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Tractometer: Online Evaluation System for Tractography [chapter]

Marc-Alexandre Côté, Arnaud Boré, Gabriel Girard, Jean-Christophe Houde, Maxime Descoteaux
2012 Lecture Notes in Computer Science  
We have developed a Tractometer: an online evaluation system for tractography processing pipelines.  ...  , q-ball, spherical deconvolution, spherical wavelets) and to different tractography parameters (masking, seeding, stopping criteria).  ...  Therefore, in the rest of the paper, we describe our new online system (url: scil.dinf.usherbrooke.ca/tractometer ) to evaluate and rank pipelines.  ... 
doi:10.1007/978-3-642-33415-3_86 fatcat:2ymlnomjzvhthmjw6c2i6wuhbe

Tractometer: Towards validation of tractography pipelines

Marc-Alexandre Côté, Gabriel Girard, Arnaud Boré, Eleftherios Garyfallidis, Jean-Christophe Houde, Maxime Descoteaux
2013 Medical Image Analysis  
We have developed the Tractometer: an online evaluation and validation system for tractography processing pipelines.  ...  Overall, we show that (i) averaging improves quality of tractography, (ii) sharp angular ODF profiles helps tractography, (iii) seeding and multi-seeding has a large impact on tractography outputs and  ...  Acknowledgments We would like to thank Compute Canada for access to High Performance Computing (HPC) resources and thank NeuroSpin for the public FiberCup dataset (url: www.lnao.fr/spip.php?  ... 
doi:10.1016/j.media.2013.03.009 pmid:23706753 fatcat:3swjkimjajfxjd3kdl4oev3xlq

Real-time multi-peak tractography for instantaneous connectivity display

Maxime Chamberland, Kevin Whittingstall, David Fortin, David Mathieu, Maxime Descoteaux
2014 Frontiers in Neuroinformatics  
We qualitatively illustrate and quantitatively evaluate our novel multi-peak RTT technique on phantom and human datasets in comparison with the state of the art offline tractography from MRtrix, which  ...  The technique runs on a single Computer Processing Unit (CPU) without the need for Graphical Unit Processing (GPU) programming.  ...  Moreover, we would like to thank Gabriel Girard, Jean-Christophe Houde, Eleftherios Garyfallidis, and Marc-Alexandre Côté of the SCIL for their help with the MRtrix and tractometer comparison.  ... 
doi:10.3389/fninf.2014.00059 pmid:24910610 pmcid:PMC4038925 fatcat:vbf53ammirbatphrrrmfa4akiu

Tractography-based connectomes are dominated by false-positive connections [article]

Klaus Maier-Hein, Peter Neher, Jean-Christophe Houde, Marc-Alexandre Cote, Eleftherios Garyfallidis, Jidan Zhong, Maxime Chamberland, Fang-Cheng Yeh, Ying Chia Lin, Qing Ji, Wilburn E. Reddick, John O. Glass (+65 others)
2016 bioRxiv   pre-print
Our results demonstrate fundamental ambiguities inherent to tract reconstruction methods based on diffusion orientation information, with critical consequences for the approach of diffusion tractography  ...  Fiber tractography based on non-invasive diffusion imaging is at the heart of connectivity studies of the human brain.  ...  The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/084137 doi: bioRxiv preprint first posted online Nov. 7, 2016; Performance metrics and evaluation The Tractometer definition  ... 
doi:10.1101/084137 fatcat:c2s4nmf2kbdrrbpdde5y5afa44

The challenge of mapping the human connectome based on diffusion tractography

Klaus H. Maier-Hein, Peter F. Neher, Jean-Christophe Houde, Marc-Alexandre Côté, Eleftherios Garyfallidis, Jidan Zhong, Maxime Chamberland, Fang-Cheng Yeh, Ying-Chia Lin, Qing Ji, Wilburn E. Reddick, John O. Glass (+65 others)
2017 Nature Communications  
Our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations.  ...  Tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. To date, the approach has not been systematically validated in ground truth studies.  ...  Performance metrics and evaluation. The Tractometer connectivity metrics 38 were used for a quantitative evaluation of the submissions.  ... 
doi:10.1038/s41467-017-01285-x pmid:29116093 pmcid:PMC5677006 fatcat:6s7zph3cdfd6xbb4aq3y6ur3my

Merged Group Tractography Evaluation with Selective Automated Group Integrated Tractography

David Q. Chen, Jidan Zhong, David J. Hayes, Brendan Behan, Matthew Walker, Peter S.-P. Hung, Mojgan Hodaie
2016 Frontiers in Neuroanatomy  
We use a merged tractography approach that permits evaluation of tractography datasets at the group level.  ...  However, correlations are not significant (p > 0.05) for unfiltered tractography.  ...  Finally, we deploy our system to the evaluation of various tractography methods in their ability to delineate neuroanatomy that are highly specific but difficult to image.  ... 
doi:10.3389/fnana.2016.00096 pmid:27790095 pmcid:PMC5061742 fatcat:gk2e3y3p2bf6rc2aaqebhfq7wi

Diffantom: whole-brain diffusion MRI phantoms derived from real datasets of the Human Connectome Project [article]

Oscar Esteban, Emmanuel Caruyer, Alessandro Daducci, Meritxell Bach-Cuadra, Maria-J. Ledesma-Carbayo, Andres Santos
2015 biorxiv/medrxiv   pre-print
SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fninf. 2016.00004  ...  ACKNOWLEDGMENTS We thank Gert Wollny for his revision of this work.  ...  While this phantom is designed for the bundle-wise evaluation of tractography (with the scores defined in the Tractometer (Côté et al., 2013) , such as geometrical coverage, valid connections, invalid  ... 
doi:10.1101/026898 fatcat:scymq3lm6bhxdeewtg5uzzvqj4

