Automated Hippocampal Subfield Segmentation at 7T MRI

Automated protocols for delineating human hippocampal subfields from 3 Tesla and 7 Tesla magnetic resonance imaging data

Researchers who study the human hippocampus are naturally interested in how its subfields function. However, many researchers are precluded from examining subfields because their manual delineation from magnetic resonance imaging (MRI) scans (still the gold standard approach) is time consuming and requires significant expertise. To help ameliorate this issue, we present here two protocols, one for 3T MRI and the other for 7T MRI, that permit automated hippocampus segmentation into six subregions, namely dentate gyrus/cornu ammonis (CA)4, CA2/3, CA1, subiculum, pre/parasubiculum, and uncus along the entire length of the hippocampus. These protocols are particularly notable relative to existing resources in that they were trained and tested using large numbers of healthy young adults (n = 140 at 3T, n = 40 at 7T) whose hippocampi were manually segmented by experts from MRI scans. Using inter-rater reliability analyses, we showed that the quality of automated segmentations produced by these protocols was high and comparable to expert manual segmenters. We provide full open access to the automated protocols, and anticipate they will save hippocampus researchers a significant amount of time. They could also help to catalyze subfield research, which is essential for gaining a full understanding of how the hippocampus functions.

Automatic segmentation of medial temporal lobe subregions in multi-scanner, multi-modality MRI of variable quality

Background

Volumetry of subregions in the medial temporal lobe (MTL) computed from automatic segmentation in MRI can track neurodegeneration in Alzheimer's disease. However, image quality may vary in MRI. Poor quality MR images can lead to unreliable segmentation of MTL subregions. Considering that different MRI contrast mechanisms and field strengths (jointly referred to as "modalities" here) offer distinct advantages in imaging different parts of the MTL, we developed a muti-modality segmentation model using both 7 tesla (7T) and 3 tesla (3T) structural MRI to obtain robust segmentation in poor-quality images.

Method

MRI modalities including 3T T1-weighted, 3T T2-weighted, 7T T1-weighted and 7T T2-weighted (7T-T2w) of 197 participants were collected from a longitudinal aging study at the Penn Alzheimer's Disease Research Center. Among them, 7T-T2w was used as the primary modality, and all other modalities were rigidly registered to the 7T-T2w. A model derived from nnU-Net took these registered modalities as input and outputted subregion segmentation in 7T-T2w space. 7T-T2w images most of which had high quality from 25 selected training participants were manually segmented to train the multi-modality model. Modality augmentation, which randomly replaced certain modalities with Gaussian noise, was applied during training to guide the model to extract information from all modalities. To compare our proposed model with a baseline single-modality model in the full dataset with mixed high/poor image quality, we evaluated the ability of derived volume/thickness measures to discriminate Amyloid+ mild cognitive impairment (A+MCI) and Amyloid- cognitively unimpaired (A-CU) groups, as well as the stability of these measurements in longitudinal data.

Results

The multi-modality model delivered good performance regardless of 7T-T2w quality, while the single-modality model under-segmented subregions in poor-quality images. The multi-modality model generally demonstrated stronger discrimination of A+MCI versus A-CU. Intra-class correlation and Bland-Altman plots demonstrate that the multi-modality model had higher longitudinal segmentation consistency in all subregions while the single-modality model had low consistency in poor-quality images.

Conclusion

The multi-modality MRI segmentation model provides an improved biomarker for neurodegeneration in the MTL that is robust to image quality. It also provides a framework for other studies which may benefit from multimodal imaging.

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

Memory impairment in Amyloidβ-status Alzheimer's disease is associated with a reduction in CA1 and dentate gyrus volume: In vivo MRI at 7T

INTRODUCTION

In Alzheimer's disease (AD), early diagnosis facilitates treatment options and leads to beneficial outcomes for patients, their carers and the healthcare system. The neuropsychological battery of the Uniform Data Set (UDSNB3.0) assesses cognition in ageing and dementia, by measuring scores across different cognitive domains such as attention, memory, processing speed, executive function and language. However, its neuroanatomical correlates have not been investigated using 7 Tesla MRI (7T MRI).

