Comparison of accuracy between FSL's FIRST and Freesurfer for caudate nucleus and putamen segmentation

Inter-Software Consistency on the Estimation of Subcortical Structure Volume in Different Age Groups

There is still little research on the consistency among the subcortical volume estimates of different software packages. It is also unclear whether there are age-related differences in the inter-software consistency. The current study aimed to examine the consistency of three commonly used automated software packages and the effect of age on inter-software consistency. We analyzed T1-weighted structural images from two public datasets, in which the subjects were divided into four age groups ranging from childhood and adolescence to late adulthood. We chose three mainstream automated software packages including FreeSurfer, CAT, and FSL, to estimate the volumes of seven subcortical structures, including thalamus, caudate, putamen, pallidum, hippocampus, amygdala, and accumbens. We used the intraclass correlation coefficient (ICC) and Pearson correlation coefficient (PCC) to quantify inter-software consistency and compared the consistency measures among the age groups. As a measure of validity, we additionally evaluated the predictive power of each software package's estimates for predicting age. The results showed good inter-software consistency in the thalamus, caudate, putamen, and hippocampus, moderate consistency in the pallidum, and poor consistency in the amygdala and accumbens. Significant differences in the inter-software consistency were not observed among the age groups in most cases. FreeSurfer exhibited higher age prediction accuracy than CAT and FSL. The current study showed that the inter-software consistency on the subcortical volume estimation varies with structures but generally not with age groups, which has important implications for the interpretation and reproducibility of neuroimaging findings.

Accurate Automated Quantification of Dopamine Transporter PET Without MRI Using Deep Learning-based Spatial Normalization

Purpose

Dopamine transporter imaging is crucial for assessing presynaptic dopaminergic neurons in Parkinson's disease (PD) and related parkinsonian disorders. While 18F-FP-CIT PET offers advantages in spatial resolution and sensitivity over 123I-β-CIT or 123I-FP-CIT SPECT imaging, accurate quantification remains essential. This study presents a novel automatic quantification method for 18F-FP-CIT PET images, utilizing an artificial intelligence (AI)-based robust PET spatial normalization (SN) technology that eliminates the need for anatomical images.

Methods

The proposed SN engine consists of convolutional neural networks, trained using 213 paired datasets of 18F-FP-CIT PET and 3D structural MRI. Remarkably, only PET images are required as input during inference. A cyclic training strategy enables backward deformation from template to individual space. An additional 89 paired 18F-FP-CIT PET and 3D MRI datasets were used to evaluate the accuracy of striatal activity quantification. MRI-based PET quantification using FIRST software was also conducted for comparison. The proposed method was also validated using 135 external datasets.

Results

The proposed AI-based method successfully generated spatially normalized 18F-FP-CIT PET images, obviating the need for CT or MRI. The striatal PET activity determined by proposed PET-only method and MRI-based PET quantification using FIRST algorithm were highly correlated, with R 2 and slope ranging 0.96-0.99 and 0.98-1.02 in both internal and external datasets.

Conclusion

Our AI-based SN method enables accurate automatic quantification of striatal activity in 18F-FP-CIT brain PET images without MRI support. This approach holds promise for evaluating presynaptic dopaminergic function in PD and related parkinsonian disorders.

Caudate nucleus volume in medicated and unmedicated patients with early- and adult-onset schizophrenia

The caudate nucleus is a part of the striatum, and striatal hyperdopaminergia is considered central to the pathophysiology of schizophrenia. How caudate volume is affected in schizophrenia and what role antipsychotics play remains unclear. In early-onset schizophrenia (EOS), where psychosis emerges during a neurodevelopmentally critical phase, the caudate may exhibit a heightened vulnerability to the effects of antipsychotic medications. We hypothesized effects of both antipsychotic medication use and age of onset on caudate in schizophrenia. We included adult patients with EOS (n = 83) and adult-onset schizophrenia (AOS) (n = 246), adult healthy controls (HC, n = 774), adolescent patients with non-affective psychosis (n = 56) and adolescent HC (n = 97). We obtained T1-weighted MRI scans using a 1.5T Siemens scanner and General Electric 3T scanners. In our main analysis, we tested for main and interaction effects of diagnosis and current antipsychotic medication use on caudate volume. Adult patients with EOS (p < 0.001) and AOS (p = 0.002) had both larger caudate than HC. Age of onset (EOS/AOS) interacted with antipsychotic use (p = 0.004) which was associated with larger caudate in EOS (p < 0.001) but not in AOS (p = 0.654). Conversely, among medicated patients only, EOS had larger caudate than AOS (p < 0.001). No other subcortical structures showed differences between medicated EOS and AOS. Medicated adolescent patients with non-affective psychosis and medicated adult patients with EOS showed similar caudate volumes. The results may indicate a schizophrenia-related and a medication-induced caudate increase, the latter restricted to patients with EOS and possibly occurring already in adolescence shortly after disease onset.

Frontal-striatal glucose metabolism and fatigue in patients with multiple sclerosis, long COVID, and COVID-19 recovered controls

This study compared brain glucose metabolism using FDG-PET in the caudate nucleus, putamen, globus pallidus, thalamus, and dorsolateral prefrontal cortex (DLPFC) among patients with Long COVID, patients with fatigue, people with multiple sclerosis (PwMS) patients with fatigue, and COVID recovered controls. PwMS exhibited greater hypometabolism compared to long COVID patients with fatigue and the COVID recovered control group in all studied brain areas except the globus pallidus (effect size range 0.7-1.5). The results showed no significant differences in glucose metabolism between patients with Long COVID and the COVID recovered control group in these regions. These findings suggest that long COVID fatigue may involve non-CNS systems, neurotransmitter imbalances, or psychological factors not captured by FDG-PET, while MS-related fatigue is associated with more severe frontal-striatal circuit dysfunction due to demyelination and neurodegeneration. Symmetrical standardized uptake values (SUVs) between hemispheres in all groups imply that fatigue in these conditions may be related to global or network-level alterations rather than hemisphere-specific changes. Future studies should employ fine-grained analysis methods, explore other brain regions, and control for confounding factors to better understand the pathophysiology of fatigue in MS and long COVID. Longitudinal studies tracking brain glucose metabolism in patients with Long COVID could provide insights into the evolution of metabolic patterns as the condition progresses.

Spatiotemporal Progression Patterns of Dopamine Availability and Deep Gray Matter Volume in Parkinson Disease-Related Cognitive Impairment

BACKGROUND AND OBJECTIVES

Cognitive impairment is a frequent nonmotor symptom in patients with Parkinson disease (PD), and early cognitive decline is often attributed to dopaminergic system dysfunction. We aimed to explore spatiotemporal progression patterns of striatal dopamine availability and regional brain volume based on cognitive status among patients with PD.

METHODS

This retrospective, cross-sectional study included patients with newly diagnosed PD who were not taking medication for this condition who visited a university-affiliated hospital in Seoul between January 2018 and December 2020. Patients were classified as having normal cognition (PD-NC), mild cognitive impairment (PD-MCI), or PD dementia (PDD) based on Seoul Neuropsychological Screening Battery-II, which includes 31 subsets covering activities of daily living and 5 cognitive domains. They all had brain imaging with MRI and PET with 18F-N-(3-fluoropropyl)-2beta-carbon ethoxy-3beta-(4-iodophenyl) nortropane at baseline. Subsequently, standardized uptake value ratios (SUVRs) for regional dopamine availability and regional gray matter volumes were obtained using automated segmentation. These metrics were compared across cognitive status groups, and spatiotemporal progression patterns were analyzed using the Subtype and Stage Inference machine learning technique.

RESULTS

Among 168 patients (mean age, 73.3 ± 6.1 years; 81 [48.2%] women), 65 had PD-NC, 65 had PD-MCI, and 38 had PDD. Patients with PD-MCI exhibited lower SUVRs (3.61 ± 1.31, p < 0.001) in the caudate than patients with PD-NC (4.43 ± 1.21) but higher SUVRs than patients with PDD (2.39 ± 1.06). Patients with PD-NC had higher thalamic SUVRs (1.55 ± 0.16, p < 0.001) than patients with both PD-MCI (1.45 ± 0.16) and PDD (1.38 ± 0.19). Regional deep gray matter volumes of the caudate (p = 0.015), putamen (p = 0.012), globus pallidus (p < 0.001), thalamus (p < 0.001), hippocampus (p < 0.001), and amygdala (p < 0.001) were more reduced in patients with PD-MCI or PDD than in patients with PD-NC, and the SUVR of the caudate correlated with caudate volume (r = 0.187, p = 0.015). Hippocampal atrophy was the initial change influencing cognitive impairment. The reduced dopamine availability of the thalamus preceded reductions in volume across most deep gray matter regions.

DISCUSSION

Our finding underscores the association between decreased dopamine availability and volume of the caudate and thalamus with cognitive dysfunction in PD. The dopamine availability of the caudate and thalamus was reduced before the volume of the caudate and thalamus was decreased, highlighting the spatiotemporal association between dopaminergic and structural pathology in cognitive impairment in PD.

Comparing Automated Subcortical Volume Estimation Methods; Amygdala Volumes Estimated by FSL and FreeSurfer Have Poor Consistency

Subcortical volumes are a promising source of biomarkers and features in biosignatures, and automated methods facilitate extracting them in large, phenotypically rich datasets. However, while extensive research has verified that the automated methods produce volumes that are similar to those generated by expert annotation, the consistency of methods with each other is understudied. Using data from the UK Biobank, we compare the estimates of subcortical volumes produced by two popular software suites: FSL and FreeSurfer. Although most subcortical volumes exhibit good to excellent consistency across the methods, the tools produce diverging estimates of amygdalar volume. Through simulation, we show that this poor consistency can lead to conflicting results, where one but not the other tool suggests statistical significance, or where both tools suggest a significant relationship but in opposite directions. Considering these issues, we discuss several ways in which care should be taken when reporting on relationships involving amygdalar volume.

