Components of variance in a multicentre functional MRI study and implications for calculation of statistical power

Efficacy of MRI data harmonization in the age of machine learning: a multicenter study across 36 datasets

Pooling publicly-available MRI data from multiple sites allows to assemble extensive groups of subjects, increase statistical power, and promote data reuse with machine learning techniques. The harmonization of multicenter data is necessary to reduce the confounding effect associated with non-biological sources of variability in the data. However, when applied to the entire dataset before machine learning, the harmonization leads to data leakage, because information outside the training set may affect model building, and potentially falsely overestimate performance. We propose a 1) measurement of the efficacy of data harmonization; 2) harmonizer transformer, i.e., an implementation of the ComBat harmonization allowing its encapsulation among the preprocessing steps of a machine learning pipeline, avoiding data leakage by design. We tested these tools using brain T1-weighted MRI data from 1740 healthy subjects acquired at 36 sites. After harmonization, the site effect was removed or reduced, and we showed the data leakage effect in predicting individual age from MRI data, highlighting that introducing the harmonizer transformer into a machine learning pipeline allows for avoiding data leakage by design.

Connectivity alterations of mesostriatal pathways in first episode psychosis

BACKGROUND AND HYPOTHESIS

Pathogenic understanding of the psychotic disorders converges on regulation of dopaminergic signaling in mesostriatocortical pathways. Functional connectivity of the mesostriatal pathways may inform us of the neuronal networks involved.

STUDY DESIGN

This longitudinal study of first episode psychosis (FEP) (49 patients, 43 controls) employed seed-based functional connectivity analyses of fMRI data collected during a naturalistic movie stimulus.

STUDY RESULTS

We identified hypoconnectivity of the dorsal striatum with the midbrain, associated with antipsychotic medication dose in FEP, in comparison with the healthy control group. The midbrain regions that showed hypoconnectivity with the dorsal striatum also showed hypoconnectivity with cerebellar regions suggested to be involved in regulation of the mesostriatocortical dopaminergic pathways. None of the baseline hypoconnectivity detected was seen at follow-up.

CONCLUSIONS

These findings extend earlier resting state findings on mesostriatal connectivity in psychotic disorders and highlight the potential for cerebellar regulation of the mesostriatocortical pathways as a target of treatment trials.

Functional network connectivity and topology during naturalistic stimulus is altered in first-episode psychosis

BACKGROUND

Psychotic disorders have been suggested to derive from dysfunctional integration of signaling between brain regions. Earlier studies have found several changes in functional network synchronization as well as altered network topology in patients with psychotic disorders. However, studies have used mainly resting-state that makes it more difficult to link functional alterations to any specific stimulus or experience. We set out to examine functional connectivity as well as graph (topological) measures and their association to symptoms in first-episode psychosis patients during movie viewing. Our goal was to understand whole-brain functional dynamics of complex naturalistic information processing in psychosis and changes in brain functional organization related to symptoms.

METHODS

71 first-episode psychosis patients and 57 control subjects watched scenes from the movie Alice in Wonderland during 3 T fMRI. We compared functional connectivity and graph measures indicating integration, segregation and centrality between groups, and examined the association between topology and symptom scores in the patient group.

RESULTS

We identified a subnetwork with predominantly decreased links of functional connectivity in first-episode psychosis patients. The subnetwork was mainly comprised of nodes of and links between the cingulo-opercular, sensorimotor and default-mode networks. In topological measures, we observed between-group differences in properties of centrality.

CONCLUSIONS

Functional brain networks are affected during naturalistic information processing already in the early stages of psychosis, concentrated in salience- and cognitive control-related hubs and subnetworks. Understanding these aberrant dynamics could add to better targeted cognitive and behavioral interventions in the early stages of psychotic disorders.

Aberrant Cortical Integration in First-Episode Psychosis During Natural Audiovisual Processing

BACKGROUND

Functional magnetic resonance imaging studies of psychotic disorders have reported both hypoactivity and hyperactivity in numerous brain regions. In line with the dysconnection hypothesis, these regions include cortical integrative hub regions. However, most earlier studies focused on a single cognitive function at a time, assessed by delivering artificial stimuli to patients with chronic psychosis. Thus, it remains unresolved whether these findings are present already in early psychosis and whether they translate to real-life-like conditions that require multisensory processing and integration.

METHODS

Scenes from the movie Alice in Wonderland (2010) were shown to 51 patients with first-episode psychosis (16 women) and 32 community-based control subjects (17 women) during 3T functional magnetic resonance imaging. We compared intersubject correlation, a measure of similarity of brain signal time courses in each voxel, between the groups. We also quantified the hubness as the number of connections each region has.

RESULTS

Intersubject correlation was significantly lower in patients with first-episode psychosis than in control subjects in the medial and lateral prefrontal, cingulate, precuneal, and parietotemporal regions, including the default mode network. Regional magnitude of between-group difference in intersubject correlation was associated with the hubness.

CONCLUSIONS

Our findings provide novel evidence for the dysconnection hypothesis by showing that during complex real-life-like stimulation, the most prominent functional alterations in psychotic disorders relate to integrative brain functions. Presence of such abnormalities in first-episode psychosis rules out long-term effects of illness or medication. These methods can be used in further studies to map widespread hub alterations in a single functional magnetic resonance imaging session and link them to potential downstream and upstream pathways.

