Accelerated Microstructure Imaging via Convex Optimization (AMICO) in crossing fibers

Mapping the microstructure properties of the local tissues in the brain is crucial to understand any pathological condition from a biological perspective. Most of the existing techniques to estimate the microstructure of the white matter assume a single axon orientation whereas numerous regions of the brain actually present a fiber-crossing configuration. The purpose of the present study is to extend a recent convex optimization framework to recover microstructure parameters in regions with multiple fibers.

Accelerated Microstructure Imaging via Convex Optimisation for regions with multiple fibres (AMICOx)

This paper reviews and extends our previous work to enable fast axonal diameter mapping from diffusion MRI data in the presence of multiple fibre populations within a voxel. Most of the existing mi-crostructure imaging techniques use non-linear algorithms to fit their data models and consequently, they are computationally expensive and usually slow. Moreover, most of them assume a single axon orientation while numerous regions of the brain actually present more complex configurations, e.g. fiber crossing. We present a flexible framework, based on convex optimisation, that enables fast and accurate reconstructions of the microstructure organisation, not limited to areas where the white matter is coherently oriented. We show through numerical simulations the ability of our method to correctly estimate the microstructure features (mean axon diameter and intra-cellular volume fraction) in crossing regions.

Graduating 4th year radiology residents' perception of optimal imaging modalities for neoplasm and trauma: a pilot study from four U.S. universities

OBJECTIVE: Our purpose was to assess 4th year radiology residents' perception of the optimal imaging modality to investigate neoplasm and trauma. MATERIALS AND METHODS: Twenty-seven 4th year radiology residents from four residency programs were surveyed. They were asked about the best imaging modality to evaluate the brain and spine, lungs, abdomen, and the musculoskeletal system. Imaging modalities available were MRI, CT, ultrasound, PET, and X-ray. All findings were compared to the ACR appropriateness criteria. RESULTS: MRI was chosen as the best imaging modality to evaluate brain, spine, abdominal, and musculoskeletal neoplasm in 96.3%, 100%, 70.4%, and 63% of residents, respectively. CT was chosen by 88.9% to evaluate neoplasm of the lung. Optimal imaging modality to evaluate trauma was CT for brain injuries (100%), spine (92.6%), lung (96.3%), abdomen (92.6%), and major musculoskeletal trauma (74.1%); MRI was chosen for sports injury (96.3%). There was agreement with ACR appropriateness criteria. CONCLUSION: Residents' perception of the best imaging modalities for neoplasm and trauma concurred with the appropriateness criteria by the ACR.

Automatic Brain Extraction in Fetal MRI using Multi-Atlas-based Segmentation

In fetal brain MRI, most of the high-resolution reconstruction algorithms rely on brain segmentation as a preprocessing step. Manual brain segmentation is however highly time-consuming and therefore not a realistic solution. In this work, we assess on a large dataset the performance of Multiple Atlas Fusion (MAF) strategies to automatically address this problem. Firstly, we show that MAF significantly increase the accuracy of brain segmentation as regards single-atlas strategy. Secondly, we show that MAF compares favorably with the most recent approach (Dice above 0.90). Finally, we show that MAF could in turn provide an enhancement in terms of reconstruction quality.

Connectivity and tissue microstructural alterations in right and left temporal lobe epilepsy revealed by diffusion spectrum imaging.

Focal epilepsy is increasingly recognized as the result of an altered brain network, both on the structural and functional levels and the characterization of these widespread brain alterations is crucial for our understanding of the clinical manifestation of seizure and cognitive deficits as well as for the management of candidates to epilepsy surgery. Tractography based on Diffusion Tensor Imaging allows non-invasive mapping of white matter tracts in vivo. Recently, diffusion spectrum imaging (DSI), based on an increased number of diffusion directions and intensities, has improved the sensitivity of tractography, notably with respect to the problem of fiber crossing and recent developments allow acquisition times compatible with clinical application. We used DSI and parcellation of the gray matter in regions of interest to build whole-brain connectivity matrices describing the mutual connections between cortical and subcortical regions in patients with focal epilepsy and healthy controls. In addition, the high angular and radial resolution of DSI allowed us to evaluate also some of the biophysical compartment models, to better understand the cause of the changes in diffusion anisotropy. Global connectivity, hub architecture and regional connectivity patterns were altered in TLE patients and showed different characteristics in RTLE vs LTLE with stronger abnormalities in RTLE. The microstructural analysis suggested that disturbed axonal density contributed more than fiber orientation to the connectivity changes affecting the temporal lobes whereas fiber orientation changes were more involved in extratemporal lobe changes. Our study provides further structural evidence that RTLE and LTLE are not symmetrical entities and DSI-based imaging could help investigate the microstructural correlate of these imaging abnormalities.