Unsupervised deep representation learning enables phenotype discovery for genetic association studies of brain imaging

Understanding the genetic architecture of brain structure is challenging, partly due to difficulties in designing robust, non-biased descriptors of brain morphology. Until recently, brain measures for genome-wide association studies (GWAS) consisted of traditionally expert-defined or software-derived image-derived phenotypes (IDPs) that are often based on theoretical preconceptions or computed from limited amounts of data. Here, we present an approach to derive brain imaging phenotypes using unsupervised deep representation learning. We train a 3-D convolutional autoencoder model with reconstruction loss on 6130 UK Biobank (UKBB) participants' T1 or T2-FLAIR (T2) brain MRIs to create a 128-dimensional representation known as Unsupervised Deep learning derived Imaging Phenotypes (UDIPs). GWAS of these UDIPs in held-out UKBB subjects (n = 22,880 discovery and n = 12,359/11,265 replication cohorts for T1/T2) identified 9457 significant SNPs organized into 97 independent genetic loci of which 60 loci were replicated. Twenty-six loci were not reported in earlier T1 and T2 IDP-based UK Biobank GWAS. We developed a perturbation-based decoder interpretation approach to show that these loci are associated with UDIPs mapped to multiple relevant brain regions. Our results established unsupervised deep learning can derive robust, unbiased, heritable, and interpretable brain imaging phenotypes.

Deep learning-based, fully automated, pediatric brain segmentation

The purpose of this study was to demonstrate the performance of a fully automated, deep learning-based brain segmentation (DLS) method in healthy controls and in patients with neurodevelopmental disorders, SCN1A mutation, under eleven. The whole, cortical, and subcortical volumes of previously enrolled 21 participants, under 11 years of age, with a SCN1A mutation, and 42 healthy controls, were obtained using a DLS method, and compared to volumes measured by Freesurfer with manual correction. Additionally, the volumes which were calculated with the DLS method between the patients and the control group. The volumes of total brain gray and white matter using DLS method were consistent with that volume which were measured by Freesurfer with manual correction in healthy controls. Among 68 cortical parcellated volume analysis, the volumes of only 7 areas measured by DLS methods were significantly different from that measured by Freesurfer with manual correction, and the differences decreased with increasing age in the subgroup analysis. The subcortical volume measured by the DLS method was relatively smaller than that of the Freesurfer volume analysis. Further, the DLS method could perfectly detect the reduced volume identified by the Freesurfer software and manual correction in patients with SCN1A mutations, compared with healthy controls. In a pediatric population, this new, fully automated DLS method is compatible with the classic, volumetric analysis with Freesurfer software and manual correction, and it can also well detect brain morphological changes in children with a neurodevelopmental disorder.

Remembering the null hypothesis when searching for brain sex differences

Human brain sex differences have fascinated scholars for centuries and become a key focus of neuroscientists since the dawn of MRI. We recently published a major review in Neuroscience and Biobehavioral Reviews showing that most male-female brain differences in humans are small and few have been reliably replicated. Although widely cited, this work was the target of a critical Commentary by DeCasien et al. (Biol Sex Differ 13:43, 2022). In this response, I update our findings and confirm the small effect sizes and pronounced scatter across recent large neuroimaging studies of human sex/gender difference. Based on the sum of data, neuroscientists would be well-advised to take the null hypothesis seriously: that men and women's brains are fundamentally similar, or "monomorphic". This perspective has important implications for how we study the genesis of behavioral and neuropsychiatric gender disparities.

Toward More Accessible Fully Automated 3D Volumetric MRI Decision Trees for the Differential Diagnosis of Multiple System Atrophy, Related Disorders, and Age-Matched Healthy Subjects

Differentiating multiple system atrophy (MSA) from related neurodegenerative movement disorders (NMD) is challenging. MRI is widely available and automated decision-tree analysis is simple, transparent, and resistant to overfitting. Using a retrospective cohort of heterogeneous clinical MRIs broadly sourced from a tertiary hospital system, we aimed to develop readily translatable and fully automated volumetric diagnostic decision-trees to facilitate early and accurate differential diagnosis of NMDs. 3DT1 MRI from 171 NMD patients (72 MSA, 49 PSP, 50 PD) and 171 matched healthy subjects were automatically segmented using Freesurfer6.0 with brainstem module. Decision trees employing substructure volumes and a novel volumetric pons-to-midbrain ratio (3D-PMR) were produced and tenfold cross-validation performed. The optimal tree separating NMD from healthy subjects selected cerebellar white matter, thalamus, putamen, striatum, and midbrain volumes as nodes. Its sensitivity was 84%, specificity 94%, accuracy 84%, and kappa 0.69 in cross-validation. The optimal tree restricted to NMD patients selected 3D-PMR, thalamus, superior cerebellar peduncle (SCP), midbrain, pons, and putamen as nodes. It yielded sensitivities/specificities of 94/84% for MSA, 72/96% for PSP, and 73/92% PD, with 79% accuracy and 0.62 kappa. There was correct classification of 16/17 MSA, 5/8 PSP, 6/8 PD autopsy-confirmed patients, and 6/8 MRIs that preceded motor symptom onset. Fully automated decision trees utilizing volumetric MRI data distinguished NMD patients from healthy subjects and MSA from other NMDs with promising accuracy, including autopsy-confirmed and pre-symptomatic subsets. Our open-source methodology is well-suited for widespread clinical translation. Assessment in even more heterogeneous retrospective and prospective cohorts is indicated.

Striatal and thalamic automatic segmentation, morphology, and clinical correlates in Parkinsonism: Parkinson's disease, multiple system atrophy and progressive supranuclear palsy

Parkinson's disease (PD), multisystem atrophy (MSA), and progressive supranuclear palsy (PSP) present similarly with bradykinesia, tremor, rigidity, and cognitive impairments. Neuroimaging studies have found differential changes in the nigrostriatal pathway in these disorders, however whether the volume and shape of specific regions within this pathway can distinguish between atypical Parkinsonian disorders remains to be determined. This paper investigates striatal and thalamic volume and morphology as distinguishing biomarkers, and their relationship to neuropsychiatric symptoms. Automatic segmentation to calculate volume and shape analysis of the caudate nucleus, putamen, and thalamus were performed in 18 PD patients, 12 MSA, 15 PSP, and 20 healthy controls, then correlated with clinical measures. PSP bilateral thalami and right putamen were significantly smaller than controls, but not MSA or PD. The left caudate and putamen significantly correlated with the Neuropsychiatric Inventory total score. Bilateral thalamus, caudate, and left putamen had significantly different morphology between groups, driven by differences between PSP and healthy controls. This study demonstrated that PSP patient striatal and thalamic volume and shape are significantly different when compared with controls. Parkinsonian disorders could not be differentiated on volumetry or morphology, however there are trends for volumetric and morphological changes associated with PD, MSA, and PSP.

Deep learning segmentation results in precise delineation of the putamen in multiple system atrophy

OBJECTIVES

The precise segmentation of atrophic structures remains challenging in neurodegenerative diseases. We determined the performance of a Deep Neural Patchwork (DNP) in comparison to established segmentation algorithms regarding the ability to delineate the putamen in multiple system atrophy (MSA), Parkinson's disease (PD), and healthy controls.

METHODS

We retrospectively included patients with MSA and PD as well as healthy controls. A DNP was trained on manual segmentations of the putamen as ground truth. For this, the cohort was randomly split into a training (N = 131) and test set (N = 120). The DNP's performance was compared with putaminal segmentations as derived by Automatic Anatomic Labelling, Freesurfer and Fastsurfer. For validation, we assessed the diagnostic accuracy of the resulting segmentations in the delineation of MSA vs. PD and healthy controls.

RESULTS

A total of 251 subjects (61 patients with MSA, 158 patients with PD, and 32 healthy controls; mean age of 61.5 ± 8.8 years) were included. Compared to the dice-coefficient of the DNP (0.96), we noted significantly weaker performance for AAL3 (0.72; p < .001), Freesurfer (0.82; p < .001), and Fastsurfer (0.84, p < .001). This was corroborated by the superior diagnostic performance of MSA vs. PD and HC of the DNP (AUC 0.93) versus the AUC of 0.88 for AAL3 (p = 0.02), 0.86 for Freesurfer (p = 0.048), and 0.85 for Fastsurfer (p = 0.04).

CONCLUSION

By utilization of a DNP, accurate segmentations of the putamen can be obtained even if substantial atrophy is present. This allows for more precise extraction of imaging parameters or shape features from the putamen in relevant patient cohorts.

CLINICAL RELEVANCE STATEMENT

Deep learning-based segmentation of the putamen was superior to currently available algorithms and is beneficial for the diagnosis of multiple system atrophy.

KEY POINTS

• A Deep Neural Patchwork precisely delineates the putamen and performs equal to human labeling in multiple system atrophy, even when pronounced putaminal volume loss is present. • The Deep Neural Patchwork-based segmentation was more capable to differentiate between multiple system atrophy and Parkinson's disease than the AAL3 atlas, Freesurfer, or Fastsurfer.

Development and validation of deep learning-based automatic brain segmentation for East Asians: A comparison with Freesurfer

Purpose

To develop and validate deep learning-based automatic brain segmentation for East Asians with comparison to data for healthy controls from Freesurfer based on a ground truth.

Methods

A total of 30 healthy participants were enrolled and underwent T1-weighted magnetic resonance imaging (MRI) using a 3-tesla MRI system. Our Neuro I software was developed based on a three-dimensional convolutional neural networks (CNNs)-based, deep-learning algorithm, which was trained using data for 776 healthy Koreans with normal cognition. Dice coefficient (D) was calculated for each brain segment and compared with control data by paired t-test. The inter-method reliability was assessed by intraclass correlation coefficient (ICC) and effect size. Pearson correlation analysis was applied to assess the relationship between D values for each method and participant ages.