METHODS

We used 7T MRI to investigate the correlations between hippocampal subfield volumes and the UDSNB3.0 in 24 individuals with Amyloidβ-status AD and 18 age-matched controls, with respective age ranges of 60 (42-76) and 62 (52-79) years. AD participants with a Medial Temporal Atrophy scale of higher than 2 on 3T MRI were excluded from the study.

RESULTS

A significant difference in the entire hippocampal volume was observed in the AD group compared to healthy controls (HC), primarily influenced by CA1, the largest hippocampal subfield. Notably, no significant difference in whole brain volume between the groups implied that hippocampal volume loss was not merely reflective of overall brain atrophy. UDSNB3.0 cognitive scores showed significant differences between AD and HC, particularly in Memory, Language, and Visuospatial domains. The volume of the Dentate Gyrus (DG) showed a significant association with the Memory and Executive domain scores in AD patients as assessed by the UDSNB3.0.. The data also suggested a non-significant trend for CA1 volume associated with UDSNB3.0 Memory, Executive, and Language domain scores in AD. In a reassessment focusing on hippocampal subfields and MoCA memory subdomains in AD, associations were observed between the DG and Cued, Uncued, and Recognition Memory subscores, whereas CA1 and Tail showed associations only with Cued memory.

DISCUSSION

This study reveals differences in the hippocampal volumes measured using 7T MRI, between individuals with early symptomatic AD compared with healthy controls. This highlights the potential of 7T MRI as a valuable tool for early AD diagnosis and the real-time monitoring of AD progression and treatment efficacy.

CLINICALTRIALS

GOV: ID NCT04992975 (Clinicaltrial.gov 2023).

Insights into hippocampal perfusion using high-resolution, multi-modal 7T MRI

We present a comprehensive study on the non-invasive measurement of hippocampal perfusion. Using high-resolution 7 tesla arterial spin labeling (ASL) data, we generated robust perfusion maps and observed significant variations in perfusion among hippocampal subfields, with CA1 exhibiting the lowest perfusion levels. Notably, these perfusion differences were robust and already detectable with 50 perfusion-weighted images per subject, acquired in 5 min. To understand the underlying factors, we examined the influence of image quality metrics, various tissue microstructure and morphometric properties, macrovasculature, and cytoarchitecture. We observed higher perfusion in regions located closer to arteries, demonstrating the influence of vascular proximity on hippocampal perfusion. Moreover, ex vivo cytoarchitectonic features based on neuronal density differences appeared to correlate stronger with hippocampal perfusion than morphometric measures like gray matter thickness. These findings emphasize the interplay between microvasculature, macrovasculature, and metabolic demand in shaping hippocampal perfusion. Our study expands the current understanding of hippocampal physiology and its relevance to neurological disorders. By providing in vivo evidence of perfusion differences between hippocampal subfields, our findings have implications for diagnosis and potential therapeutic interventions. In conclusion, our study provides a valuable resource for extensively characterizing hippocampal perfusion.

Organization of pRF size along the AP axis of the hippocampus and adjacent medial temporal cortex is related to specialization for scenes versus faces

The hippocampus is largely recognized for its integral contributions to memory processing. By contrast, its role in perceptual processing remains less clear. Hippocampal properties vary along the anterior-posterior (AP) axis. Based on past research suggesting a gradient in the scale of features processed along the AP extent of the hippocampus, the representations have been proposed to vary as a function of granularity along this axis. One way to quantify such granularity is with population receptive field (pRF) size measured during visual processing, which has so far received little attention. In this study, we compare the pRF sizes within the hippocampus to its activation for images of scenes versus faces. We also measure these functional properties in surrounding medial temporal lobe (MTL) structures. Consistent with past research, we find pRFs to be larger in the anterior than in the posterior hippocampus. Critically, our analysis of surrounding MTL regions, the perirhinal cortex, entorhinal cortex, and parahippocampal cortex shows a similar correlation between scene sensitivity and larger pRF size. These findings provide conclusive evidence for a tight relationship between the pRF size and the sensitivity to image content in the hippocampus and adjacent medial temporal cortex.

