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Beyond Crossing Fibers: Bootstrap Probabilistic Tractography Using Complex Subvoxel Fiber Geometries

Jennifer S. W. Campbell, Parya MomayyezSiahkal, Peter Savadjiev, Ilana R. Leppert, Kaleem Siddiqi, G. Bruce Pike
2014 Frontiers in Neurology  
Citation: Campbell JSW, MomayyezSiahkal P, Savadjiev P, Leppert IR, Siddiqi K and Pike GB (2014) Beyond crossing fibers: bootstrap probabilistic tractography using complex subvoxel fiber geometries.  ...  This technique is repeatedly performed within a residual bootstrap statistical process in order to efficiently quantify the uncertainty in the subvoxel geometries obtained.  ...  The authors would like to thank Dr. Stephen Frey for many helpful discussions.  ... 
doi:10.3389/fneur.2014.00216 pmid:25389414 pmcid:PMC4211389 fatcat:oegz5myv2bhgro7fz7yi5aqclu

Q-Ball of Inferior Fronto-Occipital Fasciculus and Beyond

Eduardo Caverzasi, Nico Papinutto, Bagrat Amirbekian, Mitchel S. Berger, Roland G. Henry, Gaolang Gong
2014 PLoS ONE  
In this study we present a fiber tracking dissection of the right and left IFOF by using a q-ball residual-bootstrap reconstruction of High-Angular Resolution Diffusion Imaging (HARDI) data sets in 20  ...  In conclusion q-ball tractography dissection supports a more complex definition of IFOF, which includes several subcomponents likely underlying specific function.  ...  in the residual bootstrap tractography.  ... 
doi:10.1371/journal.pone.0100274 pmid:24945305 pmcid:PMC4063757 fatcat:62mj4egcv5f53jd47tyh6b2of4

Probabilistic tractography using Lasso bootstrap

Chuyang Ye, Jerry L. Prince
2017 Medical Image Analysis  
Bootstrap provides a nonparametric approach to the estimation of FO uncertainties and residual bootstrap has been used for developing probabilistic tractography.  ...  In this work, we propose a probabilistic tractography algorithm named Lasso bootstrap tractography (LBT) for the models that incorporate sparsity.  ...  Acknowledgments This work is supported in part by NIH/NINDS 5R01NS056307, NSFC 61601461, and the "100 Talents Program" of the Chinese Academy of Sciences.  ... 
doi:10.1016/ pmid:27662597 pmcid:PMC5099091 fatcat:45ry6mxipfa2fkejnqopchfigy

Reproducibility and intercorrelation of graph theoretical measures in structural brain connectivity networks

Timo Roine, Ben Jeurissen, Daniele Perrone, Jan Aelterman, Wilfried Philips, Jan Sijbers, Alexander Leemans
2019 Medical Image Analysis  
Intrasubject variability was computed with residual bootstrapping.  ...  We studied the reproducibility and correlation in structural brain connectivity networks reconstructed with constrained spherical deconvolution based probabilistic streamlines tractography.  ...  streamlines in the residual bootstrapping sample.  ... 
doi:10.1016/ pmid:30471463 fatcat:kn5i2tedwrdrpedsth3bukwblu

Quantifying diffusion MRI tractography of the corticospinal tract in brain tumors with deterministic and probabilistic methods

Monica Bucci, Maria Luisa Mandelli, Jeffrey I. Berman, Bagrat Amirbekian, Christopher Nguyen, Mitchel S. Berger, Roland G. Henry
2013 NeuroImage: Clinical  
The corticospinal fiber tracts were delineated with DTI and q-ball models using deterministic and probabilistic algorithms.  ...  The probabilistic q-ball fiber tractography was significantly better than DTI methods in terms of sensitivity and accuracy of the course through the white matter.  ...  The deterministic and probabilistic q-ball approaches also used the FACT propagation as implemented previously with residual bootstrap for the probabilistic version (Behrens et al., 2003; Berman et al  ... 
doi:10.1016/j.nicl.2013.08.008 pmid:24273719 pmcid:PMC3815019 fatcat:minb63jilfdk7nezjbwswnwg4y

