Software

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)

Literature

These are publications relevant to some of the talks. This page is being continuously updated, so please check back for material for other talks.

Daniel Alexander

• Alexander, D. C. and Barker, G. J., Optimal imaging parameters for fibre-orientation estimation in diffusion MRI,NeuroImage,2005, 27, 357-367.
• Alexander, D. C. Multiple fibre reconstructions for diffusion MRI , Annals of the New York Academy of Sciences, 2005, 1046, 113-133
• Alexander, D. C. and Barker, G. J. and Arridge, S. R. , Detection and modeling of non-Gaussian apparent diffusion coefficient profiles in human brain data, Magnetic Resonance in Medicine, 2002, 48, 331--340
• Tuch, D. S. and Reese, T. G. and Wiegell, M. R. and Wedeen, V. J, Diffusion MRI of complex neural architecture, Neuron, 2003, 40, 885--895
• Tuch, D. S. and Reese, T. G. and Wiegell, M. R. and Makris, N and Belliveau, J. W. and Wedeen, V. J., High angular resolution diffusion imaging reveals intravoxelwhite matter fiber heterogeneity, Magnetic Resonance in Medicine, 2002, 48, 577--582
• Tournier, J-D. and Calamante, F. and Gadian, D. G. and Connelly, A., Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution, NeuroImage? , 2004, 23, 1176--1185
• Tournier, J-D. and Calamante, F. and Connelly, A., Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution,NeuroImage,2007, 35, 1459--1472
• Seunarine, K. K. and Cook, P. A. and Hall, M. G. and Embleton, K. and Parker, G. J. M. and Alexander, D. C., Exploiting peak anisotropy for tracking through complex structures., Proc. ICCV workshop on MMBIA, 2007.