Statistical harmonization corrects site effects in functional connectivity measurements from multi-site fMRI data

Acquiring resting-state functional magnetic resonance imaging (fMRI) datasets at multiple MRI scanners and clinical sites can improve statistical power and generalizability of results. However, multi-site neuroimaging studies have reported considerable nonbiological variability in fMRI measurements due to different scanner manufacturers and acquisition protocols. These undesirable sources of variability may limit power to detect effects of interest and may even result in erroneous findings. Until now, there has not been an approach that removes unwanted site effects. In this study, using a relatively large multi-site (4 sites) fMRI dataset, we investigated the impact of site effects on functional connectivity and network measures estimated by widely used connectivity metrics and brain parcellations. The protocols and image acquisition of the dataset used in this study had been homogenized using identical MRI phantom acquisitions from each of the neuroimaging sites; however, intersite acquisition effects were not completely eliminated. Indeed, in this study, we found that the magnitude of site effects depended on the choice of connectivity metric and brain atlas. Therefore, to further remove site effects, we applied ComBat, a harmonization technique previously shown to eliminate site effects in multi-site diffusion tensor imaging (DTI) and cortical thickness studies. In the current work, ComBat successfully removed site effects identified in connectivity and network measures and increased the power to detect age associations when using optimal combinations of connectivity metrics and brain atlases. Our proposed ComBat harmonization approach for fMRI-derived connectivity measures facilitates reliable and efficient analysis of retrospective and prospective multi-site fMRI neuroimaging studies.

Aberrant Cerebral Blood Flow in Response to Hunger and Satiety in Women Remitted from Anorexia Nervosa

The etiology of pathological eating in anorexia nervosa (AN) remains poorly understood. Cerebral blood flow (CBF) is an indirect marker of neuronal function. In healthy adults, fasting increases CBF, reflecting increased delivery of oxygen and glucose to support brain metabolism. This study investigated whether women remitted from restricting-type AN (RAN) have altered CBF in response to hunger that may indicate homeostatic dysregulation contributing to their ability to restrict food. We compared resting CBF measured with pulsed arterial spin labeling in 21 RAN and 16 healthy comparison women (CW) when hungry (after a 16-h fast) and after a meal. Only remitted subjects were examined to avoid the confounding effects of malnutrition on brain function. Compared to CW, RAN demonstrated a reduced difference in the Hungry − Fed CBF contrast in the right ventral striatum, right subgenual anterior cingulate cortex (p_corr < 0.05) and left posterior insula (p_unc < 0.05); RAN had decreased CBF when hungry versus fed, whereas CW had increased CBF when hungry versus fed. Moreover, decreased CBF when hungry in the left insula was associated with greater hunger ratings on the fasted day for RAN. This represents the first study to show that women remitted from AN have aberrant resting neurovascular function in homeostatic neural circuitry in response to hunger. Regions involved in homeostatic regulation showed group differences in the Hungry − Fed contrast, suggesting altered cellular energy metabolism in this circuitry that may reduce motivation to eat.

Response in taste circuitry is not modulated by hunger and satiety in women remitted from bulimia nervosa

Individuals with bulimia nervosa (BN) engage in episodes of binge eating, marked by loss of control and eating despite fullness. Does altered reward and metabolic state contribute to BN pathophysiology? Normally, hunger increases (and satiety decreases) reward salience to regulate eating. We investigated whether BN is associated with an abnormal response in a neural circuit involved in translating taste signals into motivated behavior, when hungry and fed. Twenty-six women remitted from BN (RBN) and 22 control women (CW) were administered water and sucrose during 2 counterbalanced fMRI visits, following a 16-hr fast or a standardized breakfast. Significant Group × Condition interactions were found in the left putamen, insula, and amygdala. Post hoc analyses revealed CW were significantly more responsive to taste stimuli when hungry versus fed in the left putamen and amygdala. In contrast, RBN response did not differ between conditions. Further, RBN had greater activation in the left amygdala compared with CW when fed. Findings suggest that RBN neural response to rewarding stimuli may not be modulated by metabolic state. Data raise the possibility that disinhibited eating in BN could result from a failure to devalue food reward when fed, resulting in an exaggerated response. (PsycINFO Database Record

Altered reward expectancy in individuals with recent methamphetamine dependence

BACKGROUND

Chronic methamphetamine use may lead to changes in reward-related function of the ventral striatum and caudate nucleus. Whether methamphetamine-dependent individuals show heightened reactivity to positively valenced stimuli (i.e. positive reinforcement mechanisms), or an exaggerated response to negatively valenced stimuli (i.e. driven by negative reinforcement mechanisms) remains unclear. This study investigated neural functioning of expectancy and receipt for gains and losses in adults with (METH+) and without (METH-) histories of methamphetamine dependence.

METHODS

Participants (17 METH+; 23 METH-) performed a probabilistic feedback expectancy task during blood-oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI). Participants were given visual cues probabilistically associated with monetary gain, loss, or neutral outcomes. General linear models examined the BOLD response to: (1) anticipation of gains and losses, and (2) gain and loss monetary outcomes.

RESULTS

METH+ had less BOLD response to loss anticipation than METH- in the ventral striatum and posterior caudate. METH+ also showed more BOLD response to loss outcomes than to gain outcomes in the anterior and posterior caudate, whereas METH- did not show differential responses to the valence of outcomes.

