Difference between revisions of "User:Inorton/dMRI Software List"
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=NA-MIC software= | =NA-MIC software= | ||
| − | *Slicer | + | *Slicer |
** http://www.slicer.org | ** 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= | =Open source software= | ||
| Line 13: | Line 26: | ||
** License: BSD-like | ** License: BSD-like | ||
** http://graphics.stanford.edu/projects/dti/software/ | ** http://graphics.stanford.edu/projects/dti/software/ | ||
| + | *DTI-TK | ||
| + | ** Interface: command line | ||
| + | ** License: GPL | ||
| + | ** http://www.nitrc.org/projects/dtitk | ||
* FMRIB Diffusion Toolbox | * FMRIB Diffusion Toolbox | ||
** Licence: non-commercial (http://www.fmrib.ox.ac.uk/fsl/fsl/licence.html) | ** Licence: non-commercial (http://www.fmrib.ox.ac.uk/fsl/fsl/licence.html) | ||
** http://www.fmrib.ox.ac.uk/fsl/fdt/index.html | ** http://www.fmrib.ox.ac.uk/fsl/fdt/index.html | ||
| − | |||
| − | |||
| − | |||
| − | |||
*Camino | *Camino | ||
** Interface: primarily command-line | ** Interface: primarily command-line | ||
| Line 25: | Line 38: | ||
** http://www.cs.ucl.ac.uk/research/medic/camino/ | ** http://www.cs.ucl.ac.uk/research/medic/camino/ | ||
*BrainVisa | *BrainVisa | ||
| − | ** Interface: pipeline builder | + | ** Interface: pipeline builder, GUI (Anatomist) |
** License: mix of GPL/LGPL/BSD http://brainvisa.info/doc/brainvisa/en/help/readme.html | ** License: mix of GPL/LGPL/BSD http://brainvisa.info/doc/brainvisa/en/help/readme.html | ||
** http://www.brainvisa.info/ | ** 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= | =Closed-source free software= | ||
| Line 46: | Line 70: | ||
**http://www.brainvoyager.com/products/brainvoyagerqx.html | **http://www.brainvoyager.com/products/brainvoyagerqx.html | ||
* Analyze | * Analyze | ||
| + | **http://mayoresearch.mayo.edu/mayo/research/robb_lab/analyze.cfm | ||
**http://www.analyzedirect.com/ | **http://www.analyzedirect.com/ | ||
| − | ** | + | * BrainMagix |
| − | + | **http://www.imagilys.com/ | |
| + | * Prism Clinical | ||
| + | ** http://www.prismclinical.com | ||
=Clinical Software with DTI functionality= | =Clinical Software with DTI functionality= | ||
| − | *BrainLab iPlan | + | * BrainLab iPlan |
**http://www.brainlab.com/ | **http://www.brainlab.com/ | ||
| − | *NordicNeuroLab NordicICE and BrainEx | + | * NordicNeuroLab NordicICE and BrainEx |
**http://www.nordicneurolab.com/ | **http://www.nordicneurolab.com/ | ||
| − | *Siemens "syngo DTI Tractography" | + | * Siemens "syngo DTI Tractography" |
| − | ** | + | **[[https://www.medical.siemens.com/webapp/wcs/stores/servlet/PSOptionProductDisplayView?catalogId=-11&catTree=100010,1007660,12754,1024365&langId=-11&productId=191673&productType=6&storeId=10001 link]] |
| + | * GE "DTI - complete functional neuroassessment" | ||
| + | ** [[https://www2.gehealthcare.com/portal/site/usen/menuitem.c94c459110e10489eb7d9d1074c84130/?vgnextoid=0cdb74f0f8750210VgnVCM10000024dd1403RCRD&productID=89081a8029a30210VgnVCM10000024dd1403____&channelID=ABC link]] | ||
| + | |||
| + | |||
| + | |||
| + | =dMRI File Formats= | ||
| + | ==NRRD== | ||
| + | http://teem.sourceforge.net/nrrd/format.html | ||
| + | http://www.vtk.org/Wiki/Getting_Started_with_the_NRRD_Format | ||
| + | ==Nifti== | ||
| + | [[http://groups.google.com/group/dtitk/web/data-format DTI-TK]] | ||
| + | |||
| + | [[http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1diagrams_v2.pdf Nifti Matrix storage]] | ||
| + | |||
| + | [[http://sourceforge.net/mailarchive/forum.php?thread_name=D6C04AE4-7FDC-47DA-8986-DC5C27498AB4%40uchicago.edu&forum_name=teem-users Discussion on teem-users]] | ||
Latest revision as of 16:04, 6 November 2013
Contents
NA-MIC software
- Slicer
- teem:
- the Slicer3 interactive DTI implementation is based largely on teem through the vtkTeem libraries.
- http://teem.sourceforge.net/
- ITK Tensor tools:
- 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):
- Utah 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
- 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
- Analyze
- BrainMagix
- Prism Clinical
Clinical Software with DTI functionality
- BrainLab iPlan
- NordicNeuroLab NordicICE and BrainEx
- 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]