Rachid Deriche

• M. Descoteaux, R. Deriche, T. Knoesche and A. Anwander. Deterministic and Probabilistic Tractography Based on Complex Fiber Orientation Distributions. IEEE Transactions in Medical Imaging, accepted July 6th 2008. ftp://ftp-sop.inria.fr/odyssee/Publications/2008/descoteaux-deriche:08.pdf
• M. Descoteaux and R. Deriche. High Angular Resolution Diffusion MRI Segmentation Using Region-Based Statistical Surface Evolution. Journal of Mathetical Imaging in Vision, special issue on Mathematics in Image Analysis , in press 2008. ftp://ftp-sop.inria.fr/odyssee/Publications/2008/descoteaux-deriche:08.pdf
• M. Descoteaux and R. Deriche. Mapping neuronal fiber crossings in the human brain. SPIE Newsroom , August 2008. ftp://ftp-sop.inria.fr/odyssee/Publications/2008/descoteaux-deriche-spie08.pdf
• J. Cohen-Adad, M. Descoteaux, S. Rossignol, R. D Hoge, R. Deriche and H. Benali. Detection of multiple pathways in the spinal cord using q-ball imaging , NeuroImage? , Volume 42, Issue 2, 15 August 2008, Pages 739-749. ftp://ftp-sop.inria.fr/odyssee/Publications/2008/cohen-descoteaux-etal-ni08.pdf
• P. Savadjiev, J. S.W. Campbell, M. Descoteaux, R. Deriche, G. B. Pike and K. Siddiqi. Labeling of ambiguous sub-voxel fibre bundle configurations in high angular resolution diffusion MRI. NeuroImage? , Volume 41, Issue 1, Pages 58-68, 2008 ftp://ftp-sop.inria.fr/odyssee/Publications/2008/savadjiev-campbell-etal:08.pdf
• D. Wassermann, M. Descoteaux and R. Deriche. Diffusion Maps Clustering for Magnetic Resonance Q-Ball Imaging Segmentation. International Journal on Biomedical Imaging, special issue on Recent Advances in NeuroImaging? Methodology , Volume 2008, 2008. ftp://ftp-sop.inria.fr/odyssee/Publications/2008/wassermann-descoteaux-etal:08.pdf
• M. Descoteaux, E. Angelino, S. Fitzgibbons, R. Deriche Regularized, Fast and Robust Analytical Q-Ball Imaging, Magnetic Resonance in Medicine, Volume 58, Issue 3. Pages 497-510. ftp://ftp-sop.inria.fr/odyssee/Publications/2007/descoteaux-angelino-etal:07.pdf
• Maxime Descoteaux, Elaine Angelino, Shaun Fitzgibbons, Rachid Deriche Apparent Diffusion Coefficients from High Angular Resolution Diffusion Images: Estimation and Applications Magnetic Resonance in Medicine Volume 56, Issue 2, Pages 395-410, August 2006. ftp://ftp-sop.inria.fr/odyssee/Publications/2006/descoteaux-angelino-etal:06c.pdf
• A. Ghosh, M. Descoteaux and R. Deriche. Riemannian Framework for estimating Symmetric Positive Definite 4th Order Diffusion Tensors, Medical Image Computing and Computer Assisted Intervention (MICCAI) 2008, New York, USA, September 2008. ftp://ftp-sop.inria.fr/odyssee/Publications/2008/ghosh-descoteaux-etal:08b.pdf
• A. Ghosh, E.Tsigaridas, M. Descoteaux, P. Comon,B.Mourrain and R. Deriche. A polynomial based approach to extract the maxima of an antipodally symmetric spherical function and its application to extract fiber directions from the Orientation Distribution Function in Diffusion MRI MICCAI:08 Workshop on Computational Diffusion MRI, September 10, 2008, NY ftp://ftp-sop.inria.fr/odyssee/Publications/2008/ghosh-descoteaux-etal:08c.pdf
• R. Deriche, D. Tschumperlé, C. Lenglet and M. Rousson. Variational Approaches to the Estimation, Regularization and Segmentation of Diffusion Tensor Images, in: Mathematical Models in Computer Vision: The Handbook, N. Paragios, Y. Chen, O. Faugeras (editors), Springer, 2005, chap. 32, p. 519–532. ftp://ftp-sop.inria.fr/odyssee/Publications/2005/deriche-tschumperle-etal:05.pdf
• C.A. Castaño Moraga, C. Lenglet, R. Deriche, J. Ruiz-Alzola, A Riemannian Approach to Anisotropic Filtering of Tensor Fields Signal Processing, 87(2), 263-276, February 2007 ftp://ftp-sop/odyssee/Publications/2006/castano-moraga-lenglet-etal:06.pdf
• C. Lenglet, M. Rousson, R. Deriche, DTI Segmentation by Statistical Surface Evolution, IEEE Transactions on Medical Imaging, 25(6), 685-700, June 2006 ftp://ftp-sop/odyssee/Publications/2006/lenglet-rousson-etal:06c.pdf
• C. Lenglet, M. Rousson, R. Deriche, O. Faugeras, Statistics on the Manifold of Multivariate Normal Distributions: Theory and Application to Diffusion Tensor MRI Processing, Journal of Mathematical Imaging and Vision, 25(3), 423-444, October 2006. ftp://ftp-sop.inria.fr/odyssee/Publications/2006/lenglet-rousson-etal:06.pdf
• C. Chefd'hotel, D. Tschumperlé, R. Deriche, O. Faugeras. Regularizing Flows for Constrained Matrix-Valued Images, In: Journal of Mathematical Imaging and Vision, 2004, vol. 20, no 1-2, p. 147–162. ftp://ftp-sop.inria.fr/odyssee/Publications/2004/chefdhotel-tschumperle-etal:04.pdf

