Renaud Lopes

Fractal and multifractal analysis: a review.

Over the last years, fractal and multifractal geometries were applied extensively in many medical signal (1D, 2D or 3D) analysis applications like pattern recognition, texture analysis and segmentation. Application of this geometry relies heavily on the estimation of the fractal features. Various methods were proposed to estimate the fractal dimension or multifractal spectral of a signal. This article presents an overview of these algorithms, the way they work, their benefits and their limits. The aim of this review is to explain and to categorize the various algorithms into groups and their application in the field of medical signal analysis.

Widespread epileptic networks in focal epilepsies: EEG‐fMRI study

Purpose:  To assess the extent of brain involvement during focal epileptic activity, we studied patterns of cortical and subcortical metabolic changes coinciding with interictal epileptic discharges (IEDs) using group analysis of simultaneous electroencephalography and functional magnetic resonance imaging (EEG‐fMRI) scans in patients with focal epilepsy.

Brain morphometry reproducibility in multi-center 3T MRI studies: A comparison of cross-sectional and longitudinal segmentations

Large-scale longitudinal multi-site MRI brain morphometry studies are becoming increasingly crucial to characterize both normal and clinical population groups using fully automated segmentation tools. The test-retest reproducibility of morphometry data acquired across multiple scanning sessions, and for different MR vendors, is an important reliability indicator since it defines the sensitivity of a protocol to detect longitudinal effects in a consortium. There is very limited knowledge about how across-session reliability of morphometry estimates might be affected by different 3T MRI systems. Moreover, there is a need for optimal acquisition and analysis protocols in order to reduce sample sizes. A recent study has shown that the longitudinal FreeSurfer segmentation offers improved within session test-retest reproducibility relative to the cross-sectional segmentation at one 3T site using a nonstandard multi-echo MPRAGE sequence. In this study we implement a multi-site 3T MRI morphometry protocol based on vendor provided T1 structural sequences from different vendors (3D MPRAGE on Siemens and Philips, 3D IR-SPGR on GE) implemented in 8 sites located in 4 European countries. The protocols used mild acceleration factors (1.5-2) when possible. We acquired across-session test-retest structural data of a group of healthy elderly subjects (5 subjects per site) and compared the across-session reproducibility of two full-brain automated segmentation methods based on either longitudinal or cross-sectional FreeSurfer processing. The segmentations include cortical thickness, intracranial, ventricle and subcortical volumes. Reproducibility is evaluated as absolute changes relative to the mean (%), Dice coefficient for volume overlap and intraclass correlation coefficients across two sessions. We found that this acquisition and analysis protocol gives comparable reproducibility results to previous studies that used longer acquisitions without acceleration. We also show that the longitudinal processing is systematically more reliable across sites regardless of MRI system differences. The reproducibility errors of the longitudinal segmentations are on average approximately half of those obtained with the cross sectional analysis for all volume segmentations and for entorhinal cortical thickness. No significant differences in reliability are found between the segmentation methods for the other cortical thickness estimates. The average of two MPRAGE volumes acquired within each test-retest session did not systematically improve the across-session reproducibility of morphometry estimates. Our results extend those from previous studies that showed improved reliability of the longitudinal analysis at single sites and/or with non-standard acquisition methods. The multi-site acquisition and analysis protocol presented here is promising for clinical applications since it allows for smaller sample sizes per MRI site or shorter trials in studies evaluating the role of potential biomarkers to predict disease progression or treatment effects.

