Garikoitz Lerma-Usabiaga | Basque Center on Cognition, Brain and Language (original) (raw)

Papers by Garikoitz Lerma-Usabiaga

We develop an open-source tool for the retrospective estimation of inter-volume head-motion and e... more We develop an open-source tool for the retrospective estimation of inter-volume head-motion and eddy-current distortions, typically found in diffusion MRI (dMRI) data acquired with echo-planar imaging schemes. The implementation is “open-since-inception” to ensure transparency. By leveraging the widely used DIPY package and a user-friendly interface, researchers have at their disposal an implementation combining state-of-art approaches with substantial improvements that can efficiently leverage any compliant diffusion model(s) while simultaneously accounting for susceptibility distortions.

v1.0.0 As used in "Numerosity tuning in human association cortices and local image contrast ... more v1.0.0 As used in "Numerosity tuning in human association cortices and local image contrast representations in early visual cortex".

SummaryDiffusion MRI is a complex technique, where new discoveries and implementations occur at a... more SummaryDiffusion MRI is a complex technique, where new discoveries and implementations occur at a fast pace. The expertise needed for data analyses and accurate and reproducible results is increasingly demanding and requires multidisciplinary collaborations. In the present work we introduce Reproducible Tract Profiles (RTP2): a set of flexible and automated methods to analyze anatomical MRI and diffusion weighted imaging (DWI) data for reproducible tractography. The tools read structural MRI data and process them through a succession of serialized containerized analyses. We describe the DWI algorithms used to identify white-matter tracts and their summary metrics, the flexible architecture of the platform, and the tools to programmatically access and control the computations. The combination of these three components provides an easy-to-use automatized tool developed and tested over 20 years, to obtain usable and reliable state-of-the-art diffusion metrics at the individual and grou...

See collection description. Matlab nested table format.

See collection description. Nested json.

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transpa... more dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

Lecture Notes in Computer Science, 2017

Head motion is one of the most important nuisance variables in neuroimaging, particularly in stud... more Head motion is one of the most important nuisance variables in neuroimaging, particularly in studies of clinical or special populations, such as children. However, the possibility of estimating motion in structural MRI is limited to a few specialized sites using advanced MRI acquisition techniques. Here we propose a supervised learning method to retrospectively estimate motion from plain MRI. Using sparsely labeled training data, we trained a 3D convolutional neural network to assess if voxels are corrupted by motion or not. The output of the network is a motion probability map, which we integrate across a region of interest (ROI) to obtain a scalar motion score. Using cross-validation on a dataset of n = 48 healthy children scanned at our center, and the cerebral cortex as ROI, we show that the proposed measure of motion explains away 37% of the variation in cortical thickness. We also show that the motion score is highly correlated with the results from human quality control of the scans. The proposed technique can not only be applied to current studies, but also opens up the possibility of reanalyzing large amounts of legacy datasets with motion into consideration: we applied the classifier trained on data from our center to the ABIDE dataset (autism), and managed to recover group differences that were confounded by motion.

2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), 2016

Multi-slab MRI overcomes some of the hardware limitations of today's clinical scanners (e.g., mem... more Multi-slab MRI overcomes some of the hardware limitations of today's clinical scanners (e.g., memory size), enabling the acquisition of ultra-high resolution ex vivo MRI of the whole human brain with high SNR efficiency. However, multi-slab MRI suffers from slab boundary artifacts (SBA) that can greatly bias subsequent analyses. Since SBA heavily interplays with the bias field (BF) present in MRI, we propose a Bayesian method that corrects for SBA and BF simultaneously. The method, which combines a probabilistic brain atlas with an Expectation Maximization inference algorithm, is shown to outperform state-of-the-art SBA and BF correction techniques-even when used in combination. Index Terms-Ex vivo MRI, bias field, slab boundary artifact, Venetian blind, Bayesian image enhancement * JEI is funded by a Marie Sklodowska-Curie fellowship (grant #654911).