Characterisation of anatomical properties of the human basal ganglia using magnetic resonance imaging

The detailed in-vivo characterization of subcortical brain structures is essential not only to understand the basic organizational principles of the healthy brain but also for the study of the involvement of the basal ganglia in brain disorders. The particular tissue properties of basal ganglia - most importantly their high iron content, strongly affect the contrast of magnetic resonance imaging (MRI) images, hampering the accurate automated assessment of these regions. This technical challenge explains the substantial controversy in the literature about the magnitude, directionality and neurobiological interpretation of basal ganglia structural changes estimated from MRI and computational anatomy techniques. My scientific project addresses the pertinent need for accurate automated delineation of basal ganglia using two complementary strategies: ? Empirical testing of the utility of novel imaging protocols to provide superior contrast in the basal ganglia and to quantify brain tissue properties; ? Improvement of the algorithms for the reliable automated detection of basal ganglia and thalamus Previous research demonstrated that MRI protocols based on magnetization transfer (MT) saturation maps provide optimal grey-white matter contrast in subcortical structures compared with the widely used Tl-weighted (Tlw) images (Helms et al., 2009). Under the assumption of a direct impact of brain tissue properties on MR contrast my first study addressed the question of the mechanisms underlying the regional specificities effect of the basal ganglia. I used established whole-brain voxel-based methods to test for grey matter volume differences between MT and Tlw imaging protocols with an emphasis on subcortical structures. I applied a regression model to explain the observed grey matter differences from the regionally specific impact of brain tissue properties on the MR contrast. The results of my first project prompted further methodological developments to create adequate priors for the basal ganglia and thalamus allowing optimal automated delineation of these structures in a probabilistic tissue classification framework. I established a standardized workflow for manual labelling of the basal ganglia, thalamus and cerebellar dentate to create new tissue probability maps from quantitative MR maps featuring optimal grey-white matter contrast in subcortical areas. The validation step of the new tissue priors included a comparison of the classification performance with the existing probability maps. In my third project I continued investigating the factors impacting automated brain tissue classification that result in interpretational shortcomings when using Tlw MRI data in the framework of computational anatomy. While the intensity in Tlw images is predominantly

Individual Differences in True and False Memory Retrieval Are Related to White Matter Brain Microstructure

We sometimes vividly remember things that did not happen, a phenomenon with general relevance, not only in the courtroom. It is unclear to what extent individual differences in false memories are driven by anatomical differences in memory-relevant brain regions. Here we show in humans that microstructural properties of different white matter tracts as quantified using diffusion tensor imaging are strongly correlated with true and false memory retrieval. To investigate these hypotheses, we tested a large group of participants in a version of the Deese-Roediger-McDermott paradigm (recall and recognition) and subsequently obtained diffusion tensor images. A voxel-based whole-brain level linear regression analysis was performedto relatefractional anisotropyto indices oftrue andfalse memory recall and recognition. True memory was correlated to diffusion anisotropy in the inferior longitudinal fascicle, the major connective pathway of the medial temporal lobe, whereas a greater proneness to retrieve false items was related to the superior longitudinal fascicle connecting frontoparietal structures. Our results show that individual differences in white matter microstructure underlie true and false memory performance.