Mapping brain anatomical connectivity using white matter tractography

Mariana Lazar
2010 NMR in Biomedicine  
The trajectory and terminations of white matter pathways are estimated from local orientations of nerve bundles. These orientations are obtained using measurements of water diffusion in the brain.  ...  White matter tractography is currently the only available technique for reconstructing the anatomical connectivity in the human brain non-invasively and in-vivo.  ...  Thanks go to Jens Jensen, Joseph Helpern, John Ollinger, Andy Alexander, and Aaron Field for useful discussions.  ... 
doi:10.1002/nbm.1579 pmid:20886567 pmcid:PMC4503207 fatcat:vxtc74ouufe35njl4wmwljldna

High Angular Resolution Diffusion Imaging Probabilistic Tractography of the Auditory Radiation

J.I. Berman, M.R. Lanza, L. Blaskey, J.C. Edgar, T.P.L. Roberts
2013 American Journal of Neuroradiology  
This study investigates whether HARDI fiber tracking can be used to robustly delineate the full extent of the tract.  ...  Probabilistic HARDI and DTI fiber tracking of the auditory radiation was performed with starting and filter regions automatically generated from the FreeSurfer white matter parcellation.  ...  ACKNOWLEDGMENT The authors thank Thorsten Feiweier of Siemens for providing the diffusion works in progress pulse sequence used in this study. Dr.  ... 
doi:10.3174/ajnr.a3471 pmid:23493892 pmcid:PMC3987782 fatcat:6lq2j6saane63d34cbemcwlliq

The Impact of In-Scanner Head Motion on Structural Connectivity Derived from Diffusion Tensor Imaging [article]

Graham L. Baum, David R. Roalf, Philip A. Cook, Rastko Ciric, Adon F. G. Rosen, Cedric Xia, Mark A. Elliot, Kosha Ruparel, Ragini Verma, Birkan Tunc, Ruben C. Gur, Raquel E. Gur (+2 others)
2017 bioRxiv   pre-print
Structural brain networks were constructed for each participant using both deterministic and probabilistic tractography.  ...  Nevertheless, the impact of head motion on estimates of structural connectivity derived from diffusion tractography methods remains poorly characterized.  ...  Supported by grants from the National Institute of Mental Health: R01MH107703 (TDS), R21MH106799 (DSB  ... 
doi:10.1101/185397 fatcat:7jefqwxcsffvrb774d6ozt2i4y

The impact of in-scanner head motion on structural connectivity derived from diffusion MRI

Graham L. Baum, David R. Roalf, Philip A. Cook, Rastko Ciric, Adon F.G. Rosen, Cedric Xia, Mark A. Elliott, Kosha Ruparel, Ragini Verma, Birkan Tunç, Ruben C. Gur, Raquel E. Gur (+2 others)
2018 NeuroImage  
Structural brain networks were constructed for each participant using both deterministic and probabilistic tractography.  ...  Nevertheless, the impact of head motion on estimates of structural connectivity derived from diffusion tractography methods remains poorly characterized.  ...  represent the official  ... 
doi:10.1016/j.neuroimage.2018.02.041 pmid:29486323 pmcid:PMC5911236 fatcat:x3s4gtmnqneezpymq6w6qsfy2m

Reconstruction of White Matter Tracts via Repeated Deterministic Streamline Tracking – Initial Experience

Miriam H. A. Bauer, Daniela Kuhnt, Sebastiano Barbieri, Jan Klein, Andreas Becker, Bernd Freisleben, Horst K. Hahn, Christopher Nimsky, Jean-Claude Baron
2013 PLoS ONE  
Since routinely used deterministic streamline tractography approaches often underestimate the spatial extent of white matter tracts, a novel approach to improve fiber segmentation is presented here, considering  ...  of 67.16%, 75.03% and 75.54%, using initial ROIs as combined include regions, which is clearly improved by the repeated fiber tractography method.  ...  Bartsch, PhD (Dept. of Neurosurgery, Marburg), for proofreading of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0063082 pmid:23671656 pmcid:PMC3646033 fatcat:glzd5zt4pvdgljxx4eugz3omsm

Validation of High-Resolution Tractography AgainstIn VivoTracing in the Macaque Visual Cortex

