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(URI)</option><option value="author_id">arXiv author ID</option><option value="help">Help pages</option><option value="full_text">Full text</option></select> <input id="query" name="query" type="text" value="Consagra, W"> <ul id="abstracts"><li><input checked id="abstracts-0" name="abstracts" type="radio" value="show"> <label for="abstracts-0">Show abstracts</label></li><li><input id="abstracts-1" name="abstracts" type="radio" value="hide"> <label for="abstracts-1">Hide abstracts</label></li></ul> </div> <div class="box field is-grouped is-grouped-multiline level-item"> <div class="control"> <span class="select is-small"> <select id="size" name="size"><option value="25">25</option><option selected value="50">50</option><option value="100">100</option><option value="200">200</option></select> </span> <label for="size">results per page</label>. </div> <div class="control"> <label for="order">Sort results by</label> <span class="select is-small"> <select id="order" name="order"><option selected value="-announced_date_first">Announcement date (newest first)</option><option value="announced_date_first">Announcement date (oldest first)</option><option value="-submitted_date">Submission date (newest first)</option><option value="submitted_date">Submission date (oldest first)</option><option value="">Relevance</option></select> </span> </div> <div class="control"> <button class="button is-small is-link">Go</button> </div> </div> </form> </div> </div> <ol class="breathe-horizontal" start="1"> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2409.09387">arXiv:2409.09387</a> <span> [<a href="https://arxiv.org/pdf/2409.09387">pdf</a>, <a href="https://arxiv.org/format/2409.09387">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Image and Video Processing">eess.IV</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Computer Vision and Pattern Recognition">cs.CV</span> </div> </div> <p class="title is-5 mathjax"> Estimating Neural Orientation Distribution Fields on High Resolution Diffusion MRI Scans </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/eess?searchtype=author&query=Dwedari%2C+M+M">Mohammed Munzer Dwedari</a>, <a href="/search/eess?searchtype=author&query=Consagra%2C+W">William Consagra</a>, <a href="/search/eess?searchtype=author&query=M%C3%BCller%2C+P">Philip M眉ller</a>, <a href="/search/eess?searchtype=author&query=Turgut%2C+%C3%96">脰zg眉n Turgut</a>, <a href="/search/eess?searchtype=author&query=Rueckert%2C+D">Daniel Rueckert</a>, <a href="/search/eess?searchtype=author&query=Rathi%2C+Y">Yogesh Rathi</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2409.09387v1-abstract-short" style="display: inline;"> The Orientation Distribution Function (ODF) characterizes key brain microstructural properties and plays an important role in understanding brain structural connectivity. Recent works introduced Implicit Neural Representation (INR) based approaches to form a spatially aware continuous estimate of the ODF field and demonstrated promising results in key tasks of interest when compared to conventiona… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2409.09387v1-abstract-full').style.display = 'inline'; document.getElementById('2409.09387v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2409.09387v1-abstract-full" style="display: none;"> The Orientation Distribution Function (ODF) characterizes key brain microstructural properties and plays an important role in understanding brain structural connectivity. Recent works introduced Implicit Neural Representation (INR) based approaches to form a spatially aware continuous estimate of the ODF field and demonstrated promising results in key tasks of interest when compared to conventional discrete approaches. However, traditional INR methods face difficulties when scaling to large-scale images, such as modern ultra-high-resolution MRI scans, posing challenges in learning fine structures as well as inefficiencies in training and inference speed. In this work, we propose HashEnc, a grid-hash-encoding-based estimation of the ODF field and demonstrate its effectiveness in retaining structural and textural features. We show that HashEnc achieves a 10% enhancement in image quality while requiring 3x less computational resources than current methods. Our code can be found at https://github.com/MunzerDw/NODF-HashEnc. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2409.09387v1-abstract-full').style.display = 'none'; document.getElementById('2409.09387v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 14 September, 2024; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> September 2024. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">16 pages, 8 figures, conference: Medical Image Computing and Computer-Assisted Intervention (MICCAI)</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2405.13655">arXiv:2405.13655</a> <span> [<a href="https://arxiv.org/pdf/2405.13655">pdf</a>, <a href="https://arxiv.org/format/2405.13655">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Image and Video Processing">eess.IV</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Applications">stat.AP</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Computation">stat.CO</span> </div> </div> <p class="title is-5 mathjax"> A Deep Learning Approach to Multi-Fiber Parameter Estimation and Uncertainty Quantification in Diffusion MRI </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/eess?searchtype=author&query=Consagra%2C+W">William Consagra</a>, <a href="/search/eess?searchtype=author&query=Ning%2C+L">Lipeng Ning</a>, <a href="/search/eess?searchtype=author&query=Rathi%2C+Y">Yogesh Rathi</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2405.13655v1-abstract-short" style="display: inline;"> Diffusion MRI (dMRI) is the primary