Parallel workflow tools to facilitate human brain MRI post-processing

Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues

Neural correlates of oral word reading, silent reading comprehension, and cognitive subcomponents

The ability to read is essential for cognitive development. To deepen our understanding of reading acquisition, we explored the neuroanatomical correlates (cortical thickness; CT) of word-reading fluency and sentence comprehension efficiency in Chinese with a group of typically developing children ( N = 21; 12 females and 9 males; age range 10.7–12.3 years). Then, we investigated the relationship between the CT of reading-defined regions and the cognitive subcomponents of reading to determine whether our study lends support to the multi-component model. The results demonstrated that children’s performance on oral word reading was positively correlated with CT in the left superior temporal gyrus (LSTG), left inferior temporal gyrus (LITG), left supramarginal gyrus (LSMG) and right superior temporal gyrus (RSTG). Moreover, CT in the LSTG, LSMG and LITG uniquely predicted children’s phonetic representation, phonological awareness, and orthography–phonology mapping skills, respectively. By contrast, children’s performance on sentence-reading comprehension was positively correlated with CT in the left parahippocampus (LPHP) and right calcarine fissure (RV1). As for the subcomponents of reading, CT in the LPHP was exclusively correlated with morphological awareness, whereas CT in the RV1 was correlated with orthography–semantic mapping. Taken together, these findings indicate that the reading network of typically developing children consists of multiple sub-divisions, thus providing neuroanatomical evidence in support of the multi-componential view of reading.</jats:p

Neuroimaging anomalies in asymptomatic middle cerebral artery steno-occlusive disease with normal-appearing white matter

BackgroundAsymptomatic chronic cerebrovascular steno-occlusive disease is common, but the cognitive function and alterations in the brain’s structural and functional profiles have not been well studied. This study aimed to reveal whether and how patients with asymptomatic middle cerebral artery (MCA) steno-occlusive disease and normal-appearing white matter differ in brain structural and functional profiles from normal controls and their correlations with cognitive function.MethodsIn all, 26 patients with asymptomatic MCA steno-occlusive disease and 22 healthy controls were compared for neurobehavioral assessments, brain volume, cortical thickness, fiber connectivity density (FiCD) value, and resting-state functional connectivity (FC) using multimodal MRI. We also investigated the associations between abnormal cortical thicknesses, FiCD values, and functional connectivities with the neurobehavioral assessments.ResultsPatients performed worse on memory tasks (Auditory Verbal Learning Test-Huashan version) compared with healthy controls. Patients were divided into two groups: the right group (patients with right MCA steno-occlusive disease) and the left group (patients with left MCA steno-occlusive disease). The left group showed significant cortical thinning in the left superior parietal lobule, while the right group showed significant cortical thinning in the right superior parietal lobule and caudal portion of the right middle frontal gyrus. Increased FiCD values in the superior frontal region of the left hemisphere were observed in the left group. In addition, a set of interhemispheric and intrahemispheric FC showed a significant decrease or increase in both the left and right groups. Many functional connectivity profiles were positively correlated with cognitive scores. No correlation was found between cortical thickness, FiCD values, and cognitive scores.ConclusionEven if the patients with MCA steno-occlusive disease were asymptomatic and had normal-appearing white matter, their cognitive function and structural and functional profiles had changed, especially the FC. Alterations in FC may be an important mechanism underlying the neurodegenerative process in patients with asymptomatic MCA steno-occlusive disease before structural changes occur, so FC assessment may promote the detection of network alterations, which may be used as a biomarker of disease progression and therapeutic efficacy evaluation in these patients

Alterations in brain structure and function associated with pediatric growth hormone deficiency: A multi-modal magnetic resonance imaging study

IntroductionPediatric growth hormone deficiency (GHD) is a disease resulting from impaired growth hormone/insulin-like growth factor-1 (IGF-1) axis but the effects of GHD on children’s cognitive function, brain structure and brain function were not yet fully illustrated.MethodsFull Wechsler Intelligence Scales for Children, structural imaging, diffusion tensor imaging, and resting-state functional magnetic resonance imaging were assessed in 11 children with GHD and 10 matched healthy controls.Results(1) The GHD group showed moderate cognitive impairment, and a positive correlation existed between IGF-1 levels and cognitive indices. (2) Mean diffusivity was significantly increased in both corticospinal tracts in GHD group. (3) There were significant positive correlations between IGF-1 levels and volume metrics of left thalamus, left pallidum and right putamen but a negative correlation between IGF-1 levels and cortical thickness of the occipital lobe. And IGF-1 levels negatively correlated with fractional anisotropy in the superior longitudinal fasciculus and right corticospinal tract. (4) Regional homogeneity (ReHo) in the left hippocampus/parahippocampal gyrus was negatively correlated with IGF-1 levels; the amplitude of low-frequency fluctuation (ALFF) and ReHo in the paracentral lobe, postcentral gyrus and precentral gyrus were also negatively correlated with IGF-1 levels, in which region ALFF fully mediates the effect of IGF-1 on working memory index.ConclusionMultiple subcortical, cortical structures, and regional neural activities might be influenced by serum IGF-1 levels. Thereinto, ALFF in the paracentral lobe, postcentral gyrus and precentral gyrus fully mediates the effect of IGF-1 on the working memory index

Regional Grey Matter Structure Differences between Transsexuals and Healthy Controls-A Voxel Based Morphometry Study.