DISCUSSION

METH+ individuals showed attenuated neural response to anticipated gains and losses, but their response to loss outcomes was greater than to gain outcomes. A decreased response to loss anticipation, along with a greater response to loss outcomes, suggests an altered ability to evaluate future risks and benefits based upon prior experience, which may underlie suboptimal decision-making in METH+ individuals that increases the likelihood of risky behavior.

Variance decomposition for single-subject task-based fMRI activity estimates across many sessions

Here we report an exploratory within-subject variance decomposition analysis conducted on a task-based fMRI dataset with an unusually large number of repeated measures (i.e., 500 trials in each of three different subjects) distributed across 100 functional scans and 9 to 10 different sessions. Within-subject variance was segregated into four primary components: variance across-sessions, variance across-runs within a session, variance across-blocks within a run, and residual measurement/modeling error. Our results reveal inhomogeneous and distinct spatial distributions of these variance components across significantly active voxels in grey matter. Measurement error is dominant across the whole brain. Detailed evaluation of the remaining three components shows that across-session variance is the second largest contributor to total variance in occipital cortex, while across-runs variance is the second dominant source for the rest of the brain. Network-specific analysis revealed that across-block variance contributes more to total variance in higher-order cognitive networks than in somatosensory cortex. Moreover, in some higher-order cognitive networks across-block variance can exceed across-session variance. These results help us better understand the temporal (i.e., across blocks, runs and sessions) and spatial distributions (i.e., across different networks) of within-subject natural variability in estimates of task responses in fMRI. They also suggest that different brain regions will show different natural levels of test-retest reliability even in the absence of residual artifacts and sufficiently high contrast-to-noise measurements. Further confirmation with a larger sample of subjects and other tasks is necessary to ensure generality of these results.

Auditory Hallucinations and the Brain's Resting-State Networks: Findings and Methodological Observations

In recent years, there has been increasing interest in the potential for alterations to the brain's resting-state networks (RSNs) to explain various kinds of psychopathology. RSNs provide an intriguing new explanatory framework for hallucinations, which can occur in different modalities and population groups, but which remain poorly understood. This collaboration from the International Consortium on Hallucination Research (ICHR) reports on the evidence linking resting-state alterations to auditory hallucinations (AH) and provides a critical appraisal of the methodological approaches used in this area. In the report, we describe findings from resting connectivity fMRI in AH (in schizophrenia and nonclinical individuals) and compare them with findings from neurophysiological research, structural MRI, and research on visual hallucinations (VH). In AH, various studies show resting connectivity differences in left-hemisphere auditory and language regions, as well as atypical interaction of the default mode network and RSNs linked to cognitive control and salience. As the latter are also evident in studies of VH, this points to a domain-general mechanism for hallucinations alongside modality-specific changes to RSNs in different sensory regions. However, we also observed high methodological heterogeneity in the current literature, affecting the ability to make clear comparisons between studies. To address this, we provide some methodological recommendations and options for future research on the resting state and hallucinations.

Between- and within-site variability of fMRI localizations

This study provides first data about the spatial variability of fMRI sensorimotor localizations when investigating the same subjects at different fMRI sites. Results are comparable to a previous patient study. We found a median between-site variability of about 6 mm independent of task (motor or sensory) and experimental standardization (high or low). An intraclass correlation coefficient analysis using data quality measures indicated a major influence of the fMRI site on variability. In accordance with this, within-site localization variability was considerably lower (about 3 mm). We conclude that the fMRI site is a considerable confound for localization of brain activity. However, when performed by experienced clinical fMRI experts, brain pathology does not seem to have a relevant impact on the reliability of fMRI localizations. Hum Brain Mapp 37:2151-2160, 2016. © 2016 Wiley Periodicals, Inc.

Reliability of an fMRI paradigm for emotional processing in a multisite longitudinal study

Multisite neuroimaging studies can facilitate the investigation of brain-related changes in many contexts, including patient groups that are relatively rare in the general population. Though multisite studies have characterized the reliability of brain activation during working memory and motor functional magnetic resonance imaging tasks, emotion processing tasks, pertinent to many clinical populations, remain less explored. A traveling participants study was conducted with eight healthy volunteers scanned twice on consecutive days at each of the eight North American Longitudinal Prodrome Study sites. Tests derived from generalizability theory showed excellent reliability in the amygdala ( Eρ2 = 0.82), inferior frontal gyrus (IFG; Eρ2 = 0.83), anterior cingulate cortex (ACC; Eρ2 = 0.76), insula ( Eρ2 = 0.85), and fusiform gyrus ( Eρ2 = 0.91) for maximum activation and fair to excellent reliability in the amygdala ( Eρ2 = 0.44), IFG ( Eρ2 = 0.48), ACC ( Eρ2 = 0.55), insula ( Eρ2 = 0.42), and fusiform gyrus ( Eρ2 = 0.83) for mean activation across sites and test days. For the amygdala, habituation ( Eρ2 = 0.71) was more stable than mean activation. In a second investigation, data from 111 healthy individuals across sites were aggregated in a voxelwise, quantitative meta-analysis. When compared with a mixed effects model controlling for site, both approaches identified robust activation in regions consistent with expected results based on prior single-site research. Overall, regions central to emotion processing showed strong reliability in the traveling participants study and robust activation in the aggregation study. These results support the reliability of blood oxygen level-dependent signal in emotion processing areas across different sites and scanners and may inform future efforts to increase efficiency and enhance knowledge of rare conditions in the population through multisite neuroimaging paradigms.