Presurgical MRI-Based Radiomics Models for Predicting Cerebellar Mutism Syndrome in Children With Posterior Fossa Tumors

BACKGROUND

Current studies have indicated that tumoral morphologic features are associated with cerebellar mutism syndrome (CMS), but the radiomics application in CMS is scarce.

PURPOSE

To develop a model for CMS discrimination based on multiparametric MRI radiomics in patients with posterior fossa tumors.

STUDY TYPE

Retrospective.

POPULATION

A total of 218 patients (males 132, females 86) with posterior fossa tumors, 169 of which were included in the MRI radiomics analysis. The MRI radiomics study cohort (169) was split into training (119) and testing (50) sets with a ratio of 7:3.

FIELD/SEQUENCE

All the MRI were acquired under 1.5/3.0 T scanners. T2-weighted image (T2W), T1-weighted (T1W), fluid attenuated inversion recovery (FLAIR), diffusion-weighted imaging (DWI).

ASSESSMENT

Apparent diffusion coefficient (ADC) maps were generated from DWI. Each MRI dataset generated 1561 radiomics characteristics. Feature selection was performed with univariable logistic analysis, correlation analysis, and least absolute shrinkage and selection operator (LASSO) penalized logistic regression. Significant clinical features were selected with multivariable logistic analysis and used to constructed the clinical model. Radiomics models (based on T1W, T2W, FLAIR, DWI, ADC) were constructed with selected radiomics features. The mix model was based on the multiparametric MRI radiomics features.

STATISTICAL TEST

Multivariable logistic analysis was utilized during clinical features selection. Models' performance was evaluated using the area under the receiver operating characteristic (AUC) curve. Interobserver variability was assessed using Cohen's kappa. Significant threshold was set as P < 0.05.

RESULTS

Sex (aOR = 3.72), tumor location (aOR = 2.81), hydrocephalus (aOR = 2.14), and tumor texture (aOR = 5.08) were significant features in the multivariable analysis and were used to construct the clinical model (AUC = 0.79); totally, 33 radiomics features were selected to construct radiomics models (AUC = 0.63-0.93). Seven of the 33 radiomics features were selected for the mix model (AUC = 0.93).

DATA CONCLUSION

Multiparametric MRI radiomics may be better at predicting CMS than single-parameter MRI models and clinical model.

EVIDENCE LEVEL

4.

TECHNICAL EFFICACY

2.

Novel insights into hippocampal perfusion using high-resolution, multi-modal 7T MRI

We present a comprehensive study on the non-invasive measurement of hippocampal perfusion. Using high-resolution 7 Tesla arterial spin labelling data, we generated robust perfusion maps and observed significant variations in perfusion among hippocampal subfields, with CA1 exhibiting the lowest perfusion levels. Notably, these perfusion differences were robust and detectable even within five minutes and just fifty perfusion-weighted images per subject. To understand the underlying factors, we examined the influence of image quality metrics, various tissue microstructure and morphometry properties, macrovasculature and cytoarchitecture. We observed higher perfusion in regions located closer to arteries, demonstrating the influence of vascular proximity on hippocampal perfusion. Moreover, ex vivo cytoarchitectonic features based on neuronal density differences appeared to correlate stronger with hippocampal perfusion than morphometric measures like gray matter thickness. These findings emphasize the interplay between microvasculature, macrovasculature, and metabolic demand in shaping hippocampal perfusion. Our study expands the current understanding of hippocampal physiology and its relevance to neurological disorders. By providing in vivo evidence of perfusion differences between hippocampal subfields, our findings have implications for diagnosis and potential therapeutic interventions. In conclusion, our study provides a valuable resource for extensively characterising hippocampal perfusion.