Apolipoprotein E and Recovery from Traumatic Brain Injury

The outcome from traumatic brain injury (TBI) is variable and only partly explained by known prognostic factors. This is especially true for predicting long-term outcome. Genetic factors may influence the brain`s susceptibility to injury or capacity for repair and regeneration. To examine the association of apolipoproteinE (apoE) genotype with long-term outcome, hippocampal volumes and general brain atrophy, we determined the apoE genotype from 61 TBI patients who had been injured over on average 31 years earlier. The long-term outcome was evaluated with repeated neuropsychological testing and by applying various measures of everyday functioning and quality of life. Magnetic resonance imaging (MRI) based volumetric analyses of the hippocampus and lateral ventricles were performed. In the prospective study, the purpose was to examine the association between apoE genotype and visibility of traumatic brain lesions during the first year after TBI and the ability of apoE genotype, the Glasgow Coma Score (GCS), MRI findings and duration of posttraumatic amnesia (PTA) to predict the one-year outcome. Thirty-three patients with TBI were studied and the outcome was evaluated with the Head Injury Symptom Checklist (HISC) and the Glasgow Outcome Scale extended version (GOS-E) scores one year after the injury. MRI and apoE genotyping were carried out. After three decades, neither hippocampal nor lateral ventricle volumes differed significantly in those patients with the apoE ε4 allele vs those without this allele, but the TBI patients with the apoE ε4 allele showed significantly poorer general cognitive level than those without this allele. This decline was wholly accounted for by a subgroup of patients who had developed incident or clinical dementia. In the prospective study the apoE genotype was not associated with visible MRI changes or outcome. The duration of PTA and acute MRI were the best predictors of one-year outcome in TBI. A portion of the TBI patients with the apoE ε4 allele seem to be at risk of long-term cognitive decline. This association may involve mechanisms other than those responsible for the development of brain atrophy. The early MRI and PTA have an important role in assessing the injury severity and prognosis.

DWI and complex brain network analysis predicts vascular cognitive impairment in spontaneous hypertensive rats undergoing executive function tests

The identification of biomarkers of vascular cognitive impairment is urgent for its early diagnosis. The aim of this study was to detect and monitor changes in brain structure and connectivity, and to correlate them with the decline in executive function. We examined the feasibility of early diagnostic magnetic resonance imaging (MRI) to predict cognitive impairment before onset in an animal model of chronic hypertension: Spontaneously Hypertensive Rats. Cognitive performance was tested in an operant conditioning paradigm that evaluated learning, memory, and behavioral flexibility skills. Behavioral tests were coupled with longitudinal diffusion weighted imaging acquired with 126 diffusion gradient directions and 0.3 mm(3) isometric resolution at 10, 14, 18, 22, 26, and 40 weeks after birth. Diffusion weighted imaging was analyzed in two different ways, by regional characterization of diffusion tensor imaging (DTI) indices, and by assessing changes in structural brain network organization based on Q-Ball tractography. Already at the first evaluated times, DTI scalar maps revealed significant differences in many regions, suggesting loss of integrity in white and gray matter of spontaneously hypertensive rats when compared to normotensive control rats. In addition, graph theory analysis of the structural brain network demonstrated a significant decrease of hierarchical modularity, global and local efficacy, with predictive value as shown by regional three-fold cross validation study. Moreover, these decreases were significantly correlated with the behavioral performance deficits observed at subsequent time points, suggesting that the diffusion weighted imaging and connectivity studies can unravel neuroimaging alterations even overt signs of cognitive impairment become apparent.