Guido Gerig

• Casey Goodlett, Brad Davis, Remi Jean, John Gilmore, Guido Gerig. Improved Correspondence for DTI Population Studies via Unbiased Atlas Building. Proc. MICCAI 2006, Springer LNCS vol. 4191, pp. 260 - 267.
• Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Isabelle Corouge, P.Thomas Fletcher, Sarang Joshi, Sylvain Gouttard, Guido Gerig, Medical Image Analysis 10 (2006), 786 - 798
• A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI P. Thomas Fletcher, Ran Tao, Won-Ki Jeong, and Ross T. Whitaker, Proc. IPMI 2007, Lecture Notes in Computer Science LNCS Volume 4584, Springer, pp. 346-358, 2007
• John H. Gilmore, Weili Lin, Isabella Corouge, Y. Sampath K. Vetsa, J. Keith Smith, Chaeryon Kang, Hongbin Gu, Robert M. Hamer, Jeffrey A. Lieberman, Guido Gerig, Early Postnatal Development of Corpus Callosum and Corticospinal White Matter Assessed with Quantitative Tractography, accepted AJNR-07-00044 (American Journal of Neuroradiology), Oct. 2007
• Paul A. Yushkevich, Hui Zhang, Tony J. Simon, James C. Gee, Structure-specific statistical mapping of white matter tracts, NeuroImage? , Volume 41, Issue 2, June 2008, Pages 448-461
  
  

Xavier Pennec

• X. Pennec, P. Fillard, and Nicholas Ayache. A Riemannian Framework for Tensor Computing. Int. Journal of Computer Vision 66(1), January 2006. [Preprint as INRIA RR- 5255, July 2004]
• V. Arsigny, P. Fillard, X. Pennec, and N. Ayache. Log-Euclidean Metrics for Fast and Simple Calculus on Diffusion Tensors. Magnetic Resonance in Medicine, 56(2):411-421, August 2006. PMID: 16788917.
• P. Fillard, V. Arsigny, X. Pennec, and N. Ayache. Clinical DT-MRI Estimation, Smoothing and Fiber Tracking with Log-Euclidean Metrics. IEEE Transactions on Medical Imaging, 26(11):1472-1482, November 2007. PMID: 18041263. [Preprint: INRIA Research Report RR-5607, June 2005 and ISBI 2006.]
• J.-M. Peyrat, M. Sermesant, X. Pennec, H. Delingette, C.Y. Xu, E. McVeigh? , and N. Ayache. A Computational Framework for the Statistical Analysis of Cardiac Diffusion Tensors: Application to a Small Database of Canine Hearts. IEEE Transactions on Medical Imaging, 26(11):1500-1514, November 2007. PMID: 18041265.
• N. Toussaint, J.C. Souplet, and P. Fillard. MedINRIA? : Medical Image Navigation and Research Tool by INRIA. In Proc. of MICCAI'07 Workshop on Interaction in medical image analysis and visualization, Brisbane, Australia, 2007.
• B.T. Th. Yeo, T. Vercauteren, P. Fillard, X. Pennec, P. Golland, N. Ayache, and O. Clatz. DTI Registration with Exact Finite-Strain Differential. In Proc. of the IEEE Int. Symp. on Biomed. Imaging, Paris, France, May 2008.
  
  

Carlo Pierpaoli

• Jones DK, Basser PJ. "Squashing peanuts and smashing pumpkins": how noise distorts diffusion-weighted MR data. Magn Reson Med 2004;52:979-93.
• Chang L-C, Jones DK, Pierpaoli C. RESTORE: robust estimation of tensors by outlier rejection. Magn Reson Med 2005;53:1088-95.
• Rohde GK, Barnett AS, Basser PJ, Pierpaoli C. Estimating intensity variance due to noise in registered images: applications to diffusion tensor MRI. Neuroimage 2005;26:673-84.
  
  