The benefit of minocycline on negative symptoms in early-phase psychosis in addition to standard care - extent and mechanism (BeneMin): study protocol for a randomised controlled trial

BACKGROUND

Negative symptoms of psychosis do not respond to the traditional therapy with first- or second-generation antipsychotics and are among main causes of a decrease in quality of life observed in individuals suffering from the disorder. Minocycline, a broad-spectrum tetracyclic antibiotic displaying neuroprotective properties has been suggested as a new potential therapy for negative symptoms. In the two previous clinical trials comparing minocycline and placebo, both added to the standard care, patients receiving minocycline showed increased reduction in negative symptoms. Three routes to neuroprotection by minocycline have been identified: neuroprotection against grey matter loss, anti-inflammatory action and stabilisation of glutamate receptors. However, it is not yet certain what the extent of the benefit of minocycline in psychosis is and what its mechanism is. We present a protocol for a multi-centre double-blind randomised placebo-controlled clinical trial entitled The Benefit of Minocycline on Negative Symptoms of Psychosis: Extent and Mechanism (BeneMin).

METHODS

After providing informed consent, 226 participants in the early phase of psychosis will be randomised to receive either 100 mg modified-release capsules of minocycline or similar capsules with placebo for 12 months in addition to standard care. The participants will be tested for outcome variables before and after the intervention period. The extent of benefit will be tested via clinical outcome measures, namely the Positive and Negative Syndrome Scale score, social and cognitive functioning scores, antipsychotic medication dose equivalent and level of weight gain. The mechanism of action of minocycline will be tested via blood screening for circulating cytokines and magnetic resonance imaging with three-dimensional T1-weighted rapid gradient-echo, proton density T2-weighted dual echo and T2*-weighted gradient echo planar imaging with N-back task and resting state. Eight research centres in UK and 15 National Health Service Trusts and Health Boards will be involved in recruiting participants, performing the study and analysing the data.

DISCUSSION

The BeneMin trial can inform as to whether in minocycline we have found a new and effective therapy against negative symptoms of psychosis. The European Union Clinical Trial Register: EudraCT 2010-022463-35 with the registration finalised in July 2011. The recruitment in the trial started in January 2013 with the first patient recruited in March 2013.

Altered functional response to risky choice in HIV infection

BACKGROUND

Risky decision-making is commonly observed in persons at risk for and infected with HIV and is associated with executive dysfunction. Yet it is currently unknown whether HIV alters brain processing of risk-taking decision-making.

METHODS

This study examined the neural substrate of a risky decision-making task in 21 HIV seropositive (HIV+) and 19 seronegative (HIV-) comparison participants. Functional magnetic resonance imaging was conducted while participants performed the risky-gains task, which involves choosing among safe (20 cents) and risky (40/80 cent win or loss) choices. Linear mixed effects analyses examining group and decision type were conducted. Robust regressions were performed to examine the relationship between nadir CD4 count and Kalichman sexual compulsivity and brain activation in the HIV+ group. The overlap between the task effects and robust regressions was explored.

RESULTS

Although there were no serostatus effects in behavioral performance on the risky-gains task, HIV+ individuals exhibited greater activation for risky choices in the basal ganglia, i.e. the caudate nucleus, but also in the anterior cingulate, dorsolateral prefrontal cortex, and insula relative to the HIV- group. The HIV+ group also demonstrated reduced functional responses to safe choices in the anterior cingulate and dorsolateral prefrontal cortex relative to the HIV- group. HIV+ individuals with higher nadir CD4 count and greater sexual compulsivity displayed lower differential responses to safe versus risky choices in many of these regions.

CONCLUSIONS

This study demonstrated fronto-striatal loop dysfunction associated with HIV infection during risky decision-making. Combined with similar between-group task behavior, this suggests an adaptive functional response in regions critical to reward and behavioral control in the HIV+ group. HIV-infected individuals with higher CD4 nadirs demonstrated activation patterns more similar to seronegative individuals. This suggests that the severity of past immunosuppression (CD4 nadir) may exert a legacy effect on processing of risky choices in the HIV-infected brain.

Reliability of functional magnetic resonance imaging activation during working memory in a multi-site study: analysis from the North American Prodrome Longitudinal Study

Multi-site neuroimaging studies offer an efficient means to study brain functioning in large samples of individuals with rare conditions; however, they present new challenges given that aggregating data across sites introduces additional variability into measures of interest. Assessing the reliability of brain activation across study sites and comparing statistical methods for pooling functional data are critical to ensuring the validity of aggregating data across sites. The current study used two samples of healthy individuals to assess the feasibility and reliability of aggregating multi-site functional magnetic resonance imaging (fMRI) data from a Sternberg-style verbal working memory task. Participants were recruited as part of the North American Prodrome Longitudinal Study (NAPLS), which comprises eight fMRI scanning sites across the United States and Canada. In the first study sample (n=8), one participant from each home site traveled to each of the sites and was scanned while completing the task on two consecutive days. Reliability was examined using generalizability theory. Results indicated that blood oxygen level-dependent (BOLD) signal was reproducible across sites and was highly reliable, or generalizable, across scanning sites and testing days for core working memory ROIs (generalizability ICCs=0.81 for left dorsolateral prefrontal cortex, 0.95 for left superior parietal cortex). In the second study sample (n=154), two statistical methods for aggregating fMRI data across sites for all healthy individuals recruited as control participants in the NAPLS study were compared. Control participants were scanned on one occasion at the site from which they were recruited. Results from the image-based meta-analysis (IBMA) method and mixed effects model with site covariance method both showed robust activation in expected regions (i.e. dorsolateral prefrontal cortex, anterior cingulate cortex, supplementary motor cortex, superior parietal cortex, inferior temporal cortex, cerebellum, thalamus, basal ganglia). Quantification of the similarity of group maps from these methods confirmed a very high (96%) degree of spatial overlap in results. Thus, brain activation during working memory function was reliable across the NAPLS sites and both the IBMA and mixed effects model with site covariance methods appear to be valid approaches for aggregating data across sites. These findings indicate that multi-site functional neuroimaging can offer a reliable means to increase power and generalizability of results when investigating brain function in rare populations and support the multi-site investigation of working memory function in the NAPLS study, in particular.

