3rd Party Diffusion MRI Software: Difference between revisions

From VrlWiki
Jump to navigation Jump to search
← Older editNewer edit →
Jadrian Miles (talk | contribs)
1,787 edits
Brad installed some stuff!
Jadrian Miles (talk | contribs)
1,787 edits
No edit summary
Line 8: Line 8:
! {{Hl2}} | <abbr title="Installed in $G?">inst</abbr>
! {{Hl2}} | <abbr title="Installed in $G?">inst</abbr>
! {{Hl2}} | Notes
! {{Hl2}} | Notes
|-
| [http://www.fmrib.ox.ac.uk/fsl/ FSL] || Lin, Win, Mac || {{y}} || {{y}} || GUI, plus CLI for individual processing steps.  Contains FLIRT, etc.
|-
| [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] || Java || {{y}} || {{y}} || No GUI.  CLI for individual processing steps, connected by Unix pipes.  Diverse collection of algorithmic alternatives.
|-
| [http://www.trackvis.org/ Trackvis and Diffusion Toolkit] || Lin, Win, Mac || {{n}} || {{y}} || Equivalent, respectively, to [[Brainapp]] and the [[diffusion processing pipeline]], plus a GUI for the latter.  Handles Q-ball imaging as well as DTI.  Developed at MGH.
|-
| [http://xmedcon.sourceforge.net/ XMedCon] || Lin, Win || {{y}} || {{y}} || Command-line converter for various medical imaging file formats.
|-
|-
| [http://www.slicer.org/ 3D Slicer] || Lin, Win, Mac || {{y}} || {{n}}
| [http://www.slicer.org/ 3D Slicer] || Lin, Win, Mac || {{y}} || {{n}}
|-
| [http://www.fmrib.ox.ac.uk/fsl/ FSL] || Lin, Win, Mac || {{y}} || {{y}} || GUI, plus CLI for individual processing steps.  Contains FLIRT, etc.
|-
|-
| [http://www-sop.inria.fr/asclepios/software/MedINRIA/ MedINRIA] || Lin, Win, Mac || {{n}} || {{n}}
| [http://www-sop.inria.fr/asclepios/software/MedINRIA/ MedINRIA] || Lin, Win, Mac || {{n}} || {{n}}
|-
| [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] || Java || {{y}} || {{y}} || No GUI.  CLI for individual processing steps, connected by Unix pipes.  Diverse collection of algorithmic alternatives.
|-
|-
| [http://graphics.stanford.edu/projects/dti/software/ DTI-Query] || Lin, Win, Mac || {{y}} || {{n}}
| [http://graphics.stanford.edu/projects/dti/software/ DTI-Query] || Lin, Win, Mac || {{y}} || {{n}}
Line 21: Line 25:
| [http://graphics.stanford.edu/projects/dti/software/ CINCH] || Lin, Win, Mac || {{n}} || {{n}}
| [http://graphics.stanford.edu/projects/dti/software/ CINCH] || Lin, Win, Mac || {{n}} || {{n}}
|-
|-
| [http://mristudio.org MRI Studio] (formerly DTI Studio) || Win || {{n}} || {{n}}
| [http://mristudio.org MRI Studio] (formerly DTI Studio) || Win || {{n}} || {{n}} || Interactive GUI to read/write images, compute DTIs and tractography, and create ROIs.  Supposedly also includes [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478641 Mori, et al.'s 2008 multi-subject DTI-based WM atlas].
|-
| [http://www.trackvis.org/ Trackvis and Diffusion Toolkit] || Lin, Win, Mac || {{n}} || {{y}} || Despite the name, Diffusion Toolkit is a GUI program, not a library.
|-
|-
| [http://surfer.nmr.mgh.harvard.edu/ Freesurfer] || Lin, Mac || {{n}} || {{n}} || GUI, plus CLI for individual processing steps.
| [http://surfer.nmr.mgh.harvard.edu/ Freesurfer] || Lin, Mac || {{n}} || {{n}} || GUI, plus CLI for individual processing steps.
|-
|-
| [http://www.crsltd.com/catalog/brainvoyagerqx/index.html Brain Voyager] || Lin, Win, Mac || {{n}} || {{n}} || Yet another diffusion MRI GUI program.  Commercial license for all users.
| [http://www.crsltd.com/catalog/brainvoyagerqx/index.html Brain Voyager] || Lin, Win, Mac || {{n}} || {{n}} || Yet another diffusion MRI GUI program.  Commercial license for all users.
|-
| [http://xmedcon.sourceforge.net/ XMedCon] || Lin, Win || {{y}} || {{y}} || Command-line converter for various medical imaging file formats.
|-
|-
| [http://amide.sourceforge.net AMIDE] || Lin, Win || {{y}} || {{n}} || Graphical tool similar to FSL for viewing, registration, etc.
| [http://amide.sourceforge.net AMIDE] || Lin, Win || {{y}} || {{n}} || Graphical tool similar to FSL for viewing, registration, etc.

Revision as of 18:47, 4 December 2009

This page is a repository for information about programs that other people have written to process and visualize diffusion MRI data. By examining features of these other programs, we may get inspiration for improvements in our own work.

Name Platform src inst Notes
FSL Lin, Win, Mac Y Y GUI, plus CLI for individual processing steps. Contains FLIRT, etc.
Camino Java Y Y No GUI. CLI for individual processing steps, connected by Unix pipes. Diverse collection of algorithmic alternatives.
Trackvis and Diffusion Toolkit Lin, Win, Mac N Y Equivalent, respectively, to Brainapp and the diffusion processing pipeline, plus a GUI for the latter. Handles Q-ball imaging as well as DTI. Developed at MGH.
XMedCon Lin, Win Y Y Command-line converter for various medical imaging file formats.
3D Slicer Lin, Win, Mac Y N
MedINRIA Lin, Win, Mac N N
DTI-Query Lin, Win, Mac Y N
CINCH Lin, Win, Mac N N
MRI Studio (formerly DTI Studio) Win N N Interactive GUI to read/write images, compute DTIs and tractography, and create ROIs. Supposedly also includes Mori, et al.'s 2008 multi-subject DTI-based WM atlas.
Freesurfer Lin, Mac N N GUI, plus CLI for individual processing steps.
Brain Voyager Lin, Win, Mac N N Yet another diffusion MRI GUI program. Commercial license for all users.
AMIDE Lin, Win Y N Graphical tool similar to FSL for viewing, registration, etc.
SPM Matlab Y N Designed for data sequences, as found in fMRI studies.
AFNI Lin, Mac Y N A GUI tool like Slicer mainly designed for fMRI data.

See Also

  • 3rd Party Visualization Software, which includes toolkits whose functionality is a superset of diffusion MRI processing.
  • NITRC, the NIH's Sourceforge-like repository of neuroimaging software
  • IDoImaging.com, a database of freeware medical imaging programs and libraries
Retrieved from "http://vrl.cs.brown.edu/wiki/index.php?title=3rd_Party_Diffusion_MRI_Software&oldid=3941"