Table 10:
Interfaces between Lead-DBS and other neuroimaging tools. Except for FreeSurfer, all tools are available on Windows, macOS and Linux. Necessary binaries for FSL tools were adapted to work on Windows although there is no official Windows FSL release.
| Tool Name | Tool Website | Tool Task | Type of Interface | Main Tool Publication |
|---|---|---|---|---|
| Statistic Parametric Mapping (SPM) | http://www.fil.ion.ucl.ac.uk/spm/software/spm12/ | Image Registration & Manipulation | Dependency (Matlab Path) | Friston etal. 2004 |
| FMRIB Software Library (FSL) | https://fsl.fmrib.ox.ac.uk/ | Image Registration | Necessary tools included | Woolrich et al. 2009 |
| Advanced Normalization Tools (ANTs) http://stnava.github.io/ANTs/ | Image Registration | Included | Avants etal. 2008 | |
| 3D Slicer | https://www.slicer.org/ | Image Visualization | Dependency, direct uplink via Python calls (System Path) | Fedorov etal. 2012 |
| SurfIce | https://www.nitrc.org/projects/surfice/ | Surface Visualization | Included | – |
| BRAINSFit | https://www.nitrc.org/projects/multimodereg/ | Image Registration | Included | Johnson etal. 2007 |
| FieldTrip | http://www.fieldtriptoolbox.org/ | Mesh Generation | Necessary tools adapted / included | Oostenvel et al. 2010 |
| SimBio | https://www.mrt.uni-jena.de/simbio/ | FEM Modeling | Necessary tools adapted / included | Vorwerk etal. 2018 |
| SUIT | http://www.diedrichsenlab.org/imaging/suit.htm | Specialized Registration (Brainstem) | Dependency (Matlab Path) | Diedrichsen et al. 2006 |
| FreeSurfer | https://surfer.nmr.mgh.harvard.edu/ | Surface Reconstruction (ECoG Electrodes) | Dependency (system calls) | Dale et al. 1999 |
| Computational Anatomy Toolbox (CAT) | http://www.neuro.uni-jena.de/cat/ | Surface Reconstruction (ECoG Electrodes) | Dependency (Matlab Path) | Gaser and Dahnke 2016 |
| PaCER | https://adhusch.github.io/PaCER/ | Electrode Localization | Included | Husch etal. 2017 |
| dcm2nii, dcm2niix, dicm2nii | https://www.nitrc.org/projects/dcm2nii/ | DICOM import | Included | Li et al. 2016 |
| Gibbs’ Tracker | https://www.uniklinik-freiburg.de/mr-en/research-groups/diffperf/fibertools.html | Fiber tracking | Included | Reisert etal. 2011 |
| Model-Free Mesotracker | https://bitbucket.org/reisert/mesoft_v1 | Fiber tracking | Included | Konopleva et al. 2018 |
| DSI Studio | http://dsi-studio.labsolver.org | Fiber tracking | Included | Yeh et al. 2010 |
| Gibbs’ Ringing Artifact Removal Tool | https://bitbucket.org/reisert/unring | dMRI preprocessing | Included | Kellner etal. 2015 |
| Network Based Statistics (NBS) | https://sites.google.com/site/bctnet/comparison/nbs | Graph-Theory Level Statistics | Included | Zalesky etal. 2010 |