Gender identity disorder (GID) refers to transsexual individuals who feel that their assigned biological gender is incongruent with their gender identity and this cannot be explained by any physical intersex condition. There is growing scientific interest in the last decades in studying the neuroanatomy and brain functions of transsexual individuals to better understand both the neuroanatomical features of transsexualism and the background of gender identity. So far, results are inconclusive but in general, transsexualism has been associated with a distinct neuroanatomical pattern. Studies mainly focused on male to female (MTF) transsexuals and there is scarcity of data acquired on female to male (FTM) transsexuals. Thus, our aim was to analyze structural MRI data with voxel based morphometry (VBM) obtained from both FTM and MTF transsexuals (n = 17) and compare them to the data of 18 age matched healthy control subjects (both males and females). We found differences in the regional grey matter (GM) structure of transsexual compared with control subjects, independent from their biological gender, in the cerebellum, the left angular gyrus and in the left inferior parietal lobule. Additionally, our findings showed that in several brain areas, regarding their GM volume, transsexual subjects did not differ significantly from controls sharing their gender identity but were different from those sharing their biological gender (areas in the left and right precentral gyri, the left postcentral gyrus, the left posterior cingulate, precuneus and calcarinus, the right cuneus, the right fusiform, lingual, middle and inferior occipital, and inferior temporal gyri). These results support the notion that structural brain differences exist between transsexual and healthy control subjects and that majority of these structural differences are dependent on the biological gender

Prediction of Depression in Individuals at High Familial Risk of Mood Disorders Using Functional Magnetic Resonance Imaging

Objective Bipolar disorder is a highly heritable condition. First-degree relatives of affected individuals have a more than a ten-fold increased risk of developing bipolar disorder (BD), and a three-fold risk of developing major depressive disorder (MDD) than the general population. It is unclear however whether differences in brain activation reported in BD and MDD are present before the onset of illness. Methods We studied 98 young unaffected individuals at high familial risk of BD and 58 healthy controls using functional Magnetic Resonance Imaging (fMRI) scans and a task involving executive and language processing. Twenty of the high-risk subjects subsequently developed MDD after the baseline fMRI scan. Results At baseline the high-risk subjects who later developed MDD demonstrated relatively increased activation in the insula cortex, compared to controls and high risk subjects who remained well. In the healthy controls and high-risk group who remained well, this region demonstrated reduced engagement with increasing task difficulty. The high risk subjects who subsequently developed MDD did not demonstrate this normal disengagement. Activation in this region correlated positively with measures of cyclothymia and neuroticism at baseline, but not with measures of depression. Conclusions These results suggest that increased activation of the insula can differentiate individuals at high-risk of bipolar disorder who later develop MDD from healthy controls and those at familial risk who remain well. These findings offer the potential of future risk stratification in individuals at risk of mood disorder for familial reasons

Blood-Brain Barrier Permeability of Normal Appearing White Matter in Relapsing-Remitting Multiple Sclerosis

BACKGROUND: Multiple sclerosis (MS) affects the integrity of the blood-brain barrier (BBB). Contrast-enhanced T1 weighted magnetic resonance imaging (MRI) is widely used to characterize location and extent of BBB disruptions in focal MS lesions. We employed quantitative T1 measurements before and after the intravenous injection of a paramagnetic contrast agent to assess BBB permeability in the normal appearing white matter (NAWM) in patients with relapsing-remitting MS (RR-MS). METHODOLOGY/PRINCIPAL FINDINGS: Fifty-nine patients (38 females) with RR-MS undergoing immunomodulatory treatment and nine healthy controls (4 females) underwent quantitative T1 measurements at 3 tesla before and after injection of a paramagnetic contrast agent (0.2 mmol/kg Gd-DTPA). Mean T1 values were calculated for NAWM in patients and total cerebral white matter in healthy subjects for the T1 measurements before and after injection of Gd-DTPA. The pre-injection baseline T1 of NAWM (945±55 [SD] ms) was prolonged in RR-MS relative to healthy controls (903±23 ms, p = 0.028). Gd-DTPA injection shortened T1 to a similar extent in both groups. Mean T1 of NAWM was 866±47 ms in the NAWM of RR-MS patients and 824±13 ms in the white matter of healthy controls. The regional variability of T1 values expressed as the coefficient of variation (CV) was comparable between the two groups at baseline, but not after injection of the contrast agent. After intravenous Gd-DTPA injection, T1 values in NAWM were more variable in RR-MS patients (CV = 0.198±0.046) compared to cerebral white matter of healthy controls (CV = 0.166±0.018, p = 0.046). CONCLUSIONS/SIGNIFICANCE: We found no evidence of a global BBB disruption within the NAWM of RR-MS patients undergoing immunomodulatory treatment. However, the increased variation of T1 values in NAWM after intravenous Gd-DTPA injection points to an increased regional inhomogeneity of BBB function in NAWM in relapsing-remitting MS