Results

The D values obtained from Freesurfer (ver6.0) were significantly lower than those from Neuro I. The histogram of the Freesurfer results showed remarkable differences in the distribution of D values from Neuro I. Overall, D values obtained by Freesurfer and Neuro I showed positive correlations, but the slopes and intercepts were significantly different. It was showed the largest effect sizes ranged 1.07-3.22, and ICC also showed significantly poor to moderate correlations between the two methods (0.498 ≤ ICC ≤ 0.688). For Neuro I, D values resulted in reduced residuals when fitting data to a line of best fit, and indicated consistent values corresponding to each age, even in young and older adults.

Conclusion

Freesurfer and Neuro I were not equivalent when compared to a ground truth, where Neuro I exhibited higher performance. We suggest that Neuro I is a useful alternative for the assessment of the brain volume.

Uncovering spatiotemporal patterns of atrophy in progressive supranuclear palsy using unsupervised machine learning

To better understand the pathological and phenotypic heterogeneity of progressive supranuclear palsy and the links between the two, we applied a novel unsupervised machine learning algorithm (Subtype and Stage Inference) to the largest MRI data set to date of people with clinically diagnosed progressive supranuclear palsy (including progressive supranuclear palsy-Richardson and variant progressive supranuclear palsy syndromes). Our cohort is comprised of 426 progressive supranuclear palsy cases, of which 367 had at least one follow-up scan, and 290 controls. Of the progressive supranuclear palsy cases, 357 were clinically diagnosed with progressive supranuclear palsy-Richardson, 52 with a progressive supranuclear palsy-cortical variant (progressive supranuclear palsy-frontal, progressive supranuclear palsy-speech/language, or progressive supranuclear palsy-corticobasal), and 17 with a progressive supranuclear palsy-subcortical variant (progressive supranuclear palsy-parkinsonism or progressive supranuclear palsy-progressive gait freezing). Subtype and Stage Inference was applied to volumetric MRI features extracted from baseline structural (T1-weighted) MRI scans and then used to subtype and stage follow-up scans. The subtypes and stages at follow-up were used to validate the longitudinal consistency of subtype and stage assignments. We further compared the clinical phenotypes of each subtype to gain insight into the relationship between progressive supranuclear palsy pathology, atrophy patterns, and clinical presentation. The data supported two subtypes, each with a distinct progression of atrophy: a 'subcortical' subtype, in which early atrophy was most prominent in the brainstem, ventral diencephalon, superior cerebellar peduncles, and the dentate nucleus, and a 'cortical' subtype, in which there was early atrophy in the frontal lobes and the insula alongside brainstem atrophy. There was a strong association between clinical diagnosis and the Subtype and Stage Inference subtype with 82% of progressive supranuclear palsy-subcortical cases and 81% of progressive supranuclear palsy-Richardson cases assigned to the subcortical subtype and 82% of progressive supranuclear palsy-cortical cases assigned to the cortical subtype. The increasing stage was associated with worsening clinical scores, whilst the 'subcortical' subtype was associated with worse clinical severity scores compared to the 'cortical subtype' (progressive supranuclear palsy rating scale and Unified Parkinson's Disease Rating Scale). Validation experiments showed that subtype assignment was longitudinally stable (95% of scans were assigned to the same subtype at follow-up) and individual staging was longitudinally consistent with 90% remaining at the same stage or progressing to a later stage at follow-up. In summary, we applied Subtype and Stage Inference to structural MRI data and empirically identified two distinct subtypes of spatiotemporal atrophy in progressive supranuclear palsy. These image-based subtypes were differentially enriched for progressive supranuclear palsy clinical syndromes and showed different clinical characteristics. Being able to accurately subtype and stage progressive supranuclear palsy patients at baseline has important implications for screening patients on entry to clinical trials, as well as tracking disease progression.

Multisite test-retest reliability and compatibility of brain metrics derived from FreeSurfer versions 7.1, 6.0, and 5.3

Automatic neuroimaging processing tools provide convenient and systematic methods for extracting features from brain magnetic resonance imaging scans. One tool, FreeSurfer, provides an easy-to-use pipeline to extract cortical and subcortical morphometric measures. There have been over 25 stable releases of FreeSurfer, with different versions used across published works. The reliability and compatibility of regional morphometric metrics derived from the most recent version releases have yet to be empirically assessed. Here, we used test-retest data from three public data sets to determine within-version reliability and between-version compatibility across 42 regional outputs from FreeSurfer versions 7.1, 6.0, and 5.3. Cortical thickness from v7.1 was less compatible with that of older versions, particularly along the cingulate gyrus, where the lowest version compatibility was observed (intraclass correlation coefficient 0.37-0.61). Surface area of the temporal pole, frontal pole, and medial orbitofrontal cortex, also showed low to moderate version compatibility. We confirm low compatibility between v6.0 and v5.3 of pallidum and putamen volumes, while those from v7.1 were compatible with v6.0. Replication in an independent sample showed largely similar results for measures of surface area and subcortical volumes, but had lower overall regional thickness reliability and compatibility. Batch effect correction may adjust for some inter-version effects when most sites are run with one version, but results vary when more sites are run with different versions. Age associations in a quality controlled independent sample (N = 106) revealed version differences in results of downstream statistical analysis. We provide a reference to highlight the regional metrics that may yield recent version-related inconsistencies in published findings. An interactive viewer is provided at http://data.brainescience.org/Freesurfer_Reliability/.

Secondary thalamic atrophy related to brain infarction may contribute to post-stroke cognitive impairment

BACKGROUND AND PURPOSE

The thalamus is a key brain hub that is globally connected to many cortical regions. Previous work highlights thalamic contributions to multiple cognitive functions, but few studies have measured thalamic volume changes or cognitive correlates. This study investigates associations between thalamic volumes and post-stroke cognitive function.

METHODS

Participants with non-thalamic brain infarcts (3-42 months) underwent MRI and cognitive testing. Focal infarcts and thalami were traced manually. In cases with bilateral infarcts, the side of the primary infarct volume defined the hemisphere involved. Brain parcellation and volumetrics were extracted using a standardized and previously validated neuroimaging pipeline. Age and gender-matched healthy controls provided normal comparative thalamic volumes. Thalamic atrophy was considered when the volume exceeded 2 standard deviations greater than the controls.

RESULTS

Thalamic volumes ipsilateral to the infarct in stroke patients (n=55) were smaller than left (4.4 ± 1.4 vs. 5.4 ± 0.5 cc, p < 0.001) and right (4.4 ± 1.4 vs. 5.5 ± 0.6 cc, p < 0.001) thalamic volumes in the controls. After controlling for head-size and global brain atrophy, infarct volume independently correlated with ipsilateral thalamic volume (β= -0.069, p=0.024). Left thalamic atrophy correlated significantly with poorer cognitive performance (β = 4.177, p = 0.008), after controlling for demographics and infarct volumes.

CONCLUSIONS

Our results suggest that the remote effect of infarction on ipsilateral thalamic volume is associated with global post-stroke cognitive impairment.

Robustness of radiomics to variations in segmentation methods in multimodal brain MRI

Radiomics in neuroimaging uses fully automatic segmentation to delineate the anatomical areas for which radiomic features are computed. However, differences among these segmentation methods affect radiomic features to an unknown extent. A scan-rescan dataset (n = 46) of T1-weighted and diffusion tensor images was used. Subjects were split into a sleep-deprivation and a control group. Scans were segmented using four segmentation methods from which radiomic features were computed. First, we measured segmentation agreement using the Dice-coefficient. Second, robustness and reproducibility of radiomic features were measured using the intraclass correlation coefficient (ICC). Last, difference in predictive power was assessed using the Friedman-test on performance in a radiomics-based sleep deprivation classification application. Segmentation agreement was generally high (interquartile range = 0.77–0.90) and median feature robustness to segmentation method variation was higher (ICC > 0.7) than scan-rescan reproducibility (ICC 0.3–0.8). However, classification performance differed significantly among segmentation methods (p < 0.001) ranging from 77 to 84%. Accuracy was higher for more recent deep learning-based segmentation methods. Despite high agreement among segmentation methods, subtle differences significantly affected radiomic features and their predictive power. Consequently, the effect of differences in segmentation methods should be taken into account when designing and evaluating radiomics-based research methods.

Functional connectivity of the cortico-subcortical sensorimotor loop is modulated by the severity of nigrostriatal dopaminergic denervation in Parkinson’s Disease

To assess if the severity of nigrostriatal innervation loss affects the functional connectivity (FC) of the sensorimotor cortico-striato-thalamic-cortical loop (CSTCL) in Parkinson’s Disease (PD), Resting-State functional MRI and ¹⁸F-DOPA PET data, simultaneously acquired on a hybrid PET/MRI scanner, were retrospectively analyzed in 39 PD and 16 essential tremor patients. Correlations between posterior Putamen DOPA Uptake (pPDU) and the FC of the main CSTCL hubs were assessed separately in the two groups, analyzing the differences between the two groups by a group-by-pPDU interaction analysis of the resulting clusters’ FC. Unlike in essential tremor, in PD patients pPDU correlated inversely with the FC of the thalamus with the sensorimotor cortices, and of the postcentral gyrus with the dorsal cerebellum, and directly with the FC of pre- and post-central gyri with both the superior and middle temporal gyri and the paracentral lobule, and of the caudate with the superior parietal cortex. The interaction analysis confirmed the significance of the difference between the two groups in these correlations. In PD patients, the post-central cortex FC, in the clusters correlating directly with pPDU, negatively correlated with both UPDRS motor examination score and Hoehn and Yahr stage, independent of the pPDU, suggesting that these FC changes contribute to motor impairment. In PD, nigrostriatal innervation loss correlates with a decrease in the FC within the sensorimotor network and between the sensorimotor network and the superior temporal cortices, possibly contributing to motor impairment, and with a strengthening of the thalamo-cortical FC, that may represent ineffective compensatory phenomena.

