Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain

Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain | medRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-P4HH5NV'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain View ORCID Profile Patryk Filipiak , View ORCID Profile Kamri Clarke , View ORCID Profile Timothy M. Shepherd , View ORCID Profile Mary Bruno , View ORCID Profile Dimitris G. Placantonakis , View ORCID Profile Steven H. Baete doi: https://doi.org/10.1101/2025.06.18.25329353 Patryk Filipiak 1 2 , New York, NY, USA 2 Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology , NYU Langone Health, New York, NY, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Patryk Filipiak For correspondence: patryk.filipiak{at}nyulangone.org Kamri Clarke 1 2 , New York, NY, USA 2 Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology , NYU Langone Health, New York, NY, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Kamri Clarke Timothy M. Shepherd 1 2 , New York, NY, USA 2 Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology , NYU Langone Health, New York, NY, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Timothy M. Shepherd Mary Bruno 1 2 , New York, NY, USA 2 Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology , NYU Langone Health, New York, NY, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Mary Bruno Dimitris G. Placantonakis 3 Department of Neurosurgery, Neurosurgical Laboratory for Stem Cell Research, NYU Langone Health , New York, NY, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Dimitris G. Placantonakis Steven H. Baete 1 2 , New York, NY, USA 2 Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology , NYU Langone Health, New York, NY, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Steven H. Baete Abstract Full Text Info/History Metrics Data/Code Preview PDF Abstract Peritumoral vasogenic edema of the brain is a major confounding factor for diffusion MRI tractography. Excessive fluids accumulated in edematous white matter decrease anisotropy of water self-diffusion which affects tracking algorithms. We address this hurdle with ODF-Fingerprinting (ODF-FP) — a dictionary-based fiber reconstruction algorithm that accommodates variability of neural tissue. By adding a regularization term to the ODF-FP matching formula, we boost diffusion anisotropy to improve white matter fiber identification in edematous regions. Purpose Peritumoral vasogenic edema of the brain is a major confounding factor for diffusion MRI (dMRI) tractography [ 1 ] . Excessive fluids accumulated in the extra-axonal space decrease diffusion anisotropy, causing premature termination of reconstructed White Matter (WM) fibers [ 2 ] . As a result, tractography images are often inaccurate in proximity to tumor mass, which hampers resection planning. We address this hurdle with ODF-Fingerprinting (ODF-FP) [ 3 ] — a dictionary-based fiber reconstruction algorithm that accommo-dates variability of neural tissue [ 4 ] . By adding a regularization term to the ODF-FP matching formula, we boost diffusion anisotropy to improve WM fiber tracking in edematous brain. Theory Let 𝒟 be an ODF-dictionary. We define the ODF-FP matching formula: where x is an input ODF, d j ∈ 𝒟 are dictionary ODFs (each with N j ≥ 0 crossing fibers) among which the best matching candidate is selected, and λ , μ ≥ 0 are regularization weights. Note that the added term min( d j ) boosts diffusion anisotropy by penalizing the lowest values of ODF and is intended to use only in edema regions (i.e., μ = 0 in the remaining voxels). Methods We considered dMRI of 10 brain tumor patients (51± 11 y/o) with vasogenic edema infiltrating the Arcuate Fasciculus (AF; 9 cases) or the Corticospinal Tract (CST; 7 cases). The images were acquired with a 3T Siemens Prisma (Erlangen, Germany) MR scanner at 2 × 2 × 2 mm 3 , TE/TR = 92 / 5900 ms, 60 directions at b = 300, 1100, 2500, 5000 s/mm 2 and 8 at b = 0. Our postprocessing in MRtrix3 [ 5 ] included denoising, Gibbs ringing removal, correction of B1 field inhomogeneity and eddy currents. We then executed ODF-FP with a dictionary of 10 6 items having 0 ≤ N j ≤3 crossing fibers per voxel, λ = 10 −5 , and an exploratory set of anisotropy boost factors μ ∈ { 0, 0.01, 0.02,…, 0.30} applied in manually drawn edema regions. For comparison, we processed the same images using: Constrained Spherical Deconvolution with Multi-Shell Multi-Tissue option (CSD MSMT) [ 6 ] , Free Water Elimination Diffusion Tensor Imaging (FWE DTI) [ 7 ] , Freewater estimatoR using iNtErpolated iniTialization (FERNET) [ 8 ] , Functional magnetic resonance imaging of the brain Software Library (FSL) Bedpostx [ 9 ] , and Generalized Q-sampling Imaging (GQI) [ 10 ] . For each method m , we dissected AF and CST using automated tracking in DSI Studio [ 11 ] , then calculated the respective overlap enhancements (OE) defined as normalized volumes (vol): Results Linear increment of the anisotropy boosting factor μ gradually increased OE of ODF-FP, then reached plateau within the 