Multisite longitudinal reliability of tract-based spatial statistics in diffusion tensor imaging of healthy elderly subjects

Large-scale longitudinal neuroimaging studies with diffusion imaging techniques are necessary to test and validate models of white matter neurophysiological processes that change in time, both in healthy and diseased brains. The predictive power of such longitudinal models will always be limited by the reproducibility of repeated measures acquired during different sessions. At present, there is limited quantitative knowledge about the across-session reproducibility of standard diffusion metrics in 3T multi-centric studies on subjects in stable conditions, in particular when using tract based spatial statistics and with elderly people. In this study we implemented a multi-site brain diffusion protocol in 10 clinical 3T MRI sites distributed across 4 countries in Europe (Italy, Germany, France and Greece) using vendor provided sequences from Siemens (Allegra, Trio Tim, Verio, Skyra, Biograph mMR), Philips (Achieva) and GE (HDxt) scanners. We acquired DTI data (2 × 2 × 2 mm(3), b = 700 s/mm(2), 5 b0 and 30 diffusion weighted volumes) of a group of healthy stable elderly subjects (5 subjects per site) in two separate sessions at least a week apart. For each subject and session four scalar diffusion metrics were considered: fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD) and axial (AD) diffusivity. The diffusion metrics from multiple subjects and sessions at each site were aligned to their common white matter skeleton using tract-based spatial statistics. The reproducibility at each MRI site was examined by looking at group averages of absolute changes relative to the mean (%) on various parameters: i) reproducibility of the signal-to-noise ratio (SNR) of the b0 images in centrum semiovale, ii) full brain test-retest differences of the diffusion metric maps on the white matter skeleton, iii) reproducibility of the diffusion metrics on atlas-based white matter ROIs on the white matter skeleton. Despite the differences of MRI scanner configurations across sites (vendors, models, RF coils and acquisition sequences) we found good and consistent test-retest reproducibility. White matter b0 SNR reproducibility was on average 7 ± 1% with no significant MRI site effects. Whole brain analysis resulted in no significant test-retest differences at any of the sites with any of the DTI metrics. The atlas-based ROI analysis showed that the mean reproducibility errors largely remained in the 2-4% range for FA and AD and 2-6% for MD and RD, averaged across ROIs. Our results show reproducibility values comparable to those reported in studies using a smaller number of MRI scanners, slightly different DTI protocols and mostly younger populations. We therefore show that the acquisition and analysis protocols used are appropriate for multi-site experimental scenarios.

Local fractal and multifractal features for volumic texture characterization

For texture analysis, several features such as co-occurrence matrices, Gabor filters and the wavelet transform are used. Recently, fractal geometry appeared to be an effective feature to analyze texture. But it is often restricted to 2D images, while 3D information can be very important especially in medical image processing. Moreover applications are limited to the use of fractal dimension. This study focuses on the benefits of fractal geometry in a classification method based on volumic texture analysis. The proposed methods make use of fractal and multifractal features for a 3D texture analysis of a voxel neighborhood. They are validated with synthetic data before being applied on real images. Their efficiencies are proved by comparison to some other texture features in supervised classification processes (AdaBoost and support vector machine classifiers). The results showed that features based on fractal geometry (by combining fractal and multifractal features) contributed to new texture characterization. Information on new features was useful and complementary for a classification method. This study suggests that fractal geometry can provide a new useful information in 3D texture analysis, especially in medical imaging.

A model to estimate the outcome of prostate cancer photodynamic therapy with TOOKAD Soluble WST11

Interstitial photodynamic therapy is becoming an interesting modality to treat some early stage prostate cancers. A light-sensitive drug is injected to the patient and activated by light using optical fibres inserted inside the prostate. In this work, we were interested in the characterization of the light action model for the WST11 (Tookad® Soluble) drug. A retrospective analysis was performed on results from 28 patients enrolled in phase I and II trials with the WST11 drug. A drug dose of 4 mg/kg patient, dose light of 200 J cm(-1) and wavelength of 753 nm were used. Correlation between the illuminated volume and the obtained necrosis, measured at day 7 MR images, was clearly established. This result suggests that photodynamic therapy planning is possible based on this model.