Nomograms of human hippocampal volume shifted by polygenic scores

Nomograms are important clinical tools applied widely in both developing and aging populations. They are generally constructed as normative models identifying cases as outliers to a distribution of healthy controls. Currently used normative models do not account for genetic heterogeneity. Hippocampal volume (HV) is a key endophenotype for many brain disorders. Here, we examine the impact of genetic adjustment on HV nomograms and the translational ability to detect dementia patients. Using imaging data from 35,686 healthy subjects aged 44-82 from the UK Biobank (UKB), we built HV nomograms using Gaussian process regression (GPR), which - compared to a previous method - extended the application age by 20 years, including dementia critical age ranges. Using HV polygenic scores (HV-PGS), we built genetically adjusted nomograms from participants stratified into the top and bottom 30% of HV-PGS. This shifted the nomograms in the expected directions by ~100 mm3 (2.3% of the average HV), which equates to 3 years of normal aging for a person aged ~65. Clinical impact of genetically adjusted nomograms was investigated by comparing 818 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database diagnosed as either cognitively normal (CN), having mild cognitive impairment (MCI) or Alzheimer's disease (AD) patients. While no significant change in the survival analysis was found for MCI-to-AD conversion, an average of 68% relative decrease was found in intra-diagnostic-group variance, highlighting the importance of genetic adjustment in untangling phenotypic heterogeneity.

Subcortical and hippocampal brain segmentation in 5-year-old children: validation of FSL-FIRST and FreeSurfer against manual segmentation

Developing accurate subcortical volumetric quantification tools is crucial for neurodevelopmental studies, as they could reduce the need for challenging and time‐consuming manual segmentation. In this study, the accuracy of two automated segmentation tools, FSL‐FIRST (with three different boundary correction settings) and FreeSurfer, were compared against manual segmentation of the hippocampus and subcortical nuclei, including the amygdala, thalamus, putamen, globus pallidus, caudate and nucleus accumbens, using volumetric and correlation analyses in 80 5‐year‐olds.

Both FSL‐FIRST and FreeSurfer overestimated the volume on all structures except the caudate, and the accuracy varied depending on the structure. Small structures such as the amygdala and nucleus accumbens, which are visually difficult to distinguish, produced significant overestimations and weaker correlations with all automated methods. Larger and more readily distinguishable structures such as the caudate and putamen produced notably lower overestimations and stronger correlations. Overall, the segmentations performed by FSL‐FIRST's default pipeline were the most accurate, whereas FreeSurfer's results were weaker across the structures.

In line with prior studies, the accuracy of automated segmentation tools was imperfect with respect to manually defined structures. However, apart from amygdala and nucleus accumbens, FSL‐FIRST's agreement could be considered satisfactory (Pearson correlation > 0.74, intraclass correlation coefficient (ICC) > 0.68 and Dice score coefficient (DSC) > 0.87) with highest values for the striatal structures (putamen, globus pallidus, caudate) (Pearson correlation > 0.77, ICC > 0.87 and DSC > 0.88, respectively). Overall, automated segmentation tools do not always provide satisfactory results, and careful visual inspection of the automated segmentations is strongly advised.

A framework For brain atlases: Lessons from seizure dynamics

Brain maps, or atlases, are essential tools for studying brain function and organization. The abundance of available atlases used across the neuroscience literature, however, creates an implicit challenge that may alter the hypotheses and predictions we make about neurological function and pathophysiology. Here, we demonstrate how parcellation scale, shape, anatomical coverage, and other atlas features may impact our prediction of the brain's function from its underlying structure. We show how network topology, structure-function correlation (SFC), and the power to test specific hypotheses about epilepsy pathophysiology may change as a result of atlas choice and atlas features. Through the lens of our disease system, we propose a general framework and algorithm for atlas selection. This framework aims to maximize the descriptive, explanatory, and predictive validity of an atlas. Broadly, our framework strives to provide empirical guidance to neuroscience research utilizing the various atlases published over the last century.

Longitudinal Brain Changes After Stroke and the Association With Cognitive Decline

Background

Cognitive impairment is common after stroke. So is cortical- and subcortical atrophy, with studies reporting more atrophy in the ipsilesional hemisphere than the contralesional hemisphere. The current study aimed to investigate the longitudinal associations between (I) lateralization of brain atrophy and stroke hemisphere, and (II) cognitive impairment and brain atrophy after stroke. We expected to find that (I) cortical thickness and hippocampal-, thalamic-, and caudate nucleus volumes declined more in the ipsilesional than the contralesional hemisphere up to 36 months after stroke. Furthermore, we predicted that (II) cognitive decline was associated with greater stroke volumes, and with greater cortical thickness and subcortical structural volume atrophy across the 36 months.

Methods

Stroke survivors from five Norwegian hospitals were included from the multisite-prospective “Norwegian Cognitive Impairment After Stroke” (Nor-COAST) study. Analyses were run with clinical, neuropsychological and structural magnetic resonance imaging (MRI) data from baseline, 18- and 36 months. Cortical thicknesses and subcortical volumes were obtained via FreeSurfer segmentations and stroke lesion volumes were semi-automatically derived using ITK-SNAP. Cognition was measured using MoCA.

Results

Findings from 244 stroke survivors [age = 72.2 (11.3) years, women = 55.7%, stroke severity NIHSS = 4.9 (5.0)] were included at baseline. Of these, 145 (59.4%) had an MRI scan at 18 months and 72 (49.7% of 18 months) at 36 months. Most cortices and subcortices showed a higher ipsi- compared to contralesional atrophy rate, with the effect being more prominent in the right hemisphere. Next, greater degrees of atrophy particularly in the medial temporal lobe after left-sided strokes and larger stroke lesion volumes after right-sided strokes were associated with cognitive decline over time.

Conclusion

Atrophy in the ipsilesional hemisphere was greater than in the contralesional hemisphere over time. This effect was found to be more prominent in the right hemisphere, pointing to a possible higher resilience to stroke of the left hemisphere. Lastly, greater atrophy of the cortex and subcortex, as well as larger stroke volume, were associated with worse cognition over time and should be included in risk assessments of cognitive decline after stroke.

Alteration of Cortical Volume and Thickness in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

Myalgic Encephalomyelitis/Chronic fatigue syndrome (ME/CFS) patients suffer from neurocognitive impairment. In this study, we investigated cortical volumetric and thickness changes in ME/CFS patients and healthy controls (HC). We estimated mean surface-based cortical volume and thickness from 18 ME/CFS patients who met International Consensus Criteria (ICC) and 26 HC using FreeSurfer. Vertex-wise analysis showed significant reductions in the caudal middle frontal gyrus (p = 0.0016) and precuneus (p = 0.013) thickness in ME/CFS patients compared with HC. Region based analysis of sub-cortical volumes found that amygdala volume (p = 0.002) was significantly higher in ME/CFS patients compared with HC. We also performed interaction-with-group regressions with clinical measures to test for cortical volume and thickness correlations in ME/CFS with opposite slopes to HC (abnormal). ME/CFS cortical volume and thickness regressions with fatigue, heart-rate variability, heart rate, sleep disturbance score, respiratory rate, and cognitive performance were abnormal. Our study demonstrated different cortical volume and thickness in ME/CFS patients and showed abnormal cortical volume and thickness regressions with key symptoms of ME/CFS patients.

A data-driven model of brain volume changes in progressive supranuclear palsy

The most common clinical phenotype of progressive supranuclear palsy is Richardson syndrome, characterized by levodopa unresponsive symmetric parkinsonism, with a vertical supranuclear gaze palsy, early falls and cognitive impairment. There is currently no detailed understanding of the full sequence of disease pathophysiology in progressive supranuclear palsy. Determining the sequence of brain atrophy in progressive supranuclear palsy could provide important insights into the mechanisms of disease progression, as well as guide patient stratification and monitoring for clinical trials. We used a probabilistic event-based model applied to cross-sectional structural MRI scans in a large international cohort, to determine the sequence of brain atrophy in clinically diagnosed progressive supranuclear palsy Richardson syndrome. A total of 341 people with Richardson syndrome (of whom 255 had 12-month follow-up imaging) and 260 controls were included in the study. We used a combination of 12-month follow-up MRI scans, and a validated clinical rating score (progressive supranuclear palsy rating scale) to demonstrate the longitudinal consistency and utility of the event-based model's staging system. The event-based model estimated that the earliest atrophy occurs in the brainstem and subcortical regions followed by progression caudally into the superior cerebellar peduncle and deep cerebellar nuclei, and rostrally to the cortex. The sequence of cortical atrophy progresses in an anterior to posterior direction, beginning in the insula and then the frontal lobe before spreading to the temporal, parietal and finally the occipital lobe. This in vivo ordering accords with the post-mortem neuropathological staging of progressive supranuclear palsy and was robust under cross-validation. Using longitudinal information from 12-month follow-up scans, we demonstrate that subjects consistently move to later stages over this time interval, supporting the validity of the model. In addition, both clinical severity (progressive supranuclear palsy rating scale) and disease duration were significantly correlated with the predicted subject event-based model stage (P < 0.01). Our results provide new insights into the sequence of atrophy progression in progressive supranuclear palsy and offer potential utility to stratify people with this disease on entry into clinical trials based on disease stage, as well as track disease progression.

Differences in Structural Brain Characteristics Between Individuals with Chronic Nonspecific Neck Pain and Asymptomatic Controls: A Case–Control Study

Background

Neck pain is a prevalent and costly problem, but its underlying mechanisms are poorly understood. Neuroimaging studies show alterations in brain morphometry in chronic musculoskeletal pain, but reports on neck pain are scarce.

Objective

This study investigates (1) differences in brain morphometry between individuals with chronic nonspecific neck pain and asymptomatic individuals and (2) associations between brain morphometry and patient-reported outcomes.

