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Generating Fiber Crossing Phantoms Out of Experimental DWIs [chapter]

Matthan Caan, Anne Willem de Vries, Ganesh Khedoe, Erik Akkerman, Lucas van Vliet, Kees Grimbergen, Frans Vos
2007 Lecture Notes in Computer Science  
We propose a new method for creating experimental phantom data of fiber crossings, by mixing the DWI-signals from high FA-regions with different orientation.  ...  The properties of these experimental phantoms approach the conditions of real data. These phantoms can thus serve as a 'ground truth' in validating crossing reconstruction algorithms.  ...  part of the ICT innovation program of the Ministry of Economic Affairs (EZ).  ... 
doi:10.1007/978-3-540-75757-3_21 fatcat:aumq7hi4svfhjcwuifupc2plce

A preliminary study on the effect of motion correction on HARDI reconstruction

Shireen Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig
2014 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI)  
such crossing fibers.  ...  Nonetheless, interpolation might increase the partial volume effect while not preserving the volume of the diffusion profile, whereas excluding poor DWIs may affect the ability to resolve crossing fibers  ...  The phantom was generated based on two crossing fiber bundles with a controllable separation angle.  ... 
doi:10.1109/isbi.2014.6868055 pmid:25356195 pmcid:PMC4209744 fatcat:j5obmwjy5ve5doztazz6z3rr6u

Enhancement of Fiber Orientation Distribution Reconstruction in Diffusion-Weighted Imaging by Single Channel Blind Source Separation

Min Jing, T. M. McGinnity, S. Coleman, Huaizhong Zhang, A. Fuchs, J. A. S. Kelso
2012 IEEE Transactions on Biomedical Engineering  
In diffusion-weighted imaging (DWI), reliable fiber tracking results rely on the accurate reconstruction of the fiber orientation distribution function (fODF) in each individual voxel.  ...  number of distinct fiber populations.  ...  Fig. 1 . 1 Illustration of fODF reconstruction by the SD method: (a) Synthetic DWI signal generated from two crossing fibers, (b) response function generated from a single fiber with fiber orientation  ... 
doi:10.1109/tbme.2011.2172793 pmid:22020665 fatcat:lalfvp6t25cijla67votxs6egq

Motion Is Inevitable: The Impact of Motion Correction Schemes on HARDI Reconstructions [chapter]

Shireen Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig
2014 Mathematics and Visualization  
Diffusion weighted imaging (DWI) is known to be prone to artifacts related to motion originating from subject movement, cardiac pulsation and breathing, but also to mechanical issues such as table vibrations  ...  Given the necessity for rigorous quality control and motion correction, users are often left to use simple heuristics to select correction schemes, but do not fully understand the consequences of such  ...  Conclusion Although there is excellent theoretical work on DWI acquisition parameters and ODF reconstruction schemes, as well as its effects on the quality and crossing fiber resolution, standard users  ... 
doi:10.1007/978-3-319-11182-7_15 fatcat:oqqptf6i2bcergrj2bwtjlebyq

Crossing fibers, diffractions and nonhomogeneous magnetic field: correction of artifacts by bipolar gradient pulses

Amnon Bar-Shir, Yoram Cohen
2008 Magnetic Resonance Imaging  
The present study examines the effect of diffusion pulse sequence on the signal decay and diffraction patterns observed in q-space diffusion MR performed on micron-scale phantoms of different geometries  ...  In recent years, diffusion tensor imaging (DTI) and its variants have been used to describe fiber orientations and q-space diffusion MR was proposed as a means to obtain structural information on a micron  ...  [32] have used a 50-μm phantom of crossing fibers to compare orientational uncertainty in DTI and DSI. Avram et al.  ... 
doi:10.1016/j.mri.2008.01.051 pmid:18486389 fatcat:ox6fb567ajfzdczi6yrhjqt4be

Reduced Encoding Diffusion Spectrum Imaging Implemented With a Bi-Gaussian Model

Chun-Hung Yeh, Kuan-Hung Cho, Hsuan-Cheng Lin, Jiun-Jie Wang, Ching-Po Lin
2008 IEEE Transactions on Medical Imaging  
The crossing phantom model and the manganese-enhanced rat model served as standards for accuracy assessment in RE-DSI.  ...  The errors of RE-DSI in estimating fiber orientations were close to the noise limit.  ...  ACKNOWLEDGMENT The authors are grateful to the National Science Council of Taiwan for support, and would like to thank V. J. Wedeen, W.-Y. Tseng, C. Chang, and J.-H.  ... 
doi:10.1109/tmi.2008.922189 pmid:18815093 fatcat:udriz5yxozdvroibwddhqqqc7m

Subject–Motion Correction in HARDI Acquisitions: Choices and Consequences

Shireen Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana R. Leppert, G. Bruce Pike, Guido Gerig
2014 Frontiers in Neurology  
set of DWI data, or the selection of transformation parameter 7 thresholds for detection of motion outliers.  ...  of local fiber orientations, (3) 24 global brain connectivity via Graph Diffusion Distance (GDD) and (4) the reproducibility of 25 prominent and anatomically defined fiber tracts.  ...  LIVING PHANTOM: ACQUISITION AND GOLD STANDARD GENERATION Unlike conventional MRI, where realistic phantoms exist (Collins et al., 1998) , there is no widely 235 acceptable realistic DWI phantom for the  ... 
doi:10.3389/fneur.2014.00240 pmid:25538672 pmcid:PMC4260507 fatcat:zdfveaeypvd3rjsqpwbj5pedti