A New Method for Volume Segmentation of PET Images, Based on Possibility Theory

18F-fluorodeoxyglucose positron emission tomography (18FDG PET) has become an essential technique in oncology. Accurate segmentation and uptake quantification are crucial in order to enable objective follow-up, the optimization of radiotherapy planning, and therapeutic evaluation. We have designed and evaluated a new, nearly automatic and operator-independent segmentation approach. This incorporated possibility theory, in order to take into account the uncertainty and inaccuracy inherent in the image. The approach remained independent of PET facilities since it did not require any preliminary calibration. Good results were obtained from phantom images [percent error =18.38% (mean) ±9.72% (standard deviation)]. Results on simulated and anatomopathological data sets were quantified using different similarity measures and showed the method was efficient (simulated images: Dice index =82.18% ±13.53% for SUV =2.5 ). The approach could, therefore, be an efficient and robust tool for uptake volume segmentation, and lead to new indicators for measuring volume of interest activity.

Longitudinal reproducibility of default-mode network connectivity in healthy elderly participants: A multicentric resting-state fMRI study.

To date, limited data are available regarding the inter-site consistency of test-retest reproducibility of functional connectivity measurements, in particular with regard to integrity of the Default Mode Network (DMN) in elderly participants. We implemented a harmonized resting-state fMRI protocol on 13 clinical scanners at 3.0T using vendor-provided sequences. Each site scanned a group of 5 healthy elderly participants twice, at least a week apart. We evaluated inter-site differences and test-retest reproducibility of both temporal signal-to-noise ratio (tSNR) and functional connectivity measurements derived from: i) seed-based analysis (SBA) with seed in the posterior cingulate cortex (PCC), ii) group independent component analysis (ICA) separately for each site (site ICA), and iii) consortium ICA, with group ICA across the whole consortium. Despite protocol harmonization, significant and quantitatively important inter-site differences remained in the tSNR of resting-state fMRI data; these were plausibly driven by hardware and pulse sequence differences across scanners which could not be harmonized. Nevertheless, the tSNR test-retest reproducibility in the consortium was high (ICC=0.81). The DMN was consistently extracted across all sites and analysis methods. While significant inter-site differences in connectivity scores were found, there were no differences in the associated test-retest error. Overall, ICA measurements were more reliable than PCC-SBA, with site ICA showing higher reproducibility than consortium ICA. Across the DMN nodes, the PCC yielded the most reliable measurements (≈4% test-retest error, ICC=0.85), the medial frontal cortex the least reliable (≈12%, ICC=0.82) and the lateral parietal cortices were in between (site ICA). Altogether these findings support usage of harmonized multisite studies of resting-state functional connectivity to characterize longitudinal effects in studies that assess disease progression and treatment response.

Detection of epileptic activity in fMRI without recording the EEG

EEG-fMRI localizes epileptic foci by detecting cerebral hemodynamic changes that are correlated to epileptic events visible in EEG. However, scalp EEG is insensitive to activity restricted to deep structures and recording the EEG in the scanner is complex and results in major artifacts that are difficult to remove. This study presents a new framework for identifying the BOLD manifestations of epileptic discharges without having to record the EEG. The first stage is based on the detection of epileptic events for each voxel by sparse representation in the wavelet domain. The second stage is to gather voxels according to proximity in time and space of detected activities. This technique was evaluated on data generated by superposing artificial responses at different locations and responses amplitude in the brain for 6 control subject runs. The method was able to detect effectively and consistently for responses amplitude of at least 1% above baseline. 46 runs from 15 patients with focal epilepsy were investigated. The results demonstrate that the method detected at least one concordant event in 37/41 runs. The maps of activation obtained from our method were more similar to those obtained by EEG-fMRI than to those obtained by the other method used in this context, 2D-Temporal Cluster Analysis. For 5 runs without event read on scalp EEG, 3 runs showed an activation concordant with the patients diagnostic. It may therefore be possible, at least when spikes are infrequent, to detect their BOLD manifestations without having to record the EEG.

Cerebral Hypoperfusion and Hypometabolism Detected by Arterial Spin Labeling MRI and FDG‐PET in Early‐Onset Alzheimer's Disease

Early‐onset Alzheimers disease (EOAD) is frequently associated with atypical clinical presentations and its early detection remains a challenging issue. In this study, we used arterial spin labeling (ASL), a noninvasive perfusion MRI sequence, and [18F]‐FDG‐PET to detect the perfusion and metabolic features in patients with EOAD.