0.10–0.20 range ( Figure 1 ). The improvement in shape of the reconstructed tracts was particularly visible in AF ( Figure 1A ). Quantitatively, ODF-FP with the proposed regularization term (weighted by μ = 0.15) considerably outperformed other tested methods ( Figure 2 ). Download figure Open in new tab Figure 1: Mean overlap enhancements in ODF-FP reconstruction of (A) Arcuate Fasciculus and (B) Corticospinal Tract with a range of anisotropy boost factors μ . Download figure Open in new tab Figure 2: Comparison of mean overlap ehancements in all tested methods. Discussion and Conclusion ODF-FP with the proposed modification to boost diffusion anisotropy has the potential to overcome dMRI signal distortion due to vasogenic edema. Future work should address automatic recognition of edema regions and adaptability of ODF-FP to clinically feasible dMRI acquisition protocols. Data Availability All data produced in the present study are available upon reasonable request to the authors. Acknowledgements This project was supported in part by the National Institutes of Health (NIH: R01-EB028774, R01-NS082436) and performed under the rubric of the Center for Advanced Imaging Innovation and Research (CAI 2 R, https://www.cai2r.net ), an NIBIB Biomedical Technology Resource Center (NIH P41-EB017183). References [1]. ↵ Henderson et al. , Neurosurgery , 2021 ; [2]. ↵ Koga et al. , Frontiers in Neurology , 2024 ; [3]. ↵ Baete et al. , NeuroImage , 2019 ; [4]. ↵ Filipiak et al. , MRM , 2022 ; [5]. ↵ Tournier et al. , NeuroImage , 2019 ; [6]. ↵ Jeurissen et al. , NeuroImage , 2014 ; [7]. ↵ Pasternak et al. , Springer , 2014 ; [8]. ↵ Parker et al. , PLOS One , 2020 ; [9]. ↵ Behrens et al. , NeuroImage , 2007 ; [10]. ↵ Yeh et al. , IEEE TMI , 2010 ; [11]. ↵ Yeh et al. , Nature communications , 2022 . View the discussion thread. Back to top Previous Next Posted June 20, 2025. Download PDF Data/Code Email Thank you for your interest in spreading the word about medRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain Message Subject (Your Name) has forwarded a page to you from medRxiv Message Body (Your Name) thought you would like to see this page from the medRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain Patryk Filipiak , Kamri Clarke , Timothy M. Shepherd , Mary Bruno , Dimitris G. Placantonakis , Steven H. Baete medRxiv 2025.06.18.25329353; doi: https://doi.org/10.1101/2025.06.18.25329353 Share This Article: Copy Citation Tools Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain Patryk Filipiak , Kamri Clarke , Timothy M. Shepherd , Mary Bruno , Dimitris G. Placantonakis , Steven H. Baete medRxiv 2025.06.18.25329353; doi: https://doi.org/10.1101/2025.06.18.25329353 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Radiology and Imaging Subject Areas All Articles Addiction Medicine (568) Allergy and Immunology (863) Anesthesia (297) Cardiovascular Medicine (4417) Dentistry and Oral Medicine (443) Dermatology (381) Emergency Medicine (606) Endocrinology (including Diabetes Mellitus and Metabolic Disease) (1507) Epidemiology (15209) Forensic Medicine (30) Gastroenterology (1120) Genetic and Genomic Medicine (6577) Geriatric Medicine (666) Health Economics (995) Health Informatics (4515) Health Policy (1366) Health Systems and Quality Improvement (1610) Hematology (537) HIV/AIDS (1264) Infectious Diseases (except HIV/AIDS) (15906) Intensive Care and Critical Care Medicine (1103) Medical Education (620) Medical Ethics (144) Nephrology (667) Neurology (6578) Nursing (345) Nutrition (998) Obstetrics and Gynecology (1139) Occupational and Environmental Health (955) Oncology (3321) Ophthalmology (970) Orthopedics (369) Otolaryngology (420) Pain Medicine (435) Palliative Medicine (129) Pathology (663) Pediatrics (1689) Pharmacology and Therapeutics (691) Primary Care Research (710) Psychiatry and Clinical Psychology (5425) Public and Global Health (9211) Radiology and Imaging (2192) Rehabilitation Medicine and Physical Therapy (1368) Respiratory Medicine (1194) Rheumatology (593) Sexual and Reproductive Health (709) Sports Medicine (529) Surgery (709) Toxicology (99) Transplantation (288) Urology (265) (function(){function c(){var b=a.contentDocument||a.contentWindow.document;if(b){var d=b.createElement('script');d.innerHTML="window.__CF$cv$params={r:'9feeb2e8afaeaa64',t:'MTc3OTMxNTMxNA=='};var a=document.createElement('script');a.src='/cdn-cgi/challenge-platform/scripts/jsd/main.js';document.getElementsByTagName('head')[0].appendChild(a);";b.getElementsByTagName('head')[0].appendChild(d)}}if(document.body){var a=document.createElement('iframe');a.height=1;a.width=1;a.style.position='absolute';a.style.top=0;a.style.left=0;a.style.border='none';a.style.visibility='hidden';document.body.appendChild(a);if('loading'!==document.readyState)c();else if(window.addEventListener)document.addEventListener('DOMContentLoaded',c);else{var e=document.onreadystatechange||function(){};document.onreadystatechange=function(b){e(b);'loading'!==document.readyState&&(document.onreadystatechange=e,c())}}}})();