Jerry Prince

• Alexander, D. C., Pierpaoli, C., Basser, P. J. and Gee, J. C., Spatial transformations of diffusion tensor magnetic resonance images. IEEE Transactions on Medical Imaging. 2001: 20, 1131-1139.
• Cao, Y., Miller, M., Mori, S., Winslow, R. L. and Younes, L., Diffeomorphic matching of diffusion tensor images. Proceedings of MMBIA. Proceedings of the MMBIA, New York, NY, 2006.
• Guimond, A., Guttmann, C. R. G., Warfield, S. K. and Westin, C.-F., Deformable registration of DT-MRI data based on transformation invariant tensor characteristics. Proceedings of the ISBI, 2002.
• Goh, A. and Vidal, R., Algebraic Methods for Direct and Feature Based Registration of Diffusion Tensor Images. In: Pinz, A. (Ed.). LNCS. Proceedings of the ECCV, 2006, 3, pp. 514-525.
• Jones, D. K., Griffin, L. D., Alexander, D. C., Catani, M., Horsfield, M. A., Howard, R. and Williams, S. C. R., Spatial normalization and averaging of diffusion tensor MRI data sets. Neuroimage. 2002, 17, 592-617.
• Park, H. J., Kubicki, M., Shenton, M. E., Guimond, A., McCarley? , R. W., Maier, S. E., Kikinis, R., Jolesz, F. A. and Westin, C.-F., Spatial Normalization of Diffusion Tensor MRI Using Multiple Channels. Neuroimage. 2003, 20, 1995-2009.
• Ruiz-Alzola, J., Westin, C. F., Warfield, S. K., Alberola, C., Maier, S. and Kikinis, R., Nonrigid registration of 3D tensor medical data. Medical Image Analysis. 2002, 6, 143-161.
• Xu, D., Mori, S., Shen, D., Zijl, P. C. M. v. and Davatzikos, C., Spatial Normalization of Diffusion Tensor Fields. Magnetic Resonance in Medicine. 2003, 50, 175-182.
• Zhang, H., Yushkevich, P. A., Alexander, D. C. and Gee, J. C., Deformable registration of diffusion tensor MR images with explicit orientation optimization. Medical Image Analysis. 2006, 10, 764-785.
• Jinzhong Yang, Dinggang Shen, Chandan Misra, Xiaoying Wu, Susan Resnick, Christos Davatzikos, Ragini Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, SPIE Medical Imaging, 2008
• Jinzhong Yang, Dinggang Shen, Christos Davatzikos, Ragini Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, MICCAI, 2008
• Ulas Ziyan, Mert R. Sabuncu, Lauren J. O'Donnell, Carl-Fredrik Westin, Nonlinear Registration of Diffusion MR Images Based on Fiber Bundles, MICCAI 2007
• Chiang MC, Leow AD, Dutton RA, Barysheva M, Rose S, McMahon? KL, de Zubicaray GI, Toga AW, Thompson PM. Fluid Registration of Diffusion Tensor Images Using Information Theory, IEEE Transactions on Medical Imaging, Feb. 2008.
• Angelos Barmpoutis, Baba C. Vemuri, John R. Forder: Registration of High Angular Resolution Diffusion MRI Images Using 4 th Order Tensors. MICCAI (1) 2007: 908-915.

Baba Vemuri

• References can be found at http://www.cise.ufl.edu/research/cvgmi/pub/

Ragini Verma

• Parmeshwar Khurd, Ragini Verma, Christos Davatzikos: Kernel-Based Manifold Learning for Statistical Analysis of Diffusion Tensor Images. IPMI 2007: 581-593.
• Verma, R. Khurd, P. Davatzikos, C. On Analyzing Diffusion Tensor Images by Identifying Manifold Structure Using Isomaps IEEE Transactions on Medical Imaging. Volume: 26 (6), June 2007, 772-778.
• Ragini Verma, Parmeshwar Khurd, James Loughead, Raquel Gur, Ruben Gur, Christos Davatzikos: Manifold based morphometry applied to schizophrenia, ISBI, 2008.
• Jinzhong Yang, Dinggang Shen, Chandan Misra, Xiaoying Wu, Susan Resnick, Christos Davatzikos, Ragini Verma:Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, SPIE Medical Imaging, 2008
• Jinzhong Yang, Dinggang Shen, Christos Davatzikos, Ragini Verma:Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features,MICCAI, 2008
• Peng Wang , Ragini Verma:On Classifying Disease-induced Patterns in the Brain using Diffusion Tensor Images, MICCAI, 2008
• Ragini Verma, Parmeshwar Khurd, James Loughead, Raquel Gur, Ruben Gur, Christos Davatzikos:Manifold based morphometry applied to schizophrenia, ISBI, 2008

Carl-Fredrik Westin

• Friman O, Farneback G, Westin CF. A Bayesian approach for stochastic white matter tractography. TMI 2006;25(8):965-978.
• Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. Clustering fiber tracts using normalized cuts. In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.