Hojjatollah Azadbakht, Laura M. Parkes, Hamied A. Haroon, Mark Augath, Nikos K. Logothetis, Alex de Crespigny, Helen E. D'Arceuil, Geoffrey J. M. Parker
2015 Cerebral Cortex  
On average, 74% of connections that were identified by FVE91 were reproduced by performing the most successfully optimized probabilistic diffusion MRI tractography.  ...  We performed probabilistic tractography on high angular resolution diffusion imaging data of 2 ex vivo, in vitro macaque brains.  ...  Constrained Spherical Deconvolution and Model-Based Residual Bootstrapping To perform probabilistic tractography, we first estimate the diffusion probability density function (PDF) describing the likely  ... 
doi:10.1093/cercor/bhu326 pmid:25787833 pmcid:PMC4816782 fatcat:mjwsnxio55d6rdtm7h74l3zjsu

Probabilistic tractography using Q-ball imaging and particle filtering: Application to adult and in-utero fetal brain studies

J. Pontabry, F. Rousseau, E. Oubel, C. Studholme, M. Koob, J.-L. Dietemann
2013 Medical Image Analysis  
The two key ingredients of tractography are the diffusion model (tensor, high-order tensor, Q-ball, etc.) and the means to deal with uncertainty during the tracking process (deterministic vs probabilistic  ...  In this paper, we investigate the use of an analytical Q-ball model for the diffusion data within a well-formalized particle filtering framework.  ...  Acknowledgment: The research leading to these results has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013).  ... 
doi:10.1016/ pmid:23265801 fatcat:7d5sap5isvgqhfdex7y76hjqa4

Tractography From HARDI Using an Intrinsic Unscented Kalman Filter

Guang Cheng, Hesamoddin Salehian, John R. Forder, Baba C. Vemuri
2015 IEEE Transactions on Medical Imaging  
estimation of multitensors and propagation of directional information for use in fiber tractography from diffusion weighted MR data.  ...  Lack of this key property can possibly lead to inaccuracies in the multitensor estimation as well as in the tractography.  ...  Acknowledgment The authors would like to thank Drs. Howland and M. S. Hwang for providing the Spinal Cord HARDI datasets. This research was funded by the NIH grant NS066340 to B.C.V.  ... 
doi:10.1109/tmi.2014.2355138 pmid:25203986 pmcid:PMC4280307 fatcat:at2rqok3f5g5pdezhx5xrxqzre

Modular Segregation of Structural Brain Networks Supports the Development of Executive Function in Youth

Graham L. Baum, Rastko Ciric, David R. Roalf, Richard F. Betzel, Tyler M. Moore, Russell T. Shinohara, Ari E. Kahn, Simon N. Vandekar, Petra E. Rupert, Megan Quarmley, Philip A. Cook, Mark A. Elliott (+5 others)
2017 Current Biology  
matrices (Q Yeo ) was highly significant (p<1×10 −10 ).  ...  Although these module partitions were defined in an independent dataset, using a different imaging modality, the modularity quality of the functional partition imposed on subject-level structural connectivity  ...  Acknowledgments We thank the acquisition and recruitment team, including Karthik Prabhakaran and Jeff Valdez.  ... 
doi:10.1016/j.cub.2017.04.051 pmid:28552358 pmcid:PMC5491213 fatcat:hfta6qoelzdo5ltgv77gxjopmy

Tractography and the connectome in neurosurgical treatment of gliomas: the premise, the progress, and the potential

Fraser Henderson, Kalil G. Abdullah, Ragini Verma, Steven Brem
2020 Neurosurgical Focus  
In this paper the current literature supporting the use of tractography in brain tumor surgery is summarized, highlighting important clinical studies on the application of diffusion tensor imaging (DTI  ...  The key methods of tractography in current practice and crucial white matter fiber bundles are summarized.  ...  Acknowledgments The current work is supported in part by an NIH grant (RO1 NS096606; Principal Investigators R. Verma and S. Brem).  ... 
doi:10.3171/2019.11.focus19785 pmid:32006950 pmcid:PMC7831974 fatcat:23rziwtpxrhvxef2ufm7a2tngq
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