Are power calculations useful? A multicentre neuroimaging study

There are now many reports of imaging experiments with small cohorts of typical participants that precede large-scale, often multicentre studies of psychiatric and neurological disorders. Data from these calibration experiments are sufficient to make estimates of statistical power and predictions of sample size and minimum observable effect sizes. In this technical note, we suggest how previously reported voxel-based power calculations can support decision making in the design, execution and analysis of cross-sectional multicentre imaging studies. The choice of MRI acquisition sequence, distribution of recruitment across acquisition centres, and changes to the registration method applied during data analysis are considered as examples. The consequences of modification are explored in quantitative terms by assessing the impact on sample size for a fixed effect size and detectable effect size for a fixed sample size. The calibration experiment dataset used for illustration was a precursor to the now complete Medical Research Council Autism Imaging Multicentre Study (MRC-AIMS). Validation of the voxel-based power calculations is made by comparing the predicted values from the calibration experiment with those observed in MRC-AIMS. The effect of non-linear mappings during image registration to a standard stereotactic space on the prediction is explored with reference to the amount of local deformation. In summary, power calculations offer a validated, quantitative means of making informed choices on important factors that influence the outcome of studies that consume significant resources.

Magnetic resonance imaging of a randomized controlled trial investigating predictors of recovery following psychological treatment in adolescents with moderate to severe unipolar depression: study protocol for Magnetic Resonance-Improving Mood with Psychoanalytic and Cognitive Therapies (MR-IMPACT)

BACKGROUND

Major depressive disorders (MDD) are a debilitating and pervasive group of mental illnesses afflicting many millions of people resulting in the loss of 110 million working days and more than 2,500 suicides per annum. Adolescent MDD patients attending NHS clinics show high rates of recurrence into adult life. A meta-analysis of recent research shows that psychological treatments are not as efficacious as previously thought. Modest treatment outcomes of approximately 65% of cases responding suggest that aetiological and clinical heterogeneity may hamper the better use of existing therapies and discovery of more effective treatments. Information with respect to optimal treatment choice for individuals is lacking, with no validated biomarkers to aid therapeutic decision-making.

METHODS/DESIGN

Magnetic resonance-Improving Mood with Psychoanalytic and Cognitive Therapies, the MR-IMPACT study, plans to identify brain regions implicated in the pathophysiology of depressions and examine whether there are specific behavioural or neural markers predicting remission and/or subsequent relapse in a subsample of depressed adolescents recruited to the IMPACT randomised controlled trial (Registration # ISRCTN83033550).

DISCUSSION

MR-IMPACT is an investigative biomarker component of the IMPACT pragmatic effectiveness trial. The aim of this investigation is to identify neural markers and regional indicators of the pathophysiology of and treatment response for MDD in adolescents. We anticipate that these data may enable more targeted treatment delivery by identifying those patients who may be optimal candidates for therapeutic response.

TRIAL REGISTRATION

Adjunctive study to IMPACT trial (Current Controlled Trials: ISRCTN83033550).

A survey of the sources of noise in fMRI

Functional magnetic resonance imaging (fMRI) is a noninvasive method for measuring brain function by correlating temporal changes in local cerebral blood oxygenation with behavioral measures. fMRI is used to study individuals at single time points, across multiple time points (with or without intervention), as well as to examine the variation of brain function across normal and ill populations. fMRI may be collected at multiple sites and then pooled into a single analysis. This paper describes how fMRI data is analyzed at each of these levels and describes the noise sources introduced at each level.

Variability of clinical functional MR imaging results: a multicenter study

PURPOSE

To investigate intersite variability of clinical functional magnetic resonance (MR) imaging, including influence of task standardization on variability and use of various parameters to inform the clinician whether the reliability of a given functional localization is high or low.

MATERIALS AND METHODS

Local ethics committees approved the study; all participants gave written informed consent. Eight women and seven men (mean age, 40 years) were prospectively investigated at three experienced functional MR sites with 1.5- (two sites) or 3-T (one site) MR. Nonstandardized motor and highly standardized somatosensory versions of a frequently requested clinical task (localization of the primary sensorimotor cortex) were used. Perirolandic functional MR variability was assessed (peak activation variability, center of mass [COM] variability, intraclass correlation values, overlap ratio [OR], activation size ratio). Data quality measures for functional MR images included percentage signal change (PSC), contrast-to-noise ratio (CNR), and head motion parameters. Data were analyzed with analysis of variance and a correlation analysis.

