Explanipedia

FORCE: FORward modeling for Complex microstructure Estimation Open

Rafael Neto Henriques, Alonso Ramírez-Manzanares, Patryk Filipiak, Maharshi Gor, Serge Koudoro · 2025

Diffusion Magnetic Resonance Imaging (dMRI) is a noninvasive modality that enables the study of brain tissue microstructure and the reconstruction of neural pathways. To achieve this, most reconstruction methods rely on inverse modeling te…

Clinically-feasible white matter fiber tractography in peritumoral zones with cerebral vasogenic edema Open

Patryk Filipiak, Timothy M. Shepherd, Kamri Clarke, Dimitris G. Placantonakis, Fernando E. Boada , et al. · 2025

In diffusion MRI, vasogenic edema manifests as a major fraction of isotropic water that dilutes the anisotropic intraaxonal portion of the signal. Many tractography algorithms mistake vasogenic edema for the white matter boundary and termi…

Anisotropy boosting improves ODF-Fingerprinting tractography in edematous brain Open

Patryk Filipiak, Kamri Clarke, Timothy M. Shepherd, Mary Bruno, Dimitris G. Placantonakis , et al. · 2025

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…

The effect of common parameters of bipolar stimulation on brain evoked potentials Open

Petru Isan, Samuel Deslauriers-Gauthier, Théodore Papadopoulo, Denys Fontaine, Patryk Filipiak , et al. · 2024

This study represents the first step in describing the influence of common bipolar stimulation parameters on robustness of BEPs by examining the impact of IED and IS on the N1 wave.

Improved reconstruction of crossing fibers in the mouse optic pathways with orientation distribution function fingerprinting Open

Patryk Filipiak, Thajunnisa A. Sajitha, Timothy M. Shepherd, Kamri Clarke, Hannah Goldman , et al. · 2023

Purpose The accuracy of diffusion MRI tractography reconstruction decreases in the white matter regions with crossing fibers. The optic pathways in rodents provide a challenging structure to test new diffusion tractography approaches becau…

In vivo diffusion MRI of optic pathways in 18 healthy mice Open

Patryk Filipiak, Thajunnisa A. Sajitha, Timothy M. Shepherd, Kamri Clarke, Hannah Goldman , et al. · 2023

The dataset contains manganese enhanced T1- and diffusion-weighted images of optic pathways in 18 healthy mice. All raw (Bruker) and a subset of processed (NIfTI) files are stored. AnimalsOur study was approved by the Institutional Animal …

In vivo diffusion MRI of optic pathways in 18 healthy mice Open

Patryk Filipiak, Thajunnisa A. Sajitha, Timothy M. Shepherd, Kamri Clarke, Hannah Goldman , et al. · 2023

The dataset contains manganese enhanced T1- and diffusion-weighted images of optic pathways in 18 healthy mice. All raw (Bruker) and a subset of processed (NIfTI) files are stored. AnimalsOur study was approved by the Institutional Animal …

Tractography passes the test: Results from the diffusion-simulated connectivity (disco) challenge Open

Gabriel Girard, Jonathan Rafael‐Patiño, Raphaël Truffet, Dogu Baran Aydogan, Nagesh Adluru , et al. · 2023

Identifying subcortical connectivity during brain tumor surgery: a multimodal study Open

Fabien Almairac, Petru Isan, Marie Onno, Théodore Papadopoulo, Lydiane Mondot , et al. · 2023

Validation of deep learning techniques for quality augmentation in diffusion MRI for clinical studies Open

Santiago Aja‐Fernández, Carmen Martín‐Martín, Álvaro Planchuelo‐Gómez, Abrar Faiyaz, Md Nasir Uddin , et al. · 2023

The objective of this study is to evaluate the efficacy of deep learning (DL) techniques in improving the quality of diffusion MRI (dMRI) data in clinical applications. The study aims to determine whether the use of artificial intelligence…

Diffusion Phantom Study of Fiber Crossings at Varied Angles Reconstructed with ODF-Fingerprinting Open

Patryk Filipiak, Timothy M. Shepherd, Lee Basler, Anthony Zuccolotto, Dimitris G. Placantonakis , et al. · 2023

Performance of orientation distribution function‐fingerprinting with a biophysical multicompartment diffusion model Open

Patryk Filipiak, Timothy M. Shepherd, Ying‐Chia Lin, Dimitris G. Placantonakis, Fernando E. Boada , et al. · 2022

Purpose Orientation Distribution Function (ODF) peak finding methods typically fail to reconstruct fibers crossing at shallow angles below 40°, leading to errors in tractography. ODF‐Fingerprinting (ODF‐FP) with the biophysical multicompar…