Methods

Sixty-three participants (33 pain, 11 female, mean [SD] age 35 [10] years; 30 control, 12 female, age 35 [11] years) underwent magnetic resonance imaging. Brain regions of interest (ROIs) were determined a priori, outcomes included cortical thickness and volume. Between-group differences were determined using cluster-wise correction for multiple comparisons and analyses of pain-related ROIs.

Results

Between-group differences in volume were identified in the precentral, frontal, occipital, parietal, temporal, and paracentral cortices. ROI analyses showed that parahippocampal cortical thickness was larger in the neck pain group (p=0.015, 95% CI: −0.27 to −0.03). Moderate to strong associations between volume and thickness of the cingulate cortex, prefrontal cortex, and temporal lobe and neck pain duration, pain intensity, and neck disability were identified (p-values 0.006 to 0.048).

Conclusion

Alterations in brain morphology that are associated with clinical characteristics inform the mechanisms underlying chronic nonspecific neck pain and may guide the development of more effective treatment approaches.

Hippocampal structural alterations in early-stage psychosis: Specificity and relationship to clinical outcomes

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Individuals with early-stage psychosis show reduced hippocampal volumes.

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FEP show bilateral and widespread changes, while left hemisphere is affected in CHR-P.

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However, hippocampal changes do not show a relationship with clinical outcomes.

Hippocampal dysfunctions are a core feature of schizophrenia, but conflicting evidence exists whether volumetric and morphological changes are present in early-stage psychosis and to what extent these deficits are related to clinical trajectories. In this study, we recruited individuals at clinical high risk for psychosis (CHR-P) (n = 108), patients with a first episode of psychosis (FEP) (n = 37), healthy controls (HC) (n = 70) as well as a psychiatric control group with substance abuse and affective disorders (CHR-N: n = 38). MRI-data at baseline were obtained and volumetric as well as vertex analyses of the hippocampus were carried out. Moreover, volumetric changes were examined in the amygdala, caudate, nucleus accumbens, pallidum, putamen and thalamus. In addition, we obtained follow-up functional and symptomatic assessments in CHR-P individuals to examine the question whether anatomical deficits at baseline predicted clinical trajectories. Our results show that the hippocampus is the only structure showing significant volumetric decrease in early-stage psychosis, with FEPs showing significantly smaller hippocampal volumes bilaterally alongside widespread shape changes in the vertex analysis. For the CHR-P group, volumetric decreases were confined to the left hippocampus. However, hippocampal alterations in the CHR-P group were not robustly associated with clinical outcomes, including the persistence of attenuated psychotic symptoms and functional trajectories. Accordingly, our findings highlight that dysfunctions in hippocampal anatomy are an important feature of early-stage psychosis which may, however, not be related to clinical outcomes in CHR-P participants.

MRI-based thalamic volumetry in multiple sclerosis using FSL-FIRST: Systematic assessment of common error modes

BACKGROUND AND PURPOSE

FSL's FMRIB's Integrated Registration and Segmentation Tool (FSL-FIRST) is a widely used and well-validated tool. Automated thalamic segmentation is a common application and an important longitudinal measure for multiple sclerosis (MS). However, FSL-FIRST's algorithm is based on shape models derived from non-MS groups. As such, the present study sought to systematically assess common thalamic segmentation errors made by FSL-FIRST on MRIs from people with multiple sclerosis (PwMS).

METHODS

FSL-FIRST was applied to generate thalamic segmentation masks for 890 MR images in PwMS. Images and masks were reviewed systematically to classify and quantify errors, as well as associated anatomical variations and MRI abnormalities. For cases with overt errors (n = 362), thalamic masks were corrected and quantitative volumetric differences were calculated.

RESULTS

In the entire quantitative volumetric group, the mean volumetric error of FSL-FIRST was 2.74% (0.360 ml): among only corrected cases, the mean volumetric error was 6.79% (0.894 ml). The average percent volumetric error associated with seven error types, two anatomical variants, and motions artifacts are reported. Additional analyses showed that the presence of motion artifacts or anatomical variations significantly increased the probability of error (χ²  = 18.14, p < .01 and χ²  = 64.89, p < .001, respectively). Finally, thalamus volume error was negatively associated with degree of atrophy, such that smaller thalami were systematically overestimated (r = -.28, p < .001).

CONCLUSIONS

In PwMS, FSL-FIRST thalamic segmentation miscalculates thalamic volumetry in a predictable fashion, and may be biased to overestimate highly atrophic thalami. As such, it is recommended that segmentations be reviewed and corrected manually when appropriate for specific studies.

Differences Between MR Brain Region Segmentation Methods: Impact on Single-Subject Analysis

For the segmentation of magnetic resonance brain images into anatomical regions, numerous fully automated methods have been proposed and compared to reference segmentations obtained manually. However, systematic differences might exist between the resulting segmentations, depending on the segmentation method and underlying brain atlas. This potentially results in sensitivity differences to disease and can further complicate the comparison of individual patients to normative data. In this study, we aim to answer two research questions: 1) to what extent are methods interchangeable, as long as the same method is being used for computing normative volume distributions and patient-specific volumes? and 2) can different methods be used for computing normative volume distributions and assessing patient-specific volumes? To answer these questions, we compared volumes of six brain regions calculated by five state-of-the-art segmentation methods: Erasmus MC (EMC), FreeSurfer (FS), geodesic information flows (GIF), multi-atlas label propagation with expectation–maximization (MALP-EM), and model-based brain segmentation (MBS). We applied the methods on 988 non-demented (ND) subjects and computed the correlation (PCC-v) and absolute agreement (ICC-v) on the volumes. For most regions, the PCC-v was good (>0.75), indicating that volume differences between methods in ND subjects are mainly due to systematic differences. The ICC-v was generally lower, especially for the smaller regions, indicating that it is essential that the same method is used to generate normative and patient data. To evaluate the impact on single-subject analysis, we also applied the methods to 42 patients with Alzheimer’s disease (AD). In the case where the normative distributions and the patient-specific volumes were calculated by the same method, the patient’s distance to the normative distribution was assessed with the z-score. We determined the diagnostic value of this z-score, which showed to be consistent across methods. The absolute agreement on the AD patients’ z-scores was high for regions of thalamus and putamen. This is encouraging as it indicates that the studied methods are interchangeable for these regions. For regions such as the hippocampus, amygdala, caudate nucleus and accumbens, and globus pallidus, not all method combinations showed a high ICC-z. Whether two methods are indeed interchangeable should be confirmed for the specific application and dataset of interest.

Analysis of structural brain asymmetries in attention-deficit/hyperactivity disorder in 39 datasets

OBJECTIVE

Some studies have suggested alterations of structural brain asymmetry in attention-deficit/hyperactivity disorder (ADHD), but findings have been contradictory and based on small samples. Here, we performed the largest ever analysis of brain left-right asymmetry in ADHD, using 39 datasets of the ENIGMA consortium.

METHODS

We analyzed asymmetry of subcortical and cerebral cortical structures in up to 1,933 people with ADHD and 1,829 unaffected controls. Asymmetry Indexes (AIs) were calculated per participant for each bilaterally paired measure, and linear mixed effects modeling was applied separately in children, adolescents, adults, and the total sample, to test exhaustively for potential associations of ADHD with structural brain asymmetries.

RESULTS

There was no evidence for altered caudate nucleus asymmetry in ADHD, in contrast to prior literature. In children, there was less rightward asymmetry of the total hemispheric surface area compared to controls (t = 2.1, p = .04). Lower rightward asymmetry of medial orbitofrontal cortex surface area in ADHD (t = 2.7, p = .01) was similar to a recent finding for autism spectrum disorder. There were also some differences in cortical thickness asymmetry across age groups. In adults with ADHD, globus pallidus asymmetry was altered compared to those without ADHD. However, all effects were small (Cohen's d from -0.18 to 0.18) and would not survive study-wide correction for multiple testing.

CONCLUSION

Prior studies of altered structural brain asymmetry in ADHD were likely underpowered to detect the small effects reported here. Altered structural asymmetry is unlikely to provide a useful biomarker for ADHD, but may provide neurobiological insights into the trait.

White Matter Hyperintensity Volume and Location: Associations With WM Microstructure, Brain Iron, and Cerebral Perfusion

Cerebral white matter hyperintensities (WMHs) represent macrostructural brain damage associated with various etiologies. However, the relative contributions of various etiologies to WMH volume, as assessed via different neuroimaging measures, is not well-understood. Here, we explored associations between three potential early markers of white matter hyperintensity volume. Specifically, the unique variance in total and regional WMH volumes accounted for by white matter microstructure, brain iron concentration and cerebral blood flow (CBF) was assessed. Regional volumes explored were periventricular and deep regions. Eighty healthy older adults (ages 60–86) were scanned at 3 Tesla MRI using fluid-attenuated inversion recovery, diffusion tensor imaging (DTI), multi-echo gradient-recalled echo and pseudo-continuous arterial spin labeling sequences. In a stepwise regression model, DTI-based radial diffusivity accounted for significant variance in total WMH volume (adjusted R² change = 0.136). In contrast, iron concentration (adjusted R² change = 0.043) and CBF (adjusted R² change = 0.027) made more modest improvements to the variance accounted for in total WMH volume. However, there was an interaction between iron concentration and location on WMH volume such that iron concentration predicted deep (p = 0.034) but not periventricular (p = 0.414) WMH volume. Our results suggest that WM microstructure may be a better predictor of WMH volume than either brain iron or CBF but also draws attention to the possibility that some early WMH markers may be location-specific.

