A sub+cortical fMRI-based surface parcellation

The FinnBrain multimodal neonatal template and atlas collection

The accurate processing of neonatal and infant brain MRI data is crucial for developmental neuroscience but presents unique challenges that child and adult data do not. Tissue segmentation and image coregistration accuracy can be improved by optimizing template images and related segmentation procedures. Here, we describe the construction of the FinnBrain Neonate (FBN-125) template, a multi-contrast template with T1- and T2-weighted, as well as diffusion tensor imaging-derived fractional anisotropy and mean diffusivity images. The template is symmetric, aligned to the Talairach-like MNI-152 template, and has high spatial resolution (0.5 mm³). Additionally, we provide atlas labels, constructed from manual segmentations, for cortical grey matter, white matter, cerebrospinal fluid, brainstem, cerebellum as well as the bilateral hippocampi, amygdalae, caudate nuclei, putamina, globi pallidi, and thalami. This multi-contrast template and labelled atlases aim to advance developmental neuroscience by achieving reliable means for spatial normalization and measures of neonate brain structure via automated computational methods. We also provide standard volumetric and surface co-registration files to enable investigators to transform their statistical maps to the adult MNI space, improving the consistency and comparability of neonatal studies or the use of adult MNI space atlases in neonatal neuroimaging.

Atypical co-development of the thalamus and cortex in autism: Evidence from age-related white-gray contrast change

Recent studies have shown that white-gray contrast (WGC) of either cortical or subcortical gray matter provides for accurate predictions of age in typically developing (TD) children, and that, at least for the cortex, it changes differently with age in subjects with autism spectrum disorder (ASD) compared to their TD peers. Our previous study showed different patterns of contrast change between ASD and TD in sensorimotor and association cortices. While that study was confined to the cortex, we hypothesized that subcortical structures, particularly the thalamus, were involved in the observed cortical dichotomy between lower and higher processing. The current paper investigates that hypothesis using the WGC measures from the thalamus in addition to those from the cortex. We compared age-related WGC changes in the thalamus to those in the cortex. To capture the simultaneity of this change across the two structures, we devised a metric capturing the co-development of the thalamus and cortex (CoDevTC), proportional to the magnitude of cortical and thalamic age-related WGC change. We calculated this metric for each of the subjects in a large homogeneous sample taken from the Autism Brain Imaging Data Exchange (ABIDE) (N = 434). We used structural MRI data from the largest high-quality cross-sectional sample (NYU) as well as two other large high-quality sites, GU and OHSU, all three using Siemens 3T scanners. We observed that the co-development features in ASD and TD exhibit contrasting patterns; specifically, some higher-order thalamic nuclei, such as the lateral dorsal nucleus, exhibited reduction in codevelopment with most of the cortex in ASD compared to TD. Moreover, this difference in the CoDevTC pattern correlates with a number of behavioral measures across multiple cognitive and physiological domains. The results support previous notions of altered connectivity in autism, but add more specific evidence about the heterogeneity in thalamocortical development that elucidates the mechanisms underlying the clinical features of ASD.

Abnormal stability of spontaneous neuronal activity as a predictor of diagnosis conversion from major depressive disorder to bipolar disorder

OBJECTIVE

Bipolar disorder (BD) is often misdiagnosed as major depressive disorder (MDD) in the early stage, which may lead to inappropriate treatment. This study aimed to characterize the alterations of spontaneous neuronal activity in patients with depressive episodes whose diagnosis transferred from MDD to BD.

METHODS

532 patients with MDD and 132 healthy controls (HCs) were recruited over 10 years. During the follow-up period, 75 participants with MDD transferred to BD (tBD), and 157 participants remained with the diagnosis of unipolar depression (UD). After excluding participants with poor image quality and excessive head movement, 68 participants with the diagnosis of tBD, 150 participants with the diagnosis of UD, and 130 HCs were finally included in the analysis. The dynamic amplitude of low-frequency fluctuations (dALFF) of spontaneous neuronal activity was evaluated in tBD, UD and HC using functional magnetic resonance imaging at study inclusion. Receiver operating characteristic (ROC) analysis was performed to evaluate sensitivity and specificity of the conversion prediction from MDD to BD based on dALFF.