RESULTS

Localization of perirolandic functional MR activity differed by 8 mm (peak activity) and 6 mm (COM activity) among sites. Peak activation varied up to 16.5 mm (COM range, 0.4-16.5 mm) and 45.5 mm (peak activity range, 1.8-45.5 mm). Signal strength (PSC, CNR) was significantly lower for the somatosensory task (mean PSC, 1.0% ± 0.5 [standard deviation]; mean CNR, 1.2 ± 0.4) than for the motor task (mean PSC, 2.4% ± 0.8; mean CNR, 2.9 ± 0.9) (P < .001, both). Intersite variability was larger with low signal strength (negative correlations between signal strength and peak activation variability) even if the task was highly standardized (mean OR, 22.0% ± 18.9 [somatosensory task] and 50.1% ± 18.8 [motor task]).

CONCLUSION

Clinical practice and clinical functional MR biomarker studies should consider that the center of task-specific brain activation may vary up to 16.5 mm, with the investigating site, and should maximize functional MR signal strength and evaluate reliability of local results with PSC and CNR.

Function biomedical informatics research network recommendations for prospective multicenter functional MRI studies

This report provides practical recommendations for the design and execution of multicenter functional MRI (MC-fMRI) studies based on the collective experience of the Function Biomedical Informatics Research Network (FBIRN). The study was inspired by many requests from the fMRI community to FBIRN group members for advice on how to conduct MC-fMRI studies. The introduction briefly discusses the advantages and complexities of MC-fMRI studies. Prerequisites for MC-fMRI studies are addressed before delving into the practical aspects of carefully and efficiently setting up a MC-fMRI study. Practical multisite aspects include: (i) establishing and verifying scan parameters including scanner types and magnetic fields, (ii) establishing and monitoring of a scanner quality program, (iii) developing task paradigms and scan session documentation, (iv) establishing clinical and scanner training to ensure consistency over time, (v) developing means for uploading, storing, and monitoring of imaging and other data, (vi) the use of a traveling fMRI expert, and (vii) collectively analyzing imaging data and disseminating results. We conclude that when MC-fMRI studies are organized well with careful attention to unification of hardware, software and procedural aspects, the process can be a highly effective means for accessing a desired participant demographics while accelerating scientific discovery.

The future of functional MRI in clinical medicine

In the last 20 years or so, functional MRI has matured very rapidly from being an experimental imaging method in the hands of a few labs to being a very widely available and widely used workhorse of cognitive neuroscience and clinical neuroscience research internationally. FMRI studies have had a considerable impact on our understanding of brain system phenotypes of neurological and psychiatric disorders; and some impact already on development of new therapeutics. However, the direct benefit of fMRI to individual patients with brain disorders has so far been minimal. Here I provide a personal perspective on what has already been achieved, and imagine how the further development of fMRI over the medium term might lead to even greater engagement with clinical medicine.

Effects of combining field strengths on auditory functional MRI group analysis: 1.5T and 3T

PURPOSE

To evaluate effects of combining functional magnetic resonance imaging (fMRI) data acquired from different field strengths on group analysis as a function of the number of subjects at each field strength.

MATERIALS AND METHODS

In all, 28 subjects (18 at 3T) participated in an auditory task of passively listening to a 0.75s segment of jazz music in an event-related design. Results of single-subject analysis were combined to create all possible subject combinations for a group size of eight subjects from each of the 3T and 1.5T pools, comprising subject mixtures of (3T/1.5T) 0/8, 2/6, 4/4, 6/2, and 8/0. Group analysis performance of each subject permutation was measured by receiver operating characteristic (ROC) curves and activation overlap maps.

RESULTS

While area under ROC curves, extent of activation in the gold standard region, and reliability of activation increased with the number of 3T subjects, marginal gain decreased. ROC performance overlap across mixtures was observed, indicating that some combinations of subjects markedly outperformed others. For detection of activation, 4/4 was arguably the minimum mixture level that was comparable to 3T-only group results.

CONCLUSION

Inclusion of 1.5T data does not necessarily reduce the validity of group analysis. Lower field strength data was found only to limit detection power, but did not affect specificity. Within the limits of realignment error, these results should also extend to group longitudinal analyses of subject mixtures from different field strengths.

Frontocingular dysfunction in bulimia nervosa when confronted with disease-specific stimuli

OBJECTIVE

Bulimia nervosa (BN) is characterized by dysregulation of impulse control, in other words, uncontrolled eating. Functional neuroimaging studies have been sparse and have used variable methodologies.

METHOD

Thirteen medication-free female BN patients and 13 female healthy controls were investigated by functional magnetic resonance imaging using a disease-specific food paradigm. Stimuli were rated after the scanning procedure.

RESULTS

Bulimia nervosa patients showed increased fear ratings and a trend for increased disgust. Magnetic resonance imaging data of 10 BN patients could be analysed. Three BN patients had to be excluded from the analysis because of minimal blood oxygen level dependent signals. Compared with healthy controls, BN patients showed less activation of the anterior cingulate cortex, which extended into the lateral prefrontal cortex. Furthermore, the right temporal pole showed decreased reactivity.

DISCUSSION

This study substantiates a key role of lateral prefrontal dysfunction in BN, a brain region involved in impulse control. Furthermore, the anterior cingulate cortex, which plays a key role in emotion processing, is dysfunctional. A major limitation of this study is the small sample size.