Dispositional Negative Emotionality in Childhood and Adolescence Predicts Structural Variation in the Amygdala and Caudal Anterior Cingulate During Early Adulthood: Theoretically and Empirically Based Tests

Substantial evidence implicates the amygdala and related structures in the processing of negative emotions. Furthermore, neuroimaging evidence suggests that variations in amygdala volumes are related to trait-like individual differences in neuroticism/negative emotionality, although many questions remain about the nature of such associations. We conducted planned tests of the directional prediction that dispositional negative emotionality measured at 10-17 years using parent and youth ratings on the Child and Adolescent Dispositions Scale (CADS) would predict larger volumes of the amygdala in adulthood and conducted exploratory tests of associations with other regions implicated in emotion processing. Participants were 433 twins strategically selected for neuroimaging during wave 2 from wave 1 of the Tennessee Twins Study (TTS) by oversampling on internalizing and/or externalizing psychopathology risk. Controlling for age, sex, race-ethnicity, handedness, scanner, and total brain volume, youth-rated negative emotionality positively predicted bilateral amygdala volumes after correction for multiple testing. Each unit difference of one standard deviation (SD) in negative emotionality was associated with a .12 SD unit difference in larger volumes of both amygdalae. Parent-rated negative emotionality predicted greater thickness of the left caudal/dorsal anterior cingulate cortex (β = 0.28). Associations of brain structure with negative emotionality were not moderated by sex. These results are striking because dispositions assessed at 10-17 years of age were predictive of grey matter volumes measured 12-13 years later in adulthood. Future longitudinal studies should examine the timing of amygdala/cingulate associations with dispositional negative emotionality to determine when these associations emerge during development.

Thalamic morphology predicts the onset of freezing of gait in Parkinson's disease

The onset of freezing of gait (FOG) in Parkinson's disease (PD) is a critical milestone, marked by a higher risk of falls and reduced quality of life. FOG is associated with alterations in subcortical neural circuits, yet no study has assessed whether subcortical morphology can predict the onset of clinical FOG. In this prospective multimodal neuroimaging cohort study, we performed vertex-based analysis of grey matter morphology in fifty-seven individuals with PD at study entry and two years later. We also explored the behavioral correlates and resting-state functional connectivity related to these local volume differences. At study entry, we found that freezers (N = 12) and persons who developed FOG during the course of the study (converters) (N = 9) showed local inflations in bilateral thalamus in contrast to persons who did not (non-converters) (N = 36). Longitudinally, converters (N = 7) also showed local inflation in the left thalamus, as compared to non-converters (N = 36). A model including sex, daily levodopa equivalent dose, and local thalamic inflation predicted conversion with good accuracy (AUC: 0.87, sensitivity: 88.9%, specificity: 77.8%). Exploratory analyses showed that local thalamic inflations were associated with larger medial thalamic sub-nuclei volumes and better cognitive performance. Resting-state analyses further revealed that converters had stronger thalamo-cortical coupling with limbic and cognitive regions pre-conversion, with a marked reduction in coupling over the two years. Finally, validation using the PPMI cohort suggested FOG-specific non-linear evolution of thalamic local volume. These findings provide markers of, and deeper insights into conversion to FOG, which may foster earlier intervention and better mobility for persons with PD.

Dump the "dimorphism": Comprehensive synthesis of human brain studies reveals few male-female differences beyond size

With the explosion of neuroimaging, differences between male and female brains have been exhaustively analyzed. Here we synthesize three decades of human MRI and postmortem data, emphasizing meta-analyses and other large studies, which collectively reveal few reliable sex/gender differences and a history of unreplicated claims. Males' brains are larger than females' from birth, stabilizing around 11 % in adults. This size difference accounts for other reproducible findings: higher white/gray matter ratio, intra- versus interhemispheric connectivity, and regional cortical and subcortical volumes in males. But when structural and lateralization differences are present independent of size, sex/gender explains only about 1% of total variance. Connectome differences and multivariate sex/gender prediction are largely based on brain size, and perform poorly across diverse populations. Task-based fMRI has especially failed to find reproducible activation differences between men and women in verbal, spatial or emotion processing due to high rates of false discovery. Overall, male/female brain differences appear trivial and population-specific. The human brain is not "sexually dimorphic."

A variation in the infant oxytocin receptor gene modulates infant hippocampal volumes in association with sex and prenatal maternal anxiety

Genetic variants in the oxytocin receptor (OTR) have been linked to distinct social phenotypes, psychiatric disorders and brain volume alterations in adults. However, to date, it is unknown how OTR genotype shapes prenatal brain development and whether it interacts with maternal prenatal environmental risk factors on infant brain volumes. In 105 Finnish mother-infant dyads (44 female, 11-54 days old), the association of offspring OTR genotype rs53576 and its interaction with prenatal maternal anxiety (revised Symptom Checklist 90, gestational weeks 14, 24, 34) on infant bilateral amygdalar, hippocampal and caudate volumes were probed. A sex-specific main effect of rs53576 on infant left hippocampal volumes was observed. In boys compared to girls, left hippocampal volumes were significantly larger in GG-homozygotes compared to A-allele carriers. Furthermore, genotype rs53576 and prenatal maternal anxiety significantly interacted on right hippocampal volumes irrespective of sex. Higher maternal anxiety was associated both with larger hippocampal volumes in A-allele carriers than GG-homozygotes, and, though statistically weak, also with smaller right caudate volumes in GG-homozygotes than A-allele carriers. Our study results suggest that OTR genotype enhances hippocampal neurogenesis in male GG-homozygotes. Further, prenatal maternal anxiety might induce brain alterations that render GG-homozygotes compared to A-allele carriers more vulnerable to depression.

A novel pipeline leveraging surface-based features of small subcortical structures to classify individuals with autism spectrum disorder

Autism spectrum disorder (ASD) is accompanied with widespread impairment in social-emotional functioning. Classification of ASD using sensitive morphological features derived from structural magnetic resonance imaging (MRI) of the brain may help us to better understand ASD-related mechanisms and improve related automatic diagnosis. Previous studies using T1 MRI scans in large heterogeneous ABIDE dataset with typical development (TD) controls reported poor classification accuracies (around 60%). This may because they only considered surface-based morphometry (SBM) as scalar estimates (such as cortical thickness and surface area) and ignored the neighboring intrinsic geometry information among features. In recent years, the shape-related SBM achieves great success in discovering the disease burden and progression of other brain diseases. However, when focusing on local geometry information, its high dimensionality requires careful treatment in its application to machine learning. To address the above challenges, we propose a novel pipeline for ASD classification, which mainly includes the generation of surface-based features, patch-based surface sparse coding and dictionary learning, Max-pooling and ensemble classifiers based on adaptive optimizers. The proposed pipeline may leverage the sensitivity of brain surface morphometry statistics and the efficiency of sparse coding and Max-pooling. By introducing only the surface features of bilateral hippocampus that derived from 364 male subjects with ASD and 381 age-matched TD males, this pipeline outperformed five recent MRI-based ASD classification studies with >80% accuracy in discriminating individuals with ASD from TD controls. Our results suggest shape-related SBM features may further boost the classification performance of MRI between ASD and TD.

A Review of Publicly Available Automatic Brain Segmentation Methodologies, Machine Learning Models, Recent Advancements, and Their Comparison

BACKGROUND

The noninvasive study of the structure and functions of the brain using neuroimaging techniques is increasingly being used for its clinical and research perspective. The morphological and volumetric changes in several regions and structures of brains are associated with the prognosis of neurological disorders such as Alzheimer's disease, epilepsy, schizophrenia, etc. and the early identification of such changes can have huge clinical significance. The accurate segmentation of three-dimensional brain magnetic resonance images into tissue types (i.e., grey matter, white matter, cerebrospinal fluid) and brain structures, thus, has huge importance as they can act as early biomarkers. The manual segmentation though considered the "gold standard" is time-consuming, subjective, and not suitable for bigger neuroimaging studies. Several automatic segmentation tools and algorithms have been developed over the years; the machine learning models particularly those using deep convolutional neural network (CNN) architecture are increasingly being applied to improve the accuracy of automatic methods.

PURPOSE

The purpose of the study is to understand the current and emerging state of automatic segmentation tools, their comparison, machine learning models, their reliability, and shortcomings with an intent to focus on the development of improved methods and algorithms.

METHODS

The study focuses on the review of publicly available neuroimaging tools, their comparison, and emerging machine learning models particularly those based on CNN architecture developed and published during the last five years.

CONCLUSION

Several software tools developed by various research groups and made publicly available for automatic segmentation of the brain show variability in their results in several comparison studies and have not attained the level of reliability required for clinical studies. The machine learning models particularly three dimensional fully convolutional network models can provide a robust and efficient alternative with relation to publicly available tools but perform poorly on unseen datasets. The challenges related to training, computation cost, reproducibility, and validation across distinct scanning modalities for machine learning models need to be addressed.

Cortical morphometry and neural dysfunction in Huntington's disease: a review

Numerous neuroimaging techniques have been used to identify biomarkers of disease progression in Huntington's disease (HD). To date, the earliest and most sensitive of these is caudate volume; however, it is becoming increasingly evident that numerous changes to cortical structures, and their interconnected networks, occur throughout the course of the disease. The mechanisms by which atrophy spreads from the caudate to these cortical regions remains unknown. In this review, the neuroimaging literature specific to T1-weighted and diffusion-weighted magnetic resonance imaging is summarized and new strategies for the investigation of cortical morphometry and the network spread of degeneration in HD are proposed. This new avenue of research may enable further characterization of disease pathology and could add to a suite of biomarker/s of disease progression for patient stratification that will help guide future clinical trials.