A fast and robust hippocampal subfields segmentation: HSF revealing lifespan volumetric dynamics

The hippocampal subfields, pivotal to episodic memory, are distinct both in terms of cyto- and myeloarchitectony. Studying the structure of hippocampal subfields in vivo is crucial to understand volumetric trajectories across the lifespan, from the emergence of episodic memory during early childhood to memory impairments found in older adults. However, segmenting hippocampal subfields on conventional MRI sequences is challenging because of their small size. Furthermore, there is to date no unified segmentation protocol for the hippocampal subfields, which limits comparisons between studies. Therefore, we introduced a novel segmentation tool called HSF short for hippocampal segmentation factory, which leverages an end-to-end deep learning pipeline. First, we validated HSF against currently used tools (ASHS, HIPS, and HippUnfold). Then, we used HSF on 3,750 subjects from the HCP development, young adults, and aging datasets to study the effect of age and sex on hippocampal subfields volumes. Firstly, we showed HSF to be closer to manual segmentation than other currently used tools (p < 0.001), regarding the Dice Coefficient, Hausdorff Distance, and Volumetric Similarity. Then, we showed differential maturation and aging across subfields, with the dentate gyrus being the most affected by age. We also found faster growth and decay in men than in women for most hippocampal subfields. Thus, while we introduced a new, fast and robust end-to-end segmentation tool, our neuroanatomical results concerning the lifespan trajectories of the hippocampal subfields reconcile previous conflicting results.

Ex vivo, in situ perfusion protocol for human brain fixation compatible with microscopy, MRI techniques, and anatomical studies

We present a method for human brain fixation based on simultaneous perfusion of 4% paraformaldehyde through carotids after a flush with saline. The left carotid cannula is used to perfuse the body with 10% formalin, to allow further use of the body for anatomical research or teaching. The aim of our method is to develop a vascular fixation protocol for the human brain, by adapting protocols that are commonly used in experimental animal studies. We show that a variety of histological procedures can be carried out (cyto- and myeloarchitectonics, histochemistry, immunohistochemistry, intracellular cell injection, and electron microscopy). In addition, ex vivo, ex situ high-resolution MRI (9.4T) can be obtained in the same specimens. This procedure resulted in similar morphological features to those obtained by intravascular perfusion in experimental animals, provided that the postmortem interval was under 10 h for several of the techniques used and under 4 h in the case of intracellular injections and electron microscopy. The use of intravascular fixation of the brain inside the skull provides a fixed whole human brain, perfectly fitted to the skull, with negligible deformation compared to conventional techniques. Given this characteristic of ex vivo, in situ fixation, this procedure can probably be considered the most suitable one available for ex vivo MRI scans of the brain. We describe the compatibility of the method proposed for intravascular fixation of the human brain and fixation of the donor's body for anatomical purposes. Thus, body donor programs can provide human brain tissue, while the remainder of the body can also be fixed for anatomical studies. Therefore, this method of human brain fixation through the carotid system optimizes the procurement of human brain tissue, allowing a greater understanding of human neurological diseases, while benefiting anatomy departments by making the remainder of the body available for teaching purposes.

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

Stress-related reduction of hippocampal subfield volumes in major depressive disorder: A 7-Tesla study

BACKGROUND

Major depressive disorder (MDD) is a prevalent health problem with complex pathophysiology that is not clearly understood. Prior work has implicated the hippocampus in MDD, but how hippocampal subfields influence or are affected by MDD requires further characterization with high-resolution data. This will help ascertain the accuracy and reproducibility of previous subfield findings in depression as well as correlate subfield volumes with MDD symptom scores. The objective of this study was to assess volumetric differences in hippocampal subfields between MDD patients globally and healthy controls (HC) as well as between a subset of treatment-resistant depression (TRD) patients and HC using automatic segmentation of hippocampal subfields (ASHS) software and ultra-high field MRI.

METHODS

Thirty-five MDD patients and 28 HC underwent imaging using 7-Tesla MRI. ASHS software was applied to the imaging data to perform automated hippocampal segmentation and provide volumetrics for analysis. An exploratory analysis was also performed on associations between symptom scores for diagnostic testing and hippocampal subfield volumes.

RESULTS

Compared to HC, MDD and TRD patients showed reduced right-hemisphere CA2/3 subfield volume (p = 0.01, η ² = 0.31 and p = 0.3, η ² = 0.44, respectively). Additionally, negative associations were found between subfield volumes and life-stressor checklist scores, including left CA1 (p = 0.041, f ² = 0.419), left CA4/DG (p = 0.010, f ² = 0.584), right subiculum total (p = 0.038, f ² = 0.354), left hippocampus total (p = 0.015, f ² = 0.134), and right hippocampus total (p = 0.034, f ² = 0.110). Caution should be exercised in interpreting these results due to the small sample size and low power.