Effects of Different Correlation Metrics and Preprocessing Factors on Small-World Brain Functional Networks: A Resting-State Functional MRI Study

Graph theoretical analysis of brain networks based on resting-state functional MRI (R-fMRI) has attracted a great deal of attention in recent years. These analyses often involve the selection of correlation metrics and specific preprocessing steps. However, the influence of these factors on the topological properties of functional brain networks has not been systematically examined. Here, we investigated the influences of correlation metric choice (Pearson's correlation versus partial correlation), global signal presence (regressed or not) and frequency band selection [slow-5 (0.01–0.027 Hz) versus slow-4 (0.027–0.073 Hz)] on the topological properties of both binary and weighted brain networks derived from them, and we employed test-retest (TRT) analyses for further guidance on how to choose the “best” network modeling strategy from the reliability perspective. Our results show significant differences in global network metrics associated with both correlation metrics and global signals. Analysis of nodal degree revealed differing hub distributions for brain networks derived from Pearson's correlation versus partial correlation. TRT analysis revealed that the reliability of both global and local topological properties are modulated by correlation metrics and the global signal, with the highest reliability observed for Pearson's-correlation-based brain networks without global signal removal (WOGR-PEAR). The nodal reliability exhibited a spatially heterogeneous distribution wherein regions in association and limbic/paralimbic cortices showed moderate TRT reliability in Pearson's-correlation-based brain networks. Moreover, we found that there were significant frequency-related differences in topological properties of WOGR-PEAR networks, and brain networks derived in the 0.027–0.073 Hz band exhibited greater reliability than those in the 0.01–0.027 Hz band. Taken together, our results provide direct evidence regarding the influences of correlation metrics and specific preprocessing choices on both the global and nodal topological properties of functional brain networks. This study also has important implications for how to choose reliable analytical schemes in brain network studies

Diffusion Weighted Image Denoising using overcomplete Local PCA

Diffusion Weighted Images (DWI) normally shows a low Signal to Noise Ratio (SNR) due to the presence of noise from the measurement process that complicates and biases the estimation of quantitative diffusion parameters. In this paper, a new denoising methodology is proposed that takes into consideration the multicomponent nature of multi-directional DWI datasets such as those employed in diffusion imaging. This new filter reduces random noise in multicomponent DWI by locally shrinking less significant Principal Components using an overcomplete approach. The proposed method is compared with state-of-the-art methods using synthetic and real clinical MR images, showing improved performance in terms of denoising quality and estimation of diffusion parameters.This work has been supported by the Spanish grant TIN2011-26727 from Ministerio de Ciencia e Innovacion. 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Local diffusion homogeneity (LDH): an inter-voxel diffusion MRI metric for assessing inter-subject white matter variability.

Many diffusion parameters and indices (e.g., fractional anisotropy [FA] and mean diffusivity [MD]) have been derived from diffusion magnetic resonance imaging (MRI) data. These parameters have been extensively applied as imaging markers for localizing white matter (WM) changes under various conditions (e.g., development, degeneration and disease). However, the vast majority of the existing parameters is derived from intra-voxel analyses and represents the diffusion properties solely within the voxel unit. Other types of parameters that characterize inter-voxel relationships have been largely overlooked. In the present study, we propose a novel inter-voxel metric referred to as the local diffusion homogeneity (LDH). This metric quantifies the local coherence of water molecule diffusion in a model-free manner. It can serve as an additional marker for evaluating the WM microstructural properties of the brain. To assess the distinguishing features between LDH and FA/MD, the metrics were systematically compared across space and subjects. As an example, both the LDH and FA/MD metrics were applied to measure age-related WM changes. The results indicate that LDH reveals unique inter-subject variability in specific WM regions (e.g., cerebral peduncle, internal capsule and splenium). Furthermore, there are regions in which measurements of age-related WM alterations with the LDH and FA/MD metrics yield discrepant results. These findings suggest that LDH and FA/MD have different sensitivities to specific WM microstructural properties. Taken together, the present study shows that LDH is complementary to the conventional diffusion-MRI markers and may provide additional insights into inter-subject WM variability. Further studies, however, are needed to uncover the neuronal mechanisms underlying the LDH