Lesion Induced Error on Automated Measures of Brain Volume: Data From a Pediatric Traumatic Brain Injury Cohort

Structural segmentation of T1-weighted (T1w) MRI has shown morphometric differences, both compared to controls and longitudinally, following a traumatic brain injury (TBI). While many patients with TBI present with abnormalities on structural MRI images, most neuroimaging software packages have not been systematically evaluated for accuracy in the presence of these pathology-related MRI abnormalities. The current study aimed to assess whether acute MRI lesions (MRI acquired 7–71 days post-injury) cause error in the estimates of brain volume produced by the semi-automated segmentation tool, Freesurfer. More specifically, to investigate whether this error was global, the presence of lesion-induced error in the contralesional hemisphere, where no abnormal signal was present, was measured. A dataset of 176 simulated lesion cases was generated using actual lesions from 16 pediatric TBI (pTBI) cases recruited from the emergency department and 11 typically-developing controls. Simulated lesion cases were compared to the “ground truth” of the non-lesion control-case T1w images. Using linear mixed-effects models, results showed that hemispheric measures of cortex volume were significantly lower in the contralesional-hemisphere compared to the ground truth. Interestingly, however, cortex volume (and cerebral white matter volume) were not significantly different in the lesioned hemisphere. However, percent volume difference (PVD) between the simulated lesion and ground truth showed that the magnitude of difference of cortex volume in the contralesional-hemisphere (mean PVD = 0.37%) was significantly smaller than that in the lesioned hemisphere (mean PVD = 0.47%), suggesting a small, but systematic lesion-induced error. Lesion characteristics that could explain variance in the PVD for each hemisphere were investigated. Taken together, these results suggest that the lesion-induced error caused by simulated lesions was not focal, but globally distributed. Previous post-processing approaches to adjust for lesions in structural analyses address the focal region where the lesion was located however, our results suggest that focal correction approaches are insufficient for the global error in morphometric measures of the injured brain.

Classifying multiple sclerosis patients on the basis of SDMT performance using machine learning

Objective:

To build a model to predict cognitive status reflecting structural, functional, and white matter integrity changes in early multiple sclerosis (MS).

Methods:

Based on Symbol Digit Modalities Test (SDMT) performance, 183 early MS patients were assigned “lower” or “higher” performance groups. Three-dimensional (3D)-T2, T1, diffusion weighted, and resting-state magnetic resonance imaging (MRI) data were acquired in 3T. Using Random Forest, five models were trained to classify patients into two groups based on 1—demographic/clinical, 2—lesion volume/location, 3—local/global tissue volume, 4—local/global diffusion tensor imaging, and 5—whole-brain resting-state-functional-connectivity measures. In a final model, all important features from previous models were concatenated. Area under the receiver operating characteristic curve (AUC) values were calculated to evaluate classifier performance.

Results:

The highest AUC value (0.90) was achieved by concatenating all important features from neuroimaging models. The top 10 contributing variables included volumes of bilateral nucleus accumbens and right thalamus, mean diffusivity of left cingulum-angular bundle, and functional connectivity among hubs of seven large-scale networks.

Conclusion:

These results provide an indication of a non-random brain pattern mostly compromising areas involved in attentional processes specific to patients who perform worse in SDMT. High accuracy of the final model supports this pattern as a potential neuroimaging biomarker of subtle cognitive changes in early MS.

Cannabis use in patients with early psychosis is associated with alterations in putamen and thalamic shape

Around half of patients with early psychosis have a history of cannabis use. We aimed to determine if there are neurobiological differences in these the subgroups of persons with psychosis with and without a history of cannabis use. We expected to see regional deflations in hippocampus as a neurotoxic effect and regional inflations in striatal regions implicated in addictive processes. Volumetric, T1w MRIs were acquired from people with a diagnosis psychosis with (PwP + C = 28) or without (PwP - C = 26) a history of cannabis use; and Controls with (C + C = 16) or without (C - C = 22) cannabis use. We undertook vertex-based shape analysis of the brainstem, amygdala, hippocampus, globus pallidus, nucleus accumbens, caudate, putamen, thalamus using FSL FIRST. Clusters were defined through Threshold Free Cluster Enhancement and Family Wise Error was set at p < .05. We adjusted analyses for age, sex, tobacco and alcohol use. The putamen (bilaterally) and the right thalamus showed regional enlargement in PwP + C versus PwP - C. There were no areas of regional deflation. There were no significant differences between C + C and C - C. Cannabis use in participants with psychosis is associated with morphological alterations in subcortical structures. Putamen and thalamic enlargement may be related to compulsivity in patients with a history of cannabis use.

Sex-specific association between infant caudate volumes and a polygenic risk score for major depressive disorder

Polygenic risk scores for major depressive disorder (PRS-MDD) have been identified in large genome-wide association studies, and recent findings suggest that PRS-MDD might interact with environmental risk factors to shape human limbic brain development as early as in the prenatal period. Striatal structures are crucially involved in depression; however, the association of PRS-MDD with infant striatal volumes is yet unknown. In this study, 105 Finnish mother-infant dyads (44 female, 11-54 days old) were investigated to reveal how infant PRS-MDD is associated with infant dorsal striatal volumes (caudate, putamen) and whether PRS-MDD interacts with prenatal maternal depressive symptoms (Edinburgh Postnatal Depression Scale, gestational weeks 14, 24, 34) on infant striatal volumes. A robust sex-specific main effect of PRS-MDD on bilateral infant caudate volumes was observed. PRS-MDD were more positively associated with caudate volumes in boys compared to girls. No significant interaction effects of genotype PRS-MDD with the environmental risk factor "prenatal maternal depressive symptoms" (genotype-by-environment interaction) nor significant interaction effects of genotype with prenatal maternal depressive symptoms and sex (genotype-by-environment-by-sex interaction) were found for infant dorsal striatal volumes. Our study showed that a higher PRS-MDD irrespective of prenatal exposure to maternal depressive symptoms is associated with smaller bilateral caudate volumes, an indicator of greater susceptibility to major depressive disorder, in female compared to male infants. This sex-specific polygenic effect might lay the ground for the higher prevalence of depression in women compared to men.

Accuracy of automated amygdala MRI segmentation approaches in Huntington's disease in the IMAGE-HD cohort

Smaller manually-segmented amygdala volumes have been associated with poorer motor and cognitive function in Huntington's disease (HD). Manual segmentation is the gold standard in terms of accuracy; however, automated methods may be necessary in large samples. Automated segmentation accuracy has not been determined for the amygdala in HD. We aimed to determine which of three automated approaches would most accurately segment amygdalae in HD: FreeSurfer, FIRST, and ANTS nonlinear registration followed by FIRST segmentation. T1-weighted images for the IMAGE-HD cohort including 35 presymptomatic HD (pre-HD), 36 symptomatic HD (symp-HD), and 34 healthy controls were segmented using FreeSurfer and FIRST. For the third approach, images were nonlinearly registered to an MNI template using ANTS, then segmented using FIRST. All automated methods overestimated amygdala volumes compared with manual segmentation. Dice overlap scores, indicating segmentation accuracy, were not significantly different between automated approaches. Manually segmented volumes were most statistically differentiable between groups, followed by those segmented by FreeSurfer, then ANTS/FIRST. FIRST-segmented volumes did not differ between groups. All automated methods produced a bias where volume overestimation was more severe for smaller amygdalae. This bias was subtle for FreeSurfer, but marked for FIRST, and moderate for ANTS/FIRST. Further, FreeSurfer introduced a hemispheric bias not evident with manual segmentation, producing larger right amygdalae by 8%. To assist choice of segmentation approach, we provide sample size estimation graphs based on sample size and other factors. If automated segmentation is employed in samples of the current size, FreeSurfer may effectively distinguish amygdala volume between controls and HD.

Whole Brain and Cranial Size Adjustments in Volumetric Brain Analyses of Sex- and Age-Related Trends

Our goal was to determine the influence of sex, age and the head/brain size on the compartmental brain volumes in the radiologically verified healthy population (96 subjects; 54 women and 42 men) from the Upper Silesia region in Poland. The MRI examinations were done using 3T Philips Achieva with the same T1-weighted and T2-weighted protocols. The image segmentation procedures were performed with SPM (Statistical Parameter Mapping) and FSL-FIRST software. The volumes of 14 subcortical structures for the left and right hemispheres and 4 overall volumes were calculated. The General Linear Models (GLM) analysis was used with and without the Total Brain Volume (TBV) and Intracranial Volume (ICV) parameters as the covariates to study the regional vs. global brain atrophy. After the ICV/TBV adjustments, the majority of sex differences in the specific volumes of interest (VOIs) revealed to be linked to the difference in the head/brain size parameters. The analysis also confirmed the significant effect of the aging process on the brain loss. After the TBV adjustment, the age- and sex-related volumetric trends for the gray and white matter volumes were observed: the negative age dependence of the gray matter volume is more pronounced in the males, while in case of the white matter the positive age-related trend in the female group is weaker. The local losses of the left caudate nucleus and the right thalamus are more advanced than the global brain atrophy. Different head-size correction strategies are not interchangeable and may yield various volumetric results, but when used together, facilitate studies on the regional dependencies inherent to a healthy, but aging, brain.

On brain atlas choice and automatic segmentation methods: a comparison of MAPER & FreeSurfer using three atlas databases

Several automatic image segmentation methods and few atlas databases exist for analysing structural T1-weighted magnetic resonance brain images. The impact of choosing a combination has not hitherto been described but may bias comparisons across studies. We evaluated two segmentation methods (MAPER and FreeSurfer), using three publicly available atlas databases (Hammers_mith, Desikan-Killiany-Tourville, and MICCAI 2012 Grand Challenge). For each combination of atlas and method, we conducted a leave-one-out cross-comparison to estimate the segmentation accuracy of FreeSurfer and MAPER. We also used each possible combination to segment two datasets of patients with known structural abnormalities (Alzheimer's disease (AD) and mesial temporal lobe epilepsy with hippocampal sclerosis (HS)) and their matched healthy controls. MAPER was better than FreeSurfer at modelling manual segmentations in the healthy control leave-one-out analyses in two of the three atlas databases, and the Hammers_mith atlas database transferred to new datasets best regardless of segmentation method. Both segmentation methods reliably identified known abnormalities in each patient group. Better separation was seen for FreeSurfer in the AD and left-HS datasets, and for MAPER in the right-HS dataset. We provide detailed quantitative comparisons for multiple anatomical regions, thus enabling researchers to make evidence-based decisions on their choice of atlas and segmentation method.