Using brain imaging measures in studies of procognitive pharmacologic agents in schizophrenia: psychometric and quality assurance considerations

The first phase of the Cognitive Neuroscience Treatment Research to Improve Cognition in Schizophrenia (CNTRICs) initiative focused on the identification of cognitive constructs from human and animal neuroscience that were relevant to understanding cognitive deficits in schizophrenia, as well as promising task paradigms that could be used to assess these constructs behaviorally. The current phase of CNTRICs has the goal of expanding this initial work by including measures of brain function that can augment these behavioral tasks as biomarkers to be used in drug development processing. Here we review many of the psychometric issues that need to be addressed regarding the development and inclusion of such methods in the drug development process. In addition, we review quality assurance concerns, issues associated with multicenter trials, concerns associated with potential pharmacologic confounds on imaging measures, as well as power and analysis considerations. Although review is couched in the context of the use of biomarkers for treatment studies in schizophrenia, we believe the issues and suggestions included are relevant to the entire range of neuropsychiatric disorders as well as to a wide range of imaging modalities (i.e., functional magnetic resonance imaging, positron emission tomography, event-related potentials, electroencephalography, transcranial magnetic stimulation, near infrared spectroscopy, etc.) and are relevant to both pharmacologic and psychological intervention approaches.

A procedural framework for good imaging practice in pharmacological fMRI studies applied to drug development #2: protocol optimization and best practices

Functional magnetic resonance imaging (fMRI) experiments are more complex compared with standard radiological imaging, involving additional data streams and hardware along with complex analysis methods. Here, we propose guidelines based around mitigating risks associated with the complexities of the technique at the level of the individual imaging protocol, including workable and effective quality assurance/quality control procedures and rigorous, predefined, analysis pipelines. Our aim is to provide a framework for 'good imaging practice' (GIP), enabling these requirements to be addressed at an appropriate level of detail. The development of a procedural framework for GIP in pharmaceutical fMRI studies could lead to greater acceptance of the method within industry and facilitate validation and, eventually, qualification of the technique as an imaging biomarker.

Optimal design of multi-subject blocked fMRI experiments

The design of a multi-subject fMRI experiment needs specification of the number of subjects and scanning time per subject. For example, for a blocked design with conditions A or B, fixed block length and block order ABN, where N denotes a null block, the optimal number of cycles of ABN and the optimal number of subjects have to be determined. This paper presents a method to determine the optimal number of subjects and optimal number of cycles for a blocked design based on the A-optimality criterion and a linear cost function by which the number of cycles and the number of subjects are restricted. Estimation of individual stimulus effects and estimation of contrasts between stimulus effects are both considered. The mixed-effects model is applied and analytical results for the A-optimal number of subjects and A-optimal number of cycles are obtained under the assumption of uncorrelated errors. For correlated errors with a first-order autoregressive (AR1) error structure, numerical results are presented. Our results show how the optimal number of cycles and subjects depend on the within- to between-subject variance ratio. Our method is a new approach to determine the optimal scanning time and optimal number of subjects for a multi-subject fMRI experiment. In contrast to previous results based on power analyses, the optimal number of cycles and subjects can be described analytically and costs are considered.

The Neuro/PsyGRID calibration experiment: identifying sources of variance and bias in multicenter MRI studies

Calibration experiments precede multicenter trials to identify potential sources of variance and bias. In support of future imaging studies of mental health disorders and their treatment, the Neuro/PsyGRID consortium commissioned a calibration experiment to acquire functional and structural MRI from twelve healthy volunteers attending five centers on two occasions. Measures were derived of task activation from a working memory paradigm, fractal scaling (Hurst exponent) from resting fMRI, and grey matter distributions from T(1) -weighted sequences. At each intracerebral voxel a fixed-effects analysis of variance estimated components of variance corresponding to factors of center, subject, occasion, and within-occasion order, and interactions of center-by-occasion, subject-by-occasion, and center-by-subject, the latter (since there is no intervention) a surrogate of the expected variance of the treatment effect standard error across centers. A rank order test of between-center differences was indicative of crossover or noncrossover subject-by-center interactions. In general, factors of center, subject and error variance constituted >90% of the total variance, whereas occasion, order, and all interactions were generally <5%. Subject was the primary source of variance (70%-80%) for grey-matter, with error variance the dominant component for fMRI-derived measures. Spatially, variance was broadly homogenous with the exception of fractal scaling measures which delineated white matter, related to the flip angle of the EPI sequence. Maps of P values for the associated F-tests were also derived. Rank tests were highly significant indicating the order of measures across centers was preserved. In summary, center effects should be modeled at the voxel-level using existing and long-standing statistical recommendations.

Between- and within-scanner variability in the CaliBrain study n-back cognitive task

Psychiatric neuroimaging techniques are likely to improve understanding of the brain in health and disease, but studies tend to be small, based in one imaging centre and of unclear generalisability. Multicentre studies have great appeal but face problems if functional magnetic resonance imaging (fMRI) data from different centres are to be combined. Fourteen healthy volunteers had two brain scans on different days at three scanners. Considerable effort was first made to use similar scanning sequences and standardise task implementation across centres. The n-back cognitive task was used to investigate between- and within-scanner reproducibility and reliability. Both the functional imaging and behavioural results were in good accord with the existing literature. We found no significant differences in the activation/deactivation maps between scanners, or between repeat visits to the same scanners. Between- and within-scanner reproducibility and reliability was very similar. However, the smoothness of images from the scanners differed, suggesting that smoothness equalization might further reduce inter-scanner variability. Our results for the n-back task suggest it is possible to acquire fMRI data from different scanners which allows pooling across centres, when the same field strength scanners are used and scanning sequences and paradigm implementations are standardised.