Stepwise Stochastic Dictionary Adaptation Improves Microstructure Reconstruction with Orientation Distribution Function Fingerprinting Open

Patryk Filipiak, Timothy M. Shepherd, Lee Basler, Anthony Zuccolotto, Dimitris G. Placantonakis , et al. · 2022

Towards linking diffusion MRI based macro- and microstructure measures with cortico-cortical transmission in brain tumor patients Open

Patryk Filipiak, Fabien Almairac, Théodore Papadopoulo, Denys Fontaine, Lydiane Mondot , et al. · 2020

We aimed to link macro- and microstructure measures of brain white matter obtained from diffusion MRI with effective connectivity measures based on a propagation of cortico-cortical evoked potentials induced with intrasurgical direct elect…

Diffusion MRI-based Connectivity Enriched with Microstructure Information Predicts the Propagation of Cortico-Cortical Evoked Potentials Open

Patryk Filipiak, Fabien Almairac, Théodore Papadopoulo, Denys Fontaine, Lydiane Mondot , et al. · 2020

International audience

Towards Validating Structural Connectivity in the Human Language System: An Intraoperative Cortico-Cortical Stimulation Experiment Open

Patryk Filipiak, Fabien Almairac, Théodore Papadopoulo, Denys Fontaine, Lydiane Mondot , et al. · 2019

International audience

Coarse-Grained Spatiotemporal Acquisition Design for Diffusion MRI Open

Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe , et al. · 2019

Acquisition protocols that allow to capture time-dependent changes in diffusion signal require long imaging time. We address this issue through an optimized subsampling scheme that maximizes accuracy of the spatiotemporal diffusion signal …

Reducing the number of samples in spatiotemporal dMRI acquisition design Open

Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe , et al. · 2018

Purpose Acquisition time is a major limitation in recovering brain white matter microstructure with diffusion magnetic resonance imaging. The aim of this paper is to bridge the gap between growing demands on spatiotemporal resolution of di…

fMRI Deconvolution via Temporal Regularization using a LASSO model and the LARS algorithm Open

Isa Costantini, Patryk Filipiak, Kostiantyn Maksymenko, Samuel Deslauriers‐Gauthier, Rachid Deriche · 2018

International audience

Spatio-Temporal dMRI Acquisition Design: Reducing the Number of Samples Open

Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe , et al. · 2018

Synopsis Acquisition time is a major limitation in recovering brain white matter microstructure with diffusion magnetic resonance imaging. Finding a sampling scheme that maximizes signal quality and satisfies given time constraints is NP-h…

L1-Norm Regularized Deconvolution of Functional MRI BOLD Signal Open

Isa Costantini, Patryk Filipiak, Kostiantyn Maksymenko, Samuel Deslauriers‐Gauthier, Rachid Deriche · 2018

Deconvolution methods are used to denoise the blood oxygen level-dependent (BOLD) response, the signal that forms the basis of functional MRI (fMRI). In this work we propose a novel approach based on a temporal regularized deconvolution …

Bridging Brain Structure and Function by Correlating Structural Connectivity and Cortico-Cortical Transmission Open

Fabien Almairac, Patryk Filipiak, Lavinia Slabu, Maureen Clerc, Théodore Papadopoulo , et al. · 2018

Deconvolution of fMRI BOLD signal in time-domain using an exponential operator and Lasso optimization Open

Isa Costantini, Patryk Filipiak, Kostiantyn Maksymenko, Rachid Deriche, Samuel Deslauriers‐Gauthier · 2017

Many techniques have been explored so far in the study of neural activations using the blood oxygenated level dependent (BOLD) signal. Among them, deconvolution methods have been developed in order to explore spontaneous brain activity whe…

Supplementary material from "Workshop on reconstruction schemes for magnetic resonance data: summary of findings and recommendations" Open

Esin Öztürk-Işık, Ian Marshall, Patryk Filipiak, Arnold Julian Vinoj Benjamin, Valia Guerra Ones , et al. · 2017

The high fidelity reconstruction of compressed and low-resolution magnetic resonance (MR) data is essential for simultaneously improving patient care, accuracy in diagnosis and quality in clinical research. Sponsored by the Royal Society t…

Table with the full list of participants to the workshop from Workshop on reconstruction schemes for magnetic resonance data: summary of findings and recommendations Open

Esin Öztürk-Işık, Ian Marshall, Patryk Filipiak, Arnold Julian Vinoj Benjamin, Valia Guerra Ones , et al. · 2017

The high fidelity reconstruction of compressed and low-resolution magnetic resonance (MR) data is essential for simultaneously improving patient care, accuracy in diagnosis and quality in clinical research. Sponsored by the Royal Society t…

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