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  
Here, we report the encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent).  ...  Our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations.  ...  Methods Generation of ground truth fiber bundles.  ... 
doi:10.1038/s41467-017-01285-x pmid:29116093 pmcid:PMC5677006 fatcat:6s7zph3cdfd6xbb4aq3y6ur3my

Diffusion-Weighted Images Superresolution Using High-Order SVD

Xi Wu, Zhipeng Yang, Jinrong Hu, Jing Peng, Peiyu He, Jiliu Zhou
2016 Computational and Mathematical Methods in Medicine  
Experimental results from both synthetic and real DWI datasets demonstrate that the proposed method enhances the details in reconstructed high-resolution DWI datasets and outperforms conventional techniques  ...  The proposed method was implemented on an adaptive basis which ensured a more accurate reconstruction of high-resolution DWI datasets.  ...  As shown in Figure 1 (a), this dataset is comprised of five different fiber bundles which give rise to the nonplanar configurations of bending, crossing, and kissing tracts.  ... 
doi:10.1155/2016/3647202 pmid:27635150 pmcid:PMC5008020 fatcat:o4jfrdwrgfhkppyzl7c53opbca

Fiber Density Estimation by Tensor Divergence [chapter]

Marco Reisert, Henrik Skibbe, Valerij G. Kiselev
2012 Lecture Notes in Computer Science  
However, this information is not sufficient to reconstruct the underlying fiber network, because the nature of diffusion provides only conditional fiber densities.  ...  That is, it is possible to infer the percentage of bundles that pass a voxel with a certain direction, but the absolute number of fibers is inaccessible.  ...  Skibbe is indebted to the Baden-Württemberg Stiftung for the support of this research project by the Eliteprogramme for Postdocs. Thanks to R. Umarova for providing the data.  ... 
doi:10.1007/978-3-642-33418-4_37 fatcat:7rbhl6rk6bed5pmsxfxxo7ol5e

MK-curve - Characterizing the relation between mean kurtosis and alterations in the diffusion MRI signal

Fan Zhang, Lipeng Ning, Lauren J. O'Donnell, Ofer Pasternak
2019 NeuroImage  
This is done by calculating MK for a range of synthetic DWI or b0 for each voxel, and generating curves (MK-curve) representing how alterations to the input dMRI signals affect the resulting output MK.  ...  Accordingly, two characteristic b0 values, which define a range of synthetic b0 values that generate implausible MK values, are identified on the MK-curve.  ...  Laun for making the DKI phantom data available online.  ... 
doi:10.1016/j.neuroimage.2019.04.015 pmid:30978492 pmcid:PMC6592693 fatcat:udqkm5fnpjhpjjuuiouswtnepa

Validation of diffusion MRI estimates of compartment size and volume fraction in a biomimetic brain phantom using a human MRI scanner with 300 mT/m maximum gradient strength

Qiuyun Fan, Aapo Nummenmaa, Barbara Wichtmann, Thomas Witzel, Choukri Mekkaoui, Walter Schneider, Lawrence L. Wald, Susie Y. Huang
2018 NeuroImage  
The estimated restricted volume fraction demonstrated an expected decrease along the length of the fiber bundles in accordance with the known construction of the phantom.  ...  We obtained estimates of compartment size and restricted volume fraction through a straightforward extension of the AxCaliber/ActiveAx frameworks that enables estimation of mean compartment size in fiber  ...  Funding support was also received from Chronic Effects of Neurotrauma Consortium/Veterans Affairs Rehabilitation Research & Development project F1880, U.S.  ... 
doi:10.1016/j.neuroimage.2018.01.004 pmid:29337276 pmcid:PMC6043413 fatcat:duqishlerzhqlba7wxmeedyfqi

Snake-based brain white matter fiber reconstruction

Meng Lu, Jia Di
2014 Bio-medical materials and engineering  
In fact, the proposed test performed the third best out of the ten available methods, which demonstrates that present method can accurately formulate the brain white matter fiber reconstruction.  ...  Diffusion tensor imaging (DTI) is a tractography algorithm that provides the only means of mapping white matter fibers.  ...  Experiments and results The experimental design in this study consisted of two parts: the phantom fiber tracking test and real brain white matter fiber tracking test.  ... 
doi:10.3233/bme-141114 pmid:25227001 fatcat:7bdccfopdzfkfahijvsl66l2c4

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
Fiber tractography based on non-invasive diffusion imaging is at the heart of connectivity studies of the human brain.  ...  in particular and human connectivity studies in general.  ...  simulated DWI of a brain-like geometry.  ... 
doi:10.1101/084137 fatcat:c2s4nmf2kbdrrbpdde5y5afa44

A Framework for ODF Inference by Using Fiber Tract Adaptive MPG Selection [chapter]

Hidekata Hontani, Kazunari Iwamoto, Yoshitaka Masutani
2013 Mathematics and Visualization  
The authors propose a method that selects a set of motion probing gradient (MPG) directions, which is adapted for measuring fiber tracts in some specific region of interest (ROI) with smaller number of  ...  Experimental results demonstrated that the set of MPG directions selected by our proposed method reconstructed the ODFs more accurately than an existing method based on spherical harmonics and on greedy  ...  We generated a set of artificial diffusion images, of which size was 15 × 15 × 1. Two fiber tracts cross together in each of the images as shown in Fig.1 (A) .  ... 
doi:10.1007/978-3-319-02475-2_7 fatcat:7uvryujhzrbjho64afus6zpbby
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