American Journal of Respiratory and Critical Care Medicine, 2007

Rationale: Obstructive sleep apnea (OSA) is associated with adverse cardiovascular outcomes, incl... more Rationale: Obstructive sleep apnea (OSA) is associated with adverse cardiovascular outcomes, including myocardial infarction and stroke. Atherosclerosis is a key mechanism for these cardiovascular events. Recent cross-sectional studies showed the presence of early signs of atherosclerosis in patients with OSA who were free of comorbidities. Objectives: To determine the impact of treatment with continuous positive airway pressure (CPAP) on atherosclerosis. Methods: We randomly assigned 24 patients with severe OSA (age, 46 6 6 yr) who were free of comorbidities to receive no treatment (control, n 5 12) or CPAP (n 5 12) for 4 months. Carotid intima-media thickness, arterial stiffness (evaluated by pulse-wave velocity), carotid diameter, 24-hour blood pressure monitoring, C-reactive protein, and catecholamines were determined at baseline and after 4 months. Measurements and Main Results: At baseline, all measurements were similar in both groups and did not change in the control group after 4 months. In contrast, a significant decrease occurred in carotid intimamedia thickness (707 6 105 vs. 645 6 95 mm, P 5 0.04), pulse-wave velocity (10.4 6 1.0 vs. 9.3 6 0.9 m/s, P , 0.001), C-reactive protein (3.7 6 1.8 vs. 2.0 6 1.2 mg/L, P 5 0.001), and catecholamines (365 6 125 vs. 205 6 51 ng/ml, P , 0.001) after 4 months of CPAP. Carotid diameter did not change significantly. Regarding the whole group, changes in carotid intima-media thickness were correlated with changes in catecholamines (r 5 0.41, P , 0.05). Changes in pulsewave velocity were correlated with changes in C-reactive protein (r 5 0.58, P , 0.01) and catecholamines (r 5 0.54, P , 0.01). Conclusions: The treatment of OSA significantly improves early signs of atherosclerosis, supporting the concept that OSA is an independent risk factor for atherosclerosis. Clinical trial registered with www.clinicaltrials.gov (NCT 00400543).

Working Papers on Information Systems ISSN 1535-6078, 2008

In recent papers, scholars are asking for more development in the philosophy of science for IS. I... more In recent papers, scholars are asking for more development in the philosophy of science for IS. Information Systems is a young discipline, and it has difficulties to find a stable philosophical basis. There is the double need of developing it and combining with the strong results practitioners are obtaining. Pragmatism has some remarkable qualities as a philosophical view that makes it suitable to accomplish this task. Our work proposes how recent advances on Neurophilosophical Methodology are a valid approach for IS ...

The ventral occipito-temporal (vOT) association cortex contributes significantly to recognize dif... more The ventral occipito-temporal (vOT) association cortex contributes significantly to recognize different types of visual patterns. It is widely accepted that a subset of this circuitry, including the visual word form area (VWFA), becomes trained to perform the task of rapidly identifying word forms. An important open question is the computational role of this circuitry: To what extent is part of a bottom-up hierarchical processing of information on visual word recognition and/or is involved in processing top-down signals from higher-level language regions. This doctoral dissertation thesis proposal is aimed at characterizing the vOT reading circuitry using behavioral, functional, structural and quantitative MRI indexes, and linking its computations to the other two important regions within the language network: the posterior parietal cortex (pPC) and the inferior frontal gyrus (IFG). Results revealed that two distinct word-responsive areas can be segregated in the vOT: one responsibl...

Scientific Data

The white matter tracts in the living human brain are critical for healthy function, and the diff... more The white matter tracts in the living human brain are critical for healthy function, and the diffusion MRI measured in these tracts is correlated with diverse behavioral measures. The technical skills required to analyze diffusion MRI data are complex: data acquisition requires MRI sequence development and acquisition expertise, analyzing raw-data into meaningful summary statistics requires computational neuroimaging and neuroanatomy expertise. The human white matter study field will advance faster if the tract summaries are available in plain data-science-ready format for non-diffusion MRI experts, such as statisticians, computer graphic researchers or data scientists in general. Here, we share a curated and processed dataset from three different MRI centers in a format that is data-science ready. The multisite data we share include measures of within and between MRI center variation in white-matter-tract diffusion measurements. Along with the dataset description and summary statis...

SummaryReceptive field properties measured in the reading portion of the ventral occipital-tempor... more SummaryReceptive field properties measured in the reading portion of the ventral occipital-temporal (VOT) cortex are task- and stimulus-dependent. To understand these effects, we analyzed responses in visual field-maps (V1-3, hV4, VO1) whose signals are likely inputs to the VOT. Within these maps, each voxel contains neurons that are responsive to specific regions of the visual field; these regions can be quantified using the moving bar paradigm and population receptive field (pRF) analysis. We measured pRFs using several types of contrast patterns within the bar (English words, Hebrew words, checkers, and false fonts). Word and false-font stimuli produce estimates that are as much as 3-4 deg closer to the fovea than checker stimuli in all visual field maps, becoming very pronounced in V3, hV4 and VO-1. The responses in the visual field maps suggest that the pRF shifts depend mostly on the visual characteristics of the stimulus, and may be explained by sensory signal models and thei...

PLOS Computational Biology

The Journal of Neuroscience

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of ... more White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human wholebrain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagr...