User Guide and Examples¶
Michael Notter’s User Guide
Be sure to read Michael’s excellent tutorials.
Examples¶
The following examples are literate programming documents which solve specific problems using Nipype. In some cases, the same problem is solved with multiple underlying tools.
- 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