrtrix3.reconst interfaces.mrtrix3.tracking interfaces.mrtrix3.utils interfaces.nilearn interfaces.nipy.model interfaces.nipy.preprocess interfaces.nipy.utils interfaces.nitime.analysis interfaces.petpvc interfaces.semtools.brains.classify interfaces.semtools.brains.segmentation interfaces.semtools.brains.utilities interfaces.semtools.converters interfaces.semtools.diffusion.diffusion interfaces.semtools.diffusion.gtract interfaces.semtools.diffusion.maxcurvature interfaces.semtools.diffusion.tractography.commandlineonly interfaces.semtools.diffusion.tractography.fiberprocess interfaces.semtools.diffusion.tractography.fibertrack interfaces.semtools.diffusion.tractography.ukftractography interfaces.semtools.featurecreator interfaces.semtools.filtering.denoising interfaces.semtools.filtering.featuredetection interfaces.semtools.legacy.registration interfaces.semtools.registration.brainsfit interfaces.semtools.registration.brainsresample interfaces.semtools.registration.brainsresize interfaces.semtools.registration.specialized interfaces.semtools.segmentation.specialized interfaces.semtools.utilities.brains 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 interfaces.vtkbase