RESULTS

Compared to HC, tBD exhibited elevated dALFF at left premotor cortex (PMC_L), right lateral temporal cortex (LTC_R) and right early auditory cortex (EAC_R), and UD showed reduced dALFF at PMC_L, left paracentral lobule (PCL_L), bilateral medial prefrontal cortex (mPFC), right orbital frontal cortex (OFC_R), right dorsolateral prefrontal cortex (DLPFC_R), right posterior cingulate cortex (PCC_R) and elevated dALFF at LTC_R. Furthermore, tBD exhibited elevated dALFF at PMC_L, PCL_L, bilateral mPFC, bilateral OFC, DLPFC_R, PCC_R and LTC_R than UD. In addition, ROC analysis based on dALFF in differential areas obtained an area under the curve (AUC) of 72.7%.

CONCLUSIONS

The study demonstrated the temporal dynamic abnormalities of tBD and UD in the critical regions of the somatomotor network (SMN), default mode network (DMN), and central executive network (CEN). The differential abnormal patterns of temporal dynamics between the two diseases have the potential to predict the diagnosis transition from MDD to BD.

Investigating the heterogeneity within the somatosensory-motor network and its relationship with the attention and default systems

The somatosensory-motor network (SMN) not only plays an important role in primary somatosensory and motor processing but is also central to many disorders. However, the SMN heterogeneity related to higher-order systems still remains unclear. Here, we investigated SMN heterogeneity from multiple perspectives. To characterize the SMN substructures in more detail, we used ultra-high-field functional MRI to delineate a finer-grained cortical parcellation containing 430 parcels that is more homogenous than the state-of-the-art parcellation. We personalized the new parcellation to account for individual differences and identified multiscale individual-specific brain structures. We found that the SMN subnetworks showed distinct resting-state functional connectivity (RSFC) patterns. The Hand subnetwork was central within the SMN and exhibited stronger RSFC with the attention systems than the other subnetworks, whereas the Tongue subnetwork exhibited stronger RSFC with the default systems. This two-fold differentiation was observed in the temporal ordering patterns within the SMN. Furthermore, we characterized how the distinct attention and default streams were carried forward into the functions of the SMN using dynamic causal modeling and identified two behavioral domains associated with this SMN fractionation using meta-analytic tools. Overall, our findings provided important insights into the heterogeneous SMN organization at the system level and suggested that the Hand subnetwork may be preferentially involved in exogenous processes, whereas the Tongue subnetwork may be more important in endogenous processes.

Cot-side imaging of functional connectivity in the developing brain during sleep using wearable high-density diffuse optical tomography

Studies of cortical function in newborn infants in clinical settings are extremely challenging to undertake with traditional neuroimaging approaches. Partly in response to this challenge, functional near-infrared spectroscopy (fNIRS) has become an increasingly common clinical research tool but has significant limitations including a low spatial resolution and poor depth specificity. Moreover, the bulky optical fibres required in traditional fNIRS approaches present significant mechanical challenges, particularly for the study of vulnerable newborn infants. A new generation of wearable, modular, high-density diffuse optical tomography (HD-DOT) technologies has recently emerged that overcomes many of the limitations of traditional, fibre-based and low-density fNIRS measurements. Driven by the development of this new technology, we have undertaken the first cot-side study of newborn infants using wearable HD-DOT in a clinical setting. We use this technology to study functional brain connectivity (FC) in newborn infants during sleep and assess the effect of neonatal sleep states, active sleep (AS) and quiet sleep (QS), on resting state FC. Our results demonstrate that it is now possible to obtain high-quality functional images of the neonatal brain in the clinical setting with few constraints. Our results also suggest that sleep states differentially affect FC in the neonatal brain, consistent with prior reports.

A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain

TheVirtualBrain, an open-source platform for large-scale network modeling, can be personalized to an individual using a wide range of neuroimaging modalities. With the growing number and scale of neuroimaging data sharing initiatives of both healthy and clinical populations comes an opportunity to create large and heterogeneous sets of dynamic network models to better understand individual differences in network dynamics and their impact on brain health. Here we present TheVirtualBrain-UK Biobank pipeline, a robust, automated and open-source brain image processing solution to address the expanding scope of TheVirtualBrain project. Our pipeline generates connectome-based modeling inputs compatible for use with TheVirtualBrain. We leverage the existing multimodal MRI processing pipeline from the UK Biobank made for use with a variety of brain imaging modalities. We add various features and changes to the original UK Biobank implementation specifically for informing large-scale network models, including user-defined parcellations for the construction of matching whole-brain functional and structural connectomes. Changes also include detailed reports for quality control of all modalities, a streamlined installation process, modular software packaging, updated software versions, and support for various publicly available datasets. The pipeline has been tested on various datasets from both healthy and clinical populations and is robust to the morphological changes observed in aging and dementia. In this paper, we describe these and other pipeline additions and modifications in detail, as well as how this pipeline fits into the TheVirtualBrain ecosystem.