User:Inorton/dMRI Software List

NA-MIC software

• Slicer
  • http://www.slicer.org
• teem:
  • the Slicer3 interactive DTI implementation is based largely on teem through the vtkTeem libraries.
  • http://teem.sourceforge.net/
• ITK Tensor tools:
  • http://www.itk.org/Doxygen/html/group__TensorObjects.html
• GTRACT
  • command-line tools for DTI pipeline processing
  • http://www.nitrc.org/projects/vmagnotta/
  • http://wiki.slicer.org/slicerWiki/index.php/GTRACT_V4
• UNC DTI Tools (FiberViewer):
  • http://www.niral.unc.edu/
  • http://www.ia.unc.edu/dev/download/index.htm
• Utah DTIProcess
  • http://www.nitrc.org/projects/dtiprocess/

Open source software

• BioImageSuite
  • Interface: GUI
  • License: GPL
  • http://www.bioimagesuite.org/
• DTI-query and CINCH
  • Interface: preprocessing: command line; selection: GUI
  • License: BSD-like
  • http://graphics.stanford.edu/projects/dti/software/
• DTI-TK
  • Interface: command line
  • License: GPL
  • http://www.nitrc.org/projects/dtitk
• FMRIB Diffusion Toolbox
  • Licence: non-commercial (http://www.fmrib.ox.ac.uk/fsl/fsl/licence.html)
  • http://www.fmrib.ox.ac.uk/fsl/fdt/index.html
• Camino
  • Interface: primarily command-line
  • License: OSI Artistic License 2.0
  • http://www.cs.ucl.ac.uk/research/medic/camino/
• BrainVisa
  • Interface: pipeline builder, GUI (Anatomist)
  • License: mix of GPL/LGPL/BSD http://brainvisa.info/doc/brainvisa/en/help/readme.html
  • http://www.brainvisa.info/
• DiPy
  • Interface: programming library.
  • License: New BSD (3-clause)
  • http://nipy.sourceforge.net/dipy/documentation.html
• MITK-DI
  • Interface: GUI
  • ITK-based DI processing classes including Q-ball
  • License: BSD
  • http://www.mitk.org/wiki/DiffusionImaging
• MedInria
  • License: 4-clause BSD
  • http://med.inria.fr/

Closed-source free software

• TrackVis / DTI-Toolkit
  • Purpose: DTI analysis
  • http://www.trackvis.org
• DTI Studio
  • http://www.mristudio.org/
• MevisLab
  • Purpose: module-based, domain-specific application SDK. DTI modules exist.
  • Neurosurgery application (from IEEE Viz 2010): http://www.youtube.com/watch?v=aIgFS1S97GQ
  • http://www.mevislab.de
  • nb: free version has some restrictions on module signing and number of modules.

Commercial software with DTI functionality

• Brain Voyager QX
  • http://www.brainvoyager.com/products/brainvoyagerqx.html
• Analyze
  • http://mayoresearch.mayo.edu/mayo/research/robb_lab/analyze.cfm
  • http://www.analyzedirect.com/
• BrainMagix
  • http://www.imagilys.com/
• Prism Clinical
  • http://www.prismclinical.com

Clinical Software with DTI functionality

• BrainLab iPlan
  • http://www.brainlab.com/
• NordicNeuroLab NordicICE and BrainEx
  • http://www.nordicneurolab.com/
• Siemens "syngo DTI Tractography"
  • [link]
• GE "DTI - complete functional neuroassessment"
  • [link]

dMRI File Formats

NRRD

http://teem.sourceforge.net/nrrd/format.html http://www.vtk.org/Wiki/Getting_Started_with_the_NRRD_Format

Nifti

[DTI-TK]

[Nifti Matrix storage]

[Discussion on teem-users]