imaging modality used to study brain microstructure in vivo. Reliable and computationally efficient parameter inference for common dMRI biophysical models is a challenging inverse problem, due to factors such as variable dimensionalities (reflecting the unknown number of distinct white matter fiber populations in a voxel), low signal-to-noise ratios, and non-lin… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2405.13655v1-abstract-full').style.display = 'inline'; document.getElementById('2405.13655v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2405.13655v1-abstract-full" style="display: none;"> Diffusion MRI (dMRI) is the primary imaging modality used to study brain microstructure in vivo. Reliable and computationally efficient parameter inference for common dMRI biophysical models is a challenging inverse problem, due to factors such as variable dimensionalities (reflecting the unknown number of distinct white matter fiber populations in a voxel), low signal-to-noise ratios, and non-linear forward models. These challenges have led many existing methods to use biologically implausible simplified models to stabilize estimation, for instance, assuming shared microstructure across all fiber populations within a voxel. In this work, we introduce a novel sequential method for multi-fiber parameter inference that decomposes the task into a series of manageable subproblems. These subproblems are solved using deep neural networks tailored to problem-specific structure and symmetry, and trained via simulation. The resulting inference procedure is largely amortized, enabling scalable parameter estimation and uncertainty quantification across all model parameters. Simulation studies and real imaging data analysis using the Human Connectome Project (HCP) demonstrate the advantages of our method over standard alternatives. In the case of the standard model of diffusion, our results show that under HCP-like acquisition schemes, estimates for extra-cellular parallel diffusivity are highly uncertain, while those for the intra-cellular volume fraction can be estimated with relatively high precision. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2405.13655v1-abstract-full').style.display = 'none'; document.getElementById('2405.13655v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 22 May, 2024; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> May 2024. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2307.08138">arXiv:2307.08138</a> <span> [<a href="https://arxiv.org/pdf/2307.08138">pdf</a>, <a href="https://arxiv.org/format/2307.08138">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Image and Video Processing">eess.IV</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Applications">stat.AP</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Computation">stat.CO</span> </div> </div> <p class="title is-5 mathjax"> Neural Orientation Distribution Fields for Estimation and Uncertainty Quantification in Diffusion MRI </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/eess?searchtype=author&query=Consagra%2C+W">William Consagra</a>, <a href="/search/eess?searchtype=author&query=Ning%2C+L">Lipeng Ning</a>, <a href="/search/eess?searchtype=author&query=Rathi%2C+Y">Yogesh Rathi</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2307.08138v2-abstract-short" style="display: inline;"> Inferring brain connectivity and structure \textit{in-vivo} requires accurate estimation of the orientation distribution function (ODF), which encodes key local tissue properties. However, estimating the ODF from diffusion MRI (dMRI) signals is a challenging inverse problem due to obstacles such as significant noise, high-dimensional parameter spaces, and sparse angular measurements. In this paper… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2307.08138v2-abstract-full').style.display = 'inline'; document.getElementById('2307.08138v2-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2307.08138v2-abstract-full" style="display: none;"> Inferring brain connectivity and structure \textit{in-vivo} requires accurate estimation of the orientation distribution function (ODF), which encodes key local tissue properties. However, estimating the ODF from diffusion MRI (dMRI) signals is a challenging inverse problem due to obstacles such as significant noise, high-dimensional parameter spaces, and sparse angular measurements. In this paper, we address these challenges by proposing a novel deep-learning based methodology for continuous estimation and uncertainty quantification of the spatially varying ODF field. We use a neural field (NF) to parameterize a random series representation of the latent ODFs, implicitly modeling the often ignored but valuable spatial correlation structures in the data, and thereby improving efficiency in sparse and noisy regimes. An analytic approximation to the posterior predictive distribution is derived which can be used to quantify the uncertainty in the ODF estimate at any spatial location, avoiding the need for expensive resampling-based approaches that are typically employed for this purpose. We present empirical evaluations on both synthetic and real in-vivo diffusion data, demonstrating the advantages of our method over existing approaches. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2307.08138v2-abstract-full').style.display = 'none'; document.getElementById('2307.08138v2-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 6 February, 2024; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 16 July, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> July 2023. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">code available on request</span> </p> </li> </ol> <div class="is-hidden-tablet"> <!-- feedback for mobile only --> <span class="help" 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