Tools

Diffusion analysis software available for download:

1. 3D Slicer:
http://slicer.org: Slicer2 diffusion module: Laboratory of Mathematics in Imaging, BWH Harvard Medical School
http://slicer.org: Slicer3 platform collaborative development within NA-MIC. NA-MIC wiki: http://www.na-mic.org/Wiki/index.php/Main_Page
Reads dicom data. For diffusion data, the nrrd data format is preferred.

2. MRIStudio: Susumu Mori's lab
https://www.mristudio.org/ Reads dicom data. Works on data from most scanner vendors.

3. MedINRIA: INRIA, Xavier Pennec and Pierre Fillard
http://www-sop.inria.fr/asclepios/software/MedINRIA/

4. FIberTracking: UNC Guido Gerig et al.
http://www.ia.unc.edu/dev/download/fibertracking/index.htm

5. FiberViewer: UNC Guido Gerig et al.
http://www.ia.unc.edu/dev/download/fiberviewer/index.htm

6. Volume-one:
http://www.volume-one.org/
Reads dicom data.

7. Camino: Danny Alexander
http://www.camino.org.uk

8. FSL: FMRIB's Diffusion Toolbox
http://www.fmrib.ox.ac.uk/fsl/fdt/index.html

9. CATNAP: Jerry Prince's lab
http://www.nbirn.net/tools/catnap/index.shtm
Reads dicom data. Prefers Phillips data.

10. DTI Deformable Registration: Section of Biomedical Image Analysis
https://www.rad.upenn.edu/sbia/software/index.html

11. BrainVisa (SHFJ-IFR 49 - Paris)
http://brainvisa.info/
Some plugins to BrainVisa related to the work on Q-Ball imaging developed at INRIA Odyssee are available on request. Send email to with cc to

12. The INRIA Odyssée Geodesic Connectivity Mapping Library
http://gcm.gforge.inria.fr/index.html

13. Odyssée QBall plug-in for Slicer3D 3.3
http://www-sop.inria.fr/odyssee/en/software/QBallSlicer

14. TBSS 3D skeletonization by Steve Smith (University of Oxford)
http://www.fmrib.ox.ac.uk/fsl/tbss/index.html
"Tract-Based Spatial Statistics", Audio (https://www.ipam.ucla.edu/publications/mbi2008/mbi2008_7404.mp3), Presentation (https://www.ipam.ucla.edu/publications/mbi2008/mbi2008_7404.pdf)

15. Multi-fiber reconstruction software, Bing Jian and Baba C. Vemuri
Code for Modeling and Reconstruction of Diffusion MR Images
http://code.google.com/p/diffusion-mri/