Antenatal inflammation and brain pathology in preterm infants

Chorioamnionitis is known to be an important risk factor underlying preterm delivery, and it has also been suggested to associate with brain lesions and deviant neurological development in both preterm and term infants. Cytokines are believed to be the link causing the deleterious effects of inflammation to the nervous system. Their genetic regulation has also been suggested to play a role, as interleukin (IL)-6 -174 and -572 genotypes, which partly regulate IL-6 synthesis responses, have been connected with deviant neurological development in preterm infants. We evaluated the association of histological chorioamnionitis with brain lesions, regional brain volumes, and the functioning of the auditory pathway in very low birth weight/very low gestational age (VLBW/VLGA) infants. In addition, we investigated the association between IL-6 -174 and -572 genotypes and histological chorioamnionitis, neonatal infections, and brain lesions and regional brain volumes in VLBW/VLGA infants. This study is a part of a larger multidisciplinary project PIPARI (Development and Functioning of Very Low Birth Weight Infants from Infancy to School Age), in which the survivors of a 6-year cohort of VLBW/VLGA infants (n=274) are being followed until school age in Turku University Central Hospital, Finland. Placental samples were collected in the delivery room, and were analyzed for histological inflammatory findings. Blood samples from the infants were collected and DNA was genotyped for IL-6-174 and -572 polymorphisms (GG/GC/CC). Brain ultrasound examinations were performed repeatedly in the neonatal intensive care unit and at term age, and were analysed for structural brain lesions. Brain magnetic resonance imaging was performed at term age, and was analysed for regional brain volumes. In addition, diffusion tensor imaging was performed at term, and was used to analyse fractional anisotrophy and the apparent diffusion coefficient of inferior colliculus. The brainstem auditory evoked potential recordings were carried out according to the routine clinical procedure at median age of 30 days after term age. In our study, we found that histological chorioamnionitis was not an independent risk factor for brain lesions, reduced regional brain volumes or abnormal functioning of the auditory pathway in VLBW/VLGA infants. In addition, we found that IL-6 -174 GG and -572 GC genotypes were associated with a higher incidence of histological chorioamnionitis, and that -174 CC genotype associated with higher incidence of septicaemia. The analysed IL-6 genotypes were not associated with other brain lesions, but a reduced volume of basal ganglia and thalami was associated with IL-6 -174 CC and -572 GG genotypes. In conclusion, our findings suggest that histological chorioamnionitis is not an independent risk factor for the brain development of VLBW/VLGA infants, or that the risk caused by inflammation does not exceed the risks attributed to other underlying pathologies behind preterm deliveries. In addition, our findings give reason to propose that IL-6 promoter genotypes have a role in the defence against serious infections and in the brain development of VLBW/VLGA infants.

Imaging bilinguals: When the neurosciences meet the languange sciences

The starting point of our investigation was the longstanding notion that bilingual individuals need effective mechanisms to prevent interference from one language while processing material in the other (e.g. Penfield and Roberts, 1959). To demonstrate how the prevention of interference is implemented in the brain we employed event-related brain potentials (ERPs; see Munte, Urbach, ¨ Duzel and Kutas, 2000, for an introductory review) ¨ and functional magnetic resonance imaging (fMRI) techniques, thus pursuing a combined temporal and spatial imaging approach. In contrast to previous investigations using neuroimaging techniques in bilinguals, which had been mainly concerned with the localization of the primary and secondary languages (e.g. Perani, Paulesu, Galles, Dupoux, Dehaene, Bettinardi, Cappa, Fazio and Mehler, 1998; Chee, Caplan, Soon, Sriram, Tan, Thiel and Weekes, 1999), our study addressed the dynamic aspects of bilingual language processing.

Functional connectivity of reward processing in the brain

Controversial results have been reported concerning the neural mechanisms involved in the processing of rewards and punishments. On the one hand, there is evidence suggesting that monetary gains and losses activate a similar fronto-subcortical network. On the other hand, results of recent studies imply that reward and punishment may engage distinct neural mechanisms. Using functional magnetic resonance imaging (fMRI) we investigated both regional and interregional functional connectivity patterns while participants performed a gambling task featuring unexpectedly high monetary gains and losses. Classical univariate statistical analysis showed that monetary gains and losses activated a similar fronto-striatallimbic network, in which main activation peaks were observed bilaterally in the ventral striatum. Functional connectivity analysis showed similar responses for gain and loss conditions in the insular cortex, the amygdala, and the hippocampus that correlated with the activity observed in the seed region ventral striatum, with the connectivity to the amygdala appearing more pronounced after losses. Larger functional connectivity was found to the medial orbitofrontal cortex for negative outcomes. The fact that different functional patterns were obtained with both analyses suggests that the brain activations observed in the classical univariate approach identifi es the involvement of different functional networks in the current task. These results stress the importance of studying functional connectivity in addition to standard fMRI analysis in reward-related studies.