Power calculations for multicenter imaging studies controlled by the false discovery rate

Magnetic resonance imaging (MRI) is widely used in brain imaging research (neuroimaging) to explore structural and functional changes across dispersed neural networks visible only via multisubject experiments. Multicenter investigations are an effective way to increase recruitment rates. This article describes image-based power calculations for a two-group, cross-sectional design specified by the mean effect size and its standard error, sample size, false discovery rate (FDR), and size of the network (i.e., proportion of image locations) that truly demonstrates an effect. Minimum sample size (for fixed effect size) and the minimum effect size (for fixed sample size) are calculated by specifying the acceptable power threshold. Within-center variance was estimated in five participating centers by repeat MRI scanning of 12 healthy participants from whom distributions of gray matter were estimated. The effect on outcome measures when varying FDR and the proportion of true positives is presented. Their spatial patterns reflect within-center variance, which is consistent across centers. Sample sizes 3-6 times larger are needed when detecting effects in subcortical regions compared to the neocortex. Hypothesized multicenter studies of patients with first episode psychosis and control participants were simulated with varying proportions of the cohort recruited at each center. There is little penalty to sample size for recruitment at five centers compared to the center with the lowest variance alone. At 80% power 80 participants per group are required to observe differences in gray matter in high variance regions.

Multisite reliability of cognitive BOLD data

Investigators perform multi-site functional magnetic resonance imaging studies to increase statistical power, to enhance generalizability, and to improve the likelihood of sampling relevant subgroups. Yet undesired site variation in imaging methods could off-set these potential advantages. We used variance components analysis to investigate sources of variation in the blood oxygen level-dependent (BOLD) signal across four 3-T magnets in voxelwise and region-of-interest (ROI) analyses. Eighteen participants traveled to four magnet sites to complete eight runs of a working memory task involving emotional or neutral distraction. Person variance was more than 10 times larger than site variance for five of six ROIs studied. Person-by-site interactions, however, contributed sizable unwanted variance to the total. Averaging over runs increased between-site reliability, with many voxels showing good to excellent between-site reliability when eight runs were averaged and regions of interest showing fair to good reliability. Between-site reliability depended on the specific functional contrast analyzed in addition to the number of runs averaged. Although median effect size was correlated with between-site reliability, dissociations were observed for many voxels. Brain regions where the pooled effect size was large but between-site reliability was poor were associated with reduced individual differences. Brain regions where the pooled effect size was small but between-site reliability was excellent were associated with a balance of participants who displayed consistently positive or consistently negative BOLD responses. Although between-site reliability of BOLD data can be good to excellent, acquiring highly reliable data requires robust activation paradigms, ongoing quality assurance, and careful experimental control.

Multi-site characterization of an fMRI working memory paradigm: reliability of activation indices

Neuroimaging studies are facilitated significantly when it is possible to recruit subjects and acquire data at multiple sites. However, the use of different scanners and acquisition protocols is a potential source of variability in multi-site data. In this work we present a multi-site study of the reliability of fMRI activation indices, where 10 healthy volunteers were scanned at 4 different sites while performing a working memory paradigm. Our results indicate that, even with different scanner manufacturers and field strengths, activation variability due to site differences is small compared to variability due to subject differences in this cognitive task, provided we choose an appropriate activation measure.

Mapping reliability in multicenter MRI: voxel-based morphometry and cortical thickness

Multicenter structural MRI studies can have greater statistical power than single-center studies. However, across-center differences in contrast sensitivity, spatial uniformity, etc., may lead to tissue classification or image registration differences that could reduce or wholly offset the enhanced statistical power of multicenter data. Prior work has validated volumetric multicenter MRI, but robust methods for assessing reliability and power of multisite analyses with voxel-based morphometry (VBM) and cortical thickness measurement (CORT) are not yet available. We developed quantitative methods to investigate the reproducibility of VBM and CORT to detect group differences and estimate heritability when MRI scans from different scanners running different acquisition protocols in a multicenter setup are included. The method produces brain maps displaying information such as lowest detectable effect size (or heritability) and effective number of subjects in the multicenter study. We applied the method to a five-site multicenter calibration study using scanners from four different manufacturers, running different acquisition protocols. The reliability maps showed an overall good comparability between the sites, providing a reasonable gain in sensitivity in most parts of the brain. In large parts of the cerebrum and cortex scan pooling improved heritability estimates, with "effective-N" values upto the theoretical maximum. For some areas, "optimal-pool" maps indicated that leaving out a site would give better results. The reliability maps also reveal which brain regions are in any case difficult to measure reliably (e.g., around the thalamus). These tools will facilitate the design and analysis of multisite VBM and CORT studies for detecting group differences and estimating heritability.

Pooling FMRI data: meta-analysis, mega-analysis and multi-center studies

The quantitative analysis of pooled data from related functional magnetic resonance imaging (fMRI) experiments has the potential to significantly accelerate progress in brain mapping. Such data-pooling can be achieved through meta-analysis (the pooled analysis of published results), mega-analysis (the pooled analysis of raw data) or multi-site studies, which can be seen as designed mega-analyses. Current limitations in function-location brain mapping and how data-pooling can be used to remediate them are reviewed, with particular attention to power aggregation and mitigation of false positive results. Some recently developed analysis tools for meta- and mega-analysis are also presented, and recommendations for the conduct of valid fMRI data pooling are formulated.