3rd Party Diffusion MRI Software: Difference between revisions

Latest revision as of 15:35, 2 November 2012

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
Diffusion Processing & Tractography
FSL	Lin, Win, Mac	Y	Y	GUI, plus CLI for individual processing steps. Includes implementations of mutual information linear registration, nonlinear registration, brain extraction, qball modelling, stick-and-ball modelling, probabilistic tractography. Includes numerous volumetric atlases.
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.
MedINRIA	Lin, Win, Mac	N	N
DTI-Query	Lin, Win, Mac	Y	N
CINCH	Lin, Win, Mac	N	N
Freesurfer	Lin, Mac	N	N	GUI, plus CLI for individual processing steps.
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.
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.
Image Viewing & Conversion
AFNI	Lin, Mac	Y	N	A GUI tool for viewing, transforming, and analyzing 2D slice views of images, especially DICOMs. Very powerful, commonly used for published analysis, designed around medical research and clinical uses.
OsiriX	Mac	Y	N	A less sophisticated, user-friendlier, AFNI-like GUI tool for DICOM viewing.
3D Slicer	Lin, Win, Mac	Y	N	An even less sophisticated and user-friendlier AFNI-like GUI tool.
MRIcron	Lin, Win, Mac	N	N	A GUI viewer for NIfTI. Also includes the `dcm2nii` DICOM-to-NIfTI conversion program.
XMedCon	Lin, Win	Y	Y	Command-line converter for various medical imaging file formats.
SPM	Matlab	Y	N	Designed for data sequences, as found in fMRI studies.
Diffusion Simulation
DifSim	Lin	Y	N	Low-level physics simulations of diffusion MRI response in complex micro-environments. Built on top of MCell.

@@ Line 9: / Line 9: @@
 ! {{Hl2}} | Notes
 |-
-| [http://www.slicer.org/ 3D Slicer] || Lin, Win, Mac || {{y}} || {{n}}
+| colspan=5 align=center | '''Diffusion Processing & Tractography'''
 |-
-| [http://www.fmrib.ox.ac.uk/fsl/ FSL] || Lin, Win, Mac || {{y}} || {{n}} || GUI, plus CLI for individual processing steps.  Contains FLIRT, etc.
+| [http://www.fmrib.ox.ac.uk/fsl/ FSL] || Lin, Win, Mac || {{y}} || {{y}} || GUI, plus CLI for individual processing steps.  Includes implementations of mutual information linear registration, nonlinear registration, brain extraction, qball modelling, stick-and-ball modelling, probabilistic tractography.  Includes numerous volumetric atlases.
 |-
-| [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://www.cs.ucl.ac.uk/research/medic/camino/ Camino] || Java || {{y}} || {{n}} || 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://teem.sourceforge.net/ Teem] || Lin, Win, Mac || {{y}} || {{n}} || Gordon Kindlmann's library of raster filtering utilities, under active development.
+| [http://www-sop.inria.fr/asclepios/software/MedINRIA/ MedINRIA] || Lin, Win, Mac || {{n}} || {{n}}
 |-
 | [http://graphics.stanford.edu/projects/dti/software/ DTI-Query] || Lin, Win, Mac || {{y}} || {{n}}
@@ Line 23: / Line 23: @@
 | [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://surfer.nmr.mgh.harvard.edu/ Freesurfer] || Lin, Mac || {{n}} || {{n}} || GUI, plus CLI for individual processing steps.
+|-
+| [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.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://amide.sourceforge.net AMIDE] || Lin, Win || {{y}} || {{n}} || Graphical tool similar to FSL for viewing, registration, etc.
+|-
+| colspan=5 align=center | '''Image Viewing & Conversion'''
+|-
+| [http://afni.nimh.nih.gov/afni AFNI] || Lin, Mac || {{y}} || {{n}} || A GUI tool for viewing, transforming, and analyzing 2D slice views of images, especially DICOMs.  Very powerful, commonly used for published analysis, designed around medical research and clinical uses.
+|-
+| [http://www.osirix-viewer.com OsiriX] || Mac || {{y}} || {{n}} || A less sophisticated, user-friendlier, AFNI-like GUI tool for DICOM viewing.
 |-
-| [http://www.trackvis.org/ Trackvis and Diffusion Toolkit] || Lin, Win, Mac || {{n}} || {{n}} || Despite the name, Diffusion Toolkit is a GUI program, not a library.
+| [http://www.slicer.org/ 3D Slicer] || Lin, Win, Mac || {{y}} || {{n}} || An even less sophisticated and user-friendlier AFNI-like GUI tool.
 |-
-| [http://surfer.nmr.mgh.harvard.edu/ Freesurfer] || Lin, Mac || {{n}} || {{n}} || GUI, plus CLI for individual processing steps.
+| [http://www.cabiatl.com/mricro/mricron/index.html MRIcron] || Lin, Win, Mac || {{n}} || {{n}} || A GUI viewer for NIfTI.  Also includes the <tt>dcm2nii</tt> DICOM-to-NIfTI conversion program.
 |-
-| [http://www.crsltd.com/catalog/brainvoyagerqx/index.html Brain Voyager] || Lin, Win, Mac || {{n}} || {{n}} || Commercial license for all users.
+| [http://xmedcon.sourceforge.net/ XMedCon] || Lin, Win || {{y}} || {{y}} || Command-line converter for various medical imaging file formats.
 |-
 | [http://www.fil.ion.ucl.ac.uk/spm/ SPM] || Matlab || {{y}} || {{n}} || Designed for data sequences, as found in fMRI studies.
+|-
+| colspan=5 align=center | '''Diffusion Simulation'''
+|-
+| [http://csci.ucsd.edu/projects/simulation.html DifSim] || Lin || {{y}} || {{n}} || Low-level physics simulations of diffusion MRI response in complex micro-environments. Built on top of [http://www.mcell.cnl.salk.edu/ MCell].
 |}
 == See Also ==
 * [[3rd Party Visualization Software]], which includes toolkits whose functionality is a superset of diffusion MRI processing.
+* [http://www.nitrc.org/ <abbr title="Neuroimaging Informatics Tools and Resources Clearinghouse">NITRC</abbr>], the NIH's Sourceforge-like repository of neuroimaging software
+* [http://www.idoimaging.com IDoImaging.com], a database of freeware medical imaging programs and libraries
 [[Category:Diffusion MRI]][[Category:Software]]

3rd Party Diffusion MRI Software: Difference between revisions

Latest revision as of 15:35, 2 November 2012

See Also

Navigation menu

Search