Reward networks in the brain as captured by connectivity measures

An assortment of human behaviors is thought to be driven by rewards including reinforcement learning, novelty processing, learning, decision making, economic choice, incentive motivation, and addiction. In each case the ventral tegmental area/ventral striatum (nucleus accumbens) (VTAVS) system has been implicated as a key structure by functional imaging studies, mostly on the basis of standard, univariate analyses. Here we propose that standard functional magnetic resonance imaging analysis needs to be complemented by methods that take into account the differential connectivity of the VTAVS system in the different behavioral contexts in order to describe reward based processes more appropriately. We fi rst consider the wider network for reward processing as it emerged from animal experimentation. Subsequently, an example for a method to assess functional connectivity is given. Finally, we illustrate the usefulness of such analyses by examples regarding reward valuation, reward expectation and the role of reward in addiction.

Brain Dopamine and Serotonin Receptors in the Perception of Pain. Positron Emission Tomography Studies in Healthy Subjects

The role of dopamine and serotonin in spinal pain regulation is well established. However, little is known concerning the role of brain dopamine and serotonin in the perception of pain in humans. The aim of this study was to assess the potential role of brain dopamine and serotonin in determining experimental pain sensitivity in humans using positron emission tomography (PET) and psychophysical methods. A total of 39 healthy subjects participated in the study, and PET imaging was performed to assess brain dopamine D2/D3 and serotonin 5-HT_1A receptor availability. In a separate session, sensitivity to pain and touch was assessed with traditional psychophysical methods, allowing the evaluation of potential associations between D2/D3 and 5-HT_1A binding and psychophysical responses. The subjects’ responses were also analyzed according to Signal Detection Theory, which enables separate assessment of the subject’s discriminative capacity (sensory factor) and response criterion (non-sensory factor). The study found that the D2/D3 receptor binding in the right putamen was inversely correlated with pain threshold and response criterion. 5-HT_1A binding in cingulate cortex, inferior temporal gyrus and medial prefrontal cortex was inversely correlated with discriminative capacity for touch. Additionally, the response criterion for pain and intensity rating of suprathreshold pain were inversely correlated with 5-HT_1A binding in multiple brain areas. The results suggest that brain D2/D3 receptors and 5-HT_1A receptors modulate sensitivity to pain and that the pain modulatory effects may, at least partly, be attributed to influences on the response criterion. 5-HT_1A receptors are also involved in the regulation of touch by having an effect on discriminative capacity.

The Vulnerable Brain and Very Preterm Infants - Findings from the PIPARI-Study

Preterm birth is a risk for normal brain development. Brain maturation that normally happens in the uterus is in very preterm infants a developmental challenge during their stay in a neonatal intensive care unit (NICU). Typical brain injuries of preterm infants include ischemic injuries, brain haemorrhages, ventricular dilatation (VD), and reduced brain volumes. Brain injury is a serious complication of prematurity leading to possible long term consequences for the neurodevelopment of the very low birth weight (VLBW) infant, such as cerebral palsy (CP), hearing impairments, vision problems, and delay in cognitive development.There is a need for further studies to ascertain the potential risk factors and their causal relationships to brain vulnerability, growth and development in the increasing number of surviving VLBW infants. This thesis consists of four studies evaluating the definitions, causes and consequences of brain lesions in VLBW(<1500g) or very low gestationalage (VLGA) (gestational age <32 gestational weeks) infants. We showed that the redistribution of fetal blood flow is a risk factor for smaller brain volumes at term. In addition,we showed that brain lesions related to prematurity are not associated with increased spontaneous crying behaviour or circadian rhythm development in infancy. However, the preterm infants began to fuss more often and were held more than term infants at five months of age. Furthermore, we showed that VD is associated with brain lesions and smaller brain volumes. Therefore, brain magneticresonance imaging can be recommended for infants with VD. VD together with other brain pathology is a risk factor for the onset of developmental impairments in VLBW/VLGA infants at two years of age.