Imputation Strategy for Reliable Regional MRI Morphological Measurements

Regional morphological analysis represents a crucial step in most neuroimaging studies. Results from brain segmentation techniques are intrinsically prone to certain degrees of variability, mainly as results of suboptimal segmentation. To reduce this inherent variability, the errors are often identified through visual inspection and then corrected (semi)manually. Identification and correction of incorrect segmentation could be very expensive for large-scale studies. While identification of the incorrect results can be done relatively fast even with manual inspection, the correction step is extremely time-consuming, as it requires training staff to perform laborious manual corrections. Here we frame the correction phase of this problem as a missing data problem. Instead of manually adjusting the segmentation outputs, our computational approach aims to derive accurate morphological measures by machine learning imputation. Data imputation techniques may be used to replace missing or incorrect region average values with carefully chosen imputed values, all of which are computed based on other available multivariate information. We examined our approach of correcting segmentation outputs on a cohort of 970 subjects, which were undergone an extensive, time-consuming, manual post-segmentation correction. A random forest imputation technique recovered the gold standard results with a significant accuracy (r = 0.93, p < 0.0001; when 30% of the segmentations were considered incorrect in a non-random fashion). The random forest technique proved to be most effective for big data studies (N > 250).

Higher body mass index is linked to altered hypothalamic microstructure

Animal studies suggest that obesity-related diets induce structural changes in the hypothalamus, a key brain area involved in energy homeostasis. Whether this translates to humans is however largely unknown. Using a novel multimodal approach with manual segmentation, we here show that a higher body mass index (BMI) selectively predicted higher proton diffusivity within the hypothalamus, indicative of compromised microstructure in the underlying tissue, in a well-characterized population-based cohort (n1 = 338, 48% females, age 21-78 years, BMI 18-43 kg/m²). Results were independent from confounders and confirmed in another independent sample (n2 = 236). In addition, while hypothalamic volume was not associated with obesity, we identified a sexual dimorphism and larger hypothalamic volumes in the left compared to the right hemisphere. Using two large samples of the general population, we showed that a higher BMI specifically relates to altered microstructure in the hypothalamus, independent from confounders such as age, sex and obesity-associated co-morbidities. This points to persisting microstructural changes in a key regulatory area of energy homeostasis occurring with excessive weight. Our findings may help to better understand the pathomechanisms of obesity and other eating-related disorders.

Assessment of longitudinal hippocampal atrophy in the first year after ischemic stroke using automatic segmentation techniques

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First-year hippocampal atrophy in stroke is more accelerated ipsi-lesionally.

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Volume estimation is not impacted by hemisphere side, study group, or scan timepoint.

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Segmentation method-hippocampal size interaction determines volume estimation.

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FreeSurfer/Subfields and fsl/FIRST segmentations agreed best with manual tracing.

We assessed first-year hippocampal atrophy in stroke patients and healthy controls using manual and automated segmentations: AdaBoost, FIRST (fsl/v5.0.8), FreeSurfer/v5.3 and v6.0, and Subfields (in FreeSurfer/v6.0). We estimated hippocampal volumes in 39 healthy controls and 124 stroke participants at three months, and 38 controls and 113 stroke participants at one year. We used intra-class correlation, concordance, and reduced major axis regression to assess agreement between automated and ‘Manual’ estimations. A linear mixed-effect model was used to characterize hippocampal atrophy.

Overall, hippocampal volumes were reduced by 3.9% in first-ever stroke and 9.2% in recurrent stroke at three months post-stroke, with comparable ipsi-and contra-lesional reductions in first-ever stroke. Mean atrophy rates between time points were 0.5% for controls and 1.0% for stroke patients (0.6% contra-lesionally, 1.4% ipsi-lesionally). Atrophy rates in left and right-hemisphere strokes were comparable. All methods revealed significant volume change in first-ever and ipsi-lesional stroke (p < 0.001).

Hippocampal volume estimation was not impacted by hemisphere, study group, or scan time point, but rather, by the interaction between the automated segmentation method and hippocampal size. Compared to Manual, Subfields and FIRST recorded the lowest bias. FreeSurfer/v5.3 overestimated volumes the most for large hippocampi, while FIRST was the most accurate in estimating small volumes. AdaBoost performance was average.

Our findings suggest that first-year ipsi-lesional hippocampal atrophy rate especially in first-ever stroke, is greater than atrophy rates in healthy controls and contra-lesional stroke. Subfields and FIRST can complementarily be effective in characterizing the hippocampal atrophy in healthy and stroke cohorts.

Evaluation of the intra- and inter-method agreement of brain MRI segmentation software packages: A comparison between SPM12 and FreeSurfer v6.0

PURPOSE

The lack of inter-method agreement can produce inconsistent results in neuroimaging studies. We evaluated the intra-method repeatability and the inter-method reproducibility of two widely-used automatic segmentation methods for brain MRI: the FreeSurfer (FS) and the Statistical Parametric Mapping (SPM) software packages.

METHODS

We segmented the gray matter (GM), the white matter (WM) and subcortical structures in test-retest MRI data of healthy volunteers from Kirby-21 and OASIS datasets. We used Pearson's correlation (r), Bland-Altman plot and Dice index to study intra-method repeatability and inter-method reproducibility. In order to test whether different processing methods affect the results of a neuroimaging-based group study, we carried out a statistical comparison between male and female volume measures.

RESULTS

A high correlation was found between test-retest volume measures for both SPM (r in the 0.98-0.99 range) and FS (r in the 0.95-0.99 range). A non-null bias between test-retest FS volumes was detected for GM and WM in the OASIS dataset. The inter-method reproducibility analysis measured volume correlation values in the 0.72-0.98 range and the overlap between the segmented structures assessed by the Dice index was in the 0.76-0.83 range. SPM systematically provided significantly greater GM volumes and lower WM and subcortical volumes with respect to FS. In the male vs. female brain volume comparisons, inconsistencies arose for the OASIS dataset, where the gender-related differences appear subtler with respect to the Kirby dataset.

CONCLUSIONS

The inter-method reproducibility should be evaluated before interpreting the results of neuroimaging studies.

Quantifying deep grey matter atrophy using automated segmentation approaches: A systematic review of structural MRI studies

The deep grey matter (DGM) nuclei of the brain play a crucial role in learning, behaviour, cognition, movement and memory. Although automated segmentation strategies can provide insight into the impact of multiple neurological conditions affecting these structures, such as Multiple Sclerosis (MS), Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD) and Cerebral Palsy (CP), there are a number of technical challenges limiting an accurate automated segmentation of the DGM. Namely, the insufficient contrast of T1 sequences to completely identify the boundaries of these structures, as well as the presence of iso-intense white matter lesions or extensive tissue loss caused by brain injury. Therefore in this systematic review, 269 eligible studies were analysed and compared to determine the optimal approaches for addressing these technical challenges. The automated approaches used among the reviewed studies fall into three broad categories, atlas-based approaches focusing on the accurate alignment of atlas priors, algorithmic approaches which utilise intensity information to a greater extent, and learning-based approaches that require an annotated training set. Studies that utilise freely available software packages such as FIRST, FreeSurfer and LesionTOADS were also eligible, and their performance compared. Overall, deep learning approaches achieved the best overall performance, however these strategies are currently hampered by the lack of large-scale annotated data. Improving model generalisability to new datasets could be achieved in future studies with data augmentation and transfer learning. Multi-atlas approaches provided the second-best performance overall, and may be utilised to construct a "silver standard" annotated training set for deep learning. To address the technical challenges, providing robustness to injury can be improved by using multiple channels, highly elastic diffeomorphic transformations such as LDDMM, and by following atlas-based approaches with an intensity driven refinement of the segmentation, which has been done with the Expectation Maximisation (EM) and level sets methods. Accounting for potential lesions should be achieved with a separate lesion segmentation approach, as in LesionTOADS. Finally, to address the issue of limited contrast, R2*, T2* and QSM sequences could be used to better highlight the DGM due to its higher iron content. Future studies could look to additionally acquire these sequences by retaining the phase information from standard structural scans, or alternatively acquiring these sequences for only a training set, allowing models to learn the "improved" segmentation from T1-sequences alone.

Age Prediction Based on Brain MRI Image: A Survey

Human age prediction is an interesting and applicable issue in different fields. It can be based on various criteria such as face image, DNA methylation, chest plate radiographs, knee radiographs, dental images and etc. Most of the age prediction researches have mainly been based on images. Since the image processing and Machine Learning (ML) techniques have grown up, the investigations were led to use them in age prediction problem. The implementations would be used in different fields, especially in medical applications. Brain Age Estimation (BAE) has attracted more attention in recent years and it would be so helpful in early diagnosis of some neurodegenerative diseases such as Alzheimer, Parkinson, Huntington, etc. BAE is performed on Magnetic Resonance Imaging (MRI) images to compute the brain ages. Studies based on brain MRI shows that there is a relation between accelerated aging and accelerated brain atrophy. This refers to the effects of neurodegenerative diseases on brain structure while making the whole of it older. This paper reviews and summarizes the main approaches for age prediction based on brain MRI images including preprocessing methods, useful tools used in different research works and the estimation algorithms. We categorize the BAE methods based on two factors, first the way of processing MRI images, which includes pixel-based, surface-based, or voxel-based methods and second, the generation of ML algorithms that includes traditional or Deep Learning (DL) methods. The modern techniques as DL methods help MRI based age prediction to get results that are more accurate. In recent years, more precise and statistical ML approaches have been utilized with the help of related tools for simplifying computations and getting accurate results. Pros and cons of each research and the challenges in each work are expressed and some guidelines and deliberations for future research are suggested.