Limits to anatomical accuracy of diffusion tractography using modern approaches [article]

Kurt G Schilling, Vishwesh Nath, Colin Hansen, Prasanna Parvathaneni, Justin Blaber, Yurui Gao, Peter Neher, Dogu Baran Aydogan, Yonggang Shi, Mario Ocampo-Pineda, Simona Schiavi, Alessandro Daducci (+30 others)
2018 bioRxiv   pre-print
data alone, and highlight the need for alternative or combinatorial strategies to accurately map the fiber pathways of the brain.  ...  To test whether these advances improve tractography accuracy, we organized the ISBI 2018 3D Validation of Tractography with Experimental MRI (3D VoTEM) challenge.  ...  We thank Synaptive Medical for providing the anisotropic diffusion phantom, and for expertise on its use in research.  ... 
doi:10.1101/392571 fatcat:xjlj4ypm6fhetcirf67vooghwe

Limits to anatomical accuracy of diffusion tractography using modern approaches

Kurt G. Schilling, Vishwesh Nath, Colin Hansen, Prasanna Parvathaneni, Justin Blaber, Yurui Gao, Peter Neher, Dogu Baran Aydogan, Yonggang Shi, Mario Ocampo-Pineda, Simona Schiavi, Alessandro Daducci (+30 others)
2019 NeuroImage  
data alone, and highlight the need for alternative or combinatorial strategies to accurately map the fiber pathways of the brain.  ...  To test whether these advances improve tractography accuracy, we organized the 3-D Validation of Tractography with Experimental MRI (3D-VoTEM) challenge at the ISBI 2018 conference.  ...  We thank Synaptive Medical for providing the anisotropic diffusion phantom, and for expertise on its use in research.  ... 
doi:10.1016/j.neuroimage.2018.10.029 pmid:30317017 pmcid:PMC6551229 fatcat:5fzvjx3llrd37emsuhfzukbaxe

Track Orientation Density Imaging (TODI) and Track Orientation Distribution (TOD) based tractography

Thijs Dhollander, Louise Emsell, Wim Van Hecke, Frederik Maes, Stefan Sunaert, Paul Suetens
2014 NeuroImage  
Generating a higher amount of tracks allows for a more accurate depiction of the underlying distribution.  ...  Many modern methods can handle complex fiber architecture and take on a probabilistic approach to account for different sources of uncertainty.  ...  More recently, it was also employed as part of a newly proposed strategy to evaluate tractography pipelines, named Tractometer (Côté et al., 2012 (Côté et al., , 2013 .  ... 
doi:10.1016/j.neuroimage.2013.12.047 pmid:24389015 fatcat:mwqychjadzgpvdsrgzbaexpcdu

COMMIT: Convex Optimization Modeling for Microstructure Informed Tractography

Alessandro Daducci, Alessandro Dal Palu, Alia Lemkaddem, Jean-Philippe Thiran
2015 IEEE Transactions on Medical Imaging  
The effectiveness of our approach has been evaluated both on a realistic phantom with known ground-truth and in-vivo brain data.  ...  In this article, we present a novel framework to reestablish the link between tractography and tissue microstructure.  ...  We are also thankful to Dr Gavin Winston for sharing the in-vivo data and to Dr Nicolas Kunz for processing it with NODDI.  ... 
doi:10.1109/tmi.2014.2352414 pmid:25167548 fatcat:cvvifjz7orhrhl6qyfr2htrl2e

Fiber estimation and tractography in diffusion MRI: Development of simulated brain images and comparison of multi-fiber analysis methods at clinical b-values

Bryce Wilkins, Namgyun Lee, Niharika Gajawelli, Meng Law, Natasha Leporé
2015 NeuroImage  
The synthetic data sets, ground-truth, and tools for quantitative evaluation are publically available on the NITRC website as the project "Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of  ...  For example, while all methods recovered similar tractography of prominent white matter pathways of limited fiber crossing, CSD (which had the highest fiber detection rate, especially for voxels containing  ...  We additionally thank Iman for generous assistance with the CSA method. Illustrations of tractography were prepared using TrackVis (http://www.trackvis.org; Wang et al., 2007) .  ... 
doi:10.1016/j.neuroimage.2014.12.060 pmid:25555998 pmcid:PMC4600612 fatcat:q3fdo7af6fgtlntdprs7bqyjiu

Mapping population-based structural connectomes

Zhengwu Zhang, Maxime Descoteaux, Jingwen Zhang, Gabriel Girard, Maxime Chamberland, David Dunson, Anuj Srivastava, Hongtu Zhu
2018 NeuroImage  
Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a  ...  A robust tractography algorithm and and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness  ...  We also thank Kevin Whittingstall and the Sherbrooke Molecular Imaging Center for the acquisition of the test-retest data.  ... 
doi:10.1016/j.neuroimage.2017.12.064 pmid:29355769 pmcid:PMC5910206 fatcat:zm3436yv7newzbv2pqyq63vwae

Towards quantitative brain connectomics: microstructure informed tractography via convex optimization

Muhamed Barakovic
2019
Thanks also to Marco, Gaetan, Mariam, Francesco for the enjoyable time spent together. Thanks to all my other colleagues in Lausanne  ...  Another person that changed a bit my perspective of life is Thomas Yu; thanks for being positive all the time and coming and asking all kind of questions and proposing suggestions; you are a great person  ...  To quantitatively evaluate the tractography results submitted by the various groups, the Tractometer connectivity metrics [68] were used.  ... 
doi:10.5075/epfl-thesis-7397 fatcat:bw2i6ubj55b4zjkgl4fnzvwxiu