CONCLUSION

Determining biomarkers for MDD and TRD pathophysiology through segmentation on high-resolution MRI data and understanding the effects of stress on these regions can enable better assessment of biological response to treatment selection and may elucidate the underlying mechanisms of depression.

Psychosocial factors and hippocampal subfields: The Medea-7T study

Specific subfields within the hippocampus have shown vulnerability to chronic stress, highlighting the importance of looking regionally within the hippocampus to understand the role of psychosocial factors in the development of neurodegenerative diseases. A systematic review on psychosocial factors and hippocampal subfield volumes was performed and showed inconsistent results, highlighting the need for future studies to explore this relationship. The current study aimed to explore the association of psychosocial factors with hippocampal (subfield) volumes, using high-field 7T MRI. Data were from the Memory Depression and Aging (Medea)-7T study, which included 333 participants without dementia. Hippocampal subfields were automatically segmented from T2-weighted images using ASHS software. Generalized linear models accounting for correlated outcomes were used to assess the association between subfields (i.e., entorhinal cortex, subiculum, Cornu Ammonis [CA]1, CA2, CA3, dentate gyrus, and tail) and each psychosocial factor (i.e., depressive symptoms, anxiety symptoms, childhood maltreatment, recent stressful life events, and social support), adjusted for age, sex, and intracranial volume. Neither depression nor anxiety was associated with specific hippocampal (subfield) volumes. A trend for lower total hippocampal volume was found in those reporting childhood maltreatment, and a trend for higher total hippocampal volume was found in those who experienced a recent stressful life event. Among subfields, low social support was associated with lower volume in the CA3 (B = -0.43, 95% CI: -0.72; -0.15). This study suggests possible differential effects among hippocampal (subfield) volumes and psychosocial factors.

High-resolution atlasing and segmentation of the subcortex: Review and perspective on challenges and opportunities created by machine learning

This paper reviews almost three decades of work on atlasing and segmentation methods for subcortical structures in human brain MRI. In writing this survey, we have three distinct aims. First, to document the evolution of digital subcortical atlases of the human brain, from the early MRI templates published in the nineties, to the complex multi-modal atlases at the subregion level that are available today. Second, to provide a detailed record of related efforts in the automated segmentation front, from earlier atlas-based methods to modern machine learning approaches. And third, to present a perspective on the future of high-resolution atlasing and segmentation of subcortical structures in in vivo human brain MRI, including open challenges and opportunities created by recent developments in machine learning.

Activity in perirhinal and entorhinal cortex predicts perceived visual similarities among category exemplars with highest precision

Vision neuroscience has made great strides in understanding the hierarchical organization of object representations along the ventral visual stream (VVS). How VVS representations capture fine-grained visual similarities between objects that observers subjectively perceive has received limited examination so far. In the current study, we addressed this question by focussing on perceived visual similarities among subordinate exemplars of real-world categories. We hypothesized that these perceived similarities are reflected with highest fidelity in neural activity patterns downstream from inferotemporal regions, namely in perirhinal (PrC) and anterolateral entorhinal cortex (alErC) in the medial temporal lobe. To address this issue with functional magnetic resonance imaging (fMRI), we administered a modified 1-back task that required discrimination between category exemplars as well as categorization. Further, we obtained observer-specific ratings of perceived visual similarities, which predicted behavioural discrimination performance during scanning. As anticipated, we found that activity patterns in PrC and alErC predicted the structure of perceived visual similarity relationships among category exemplars, including its observer-specific component, with higher precision than any other VVS region. Our findings provide new evidence that subjective aspects of object perception that rely on fine-grained visual differentiation are reflected with highest fidelity in the medial temporal lobe.

7T versus 3T MRI in the presurgical evaluation of patients with drug-resistant epilepsy

BACKGROUND AND PURPOSE

MRI has a crucial role in presurgical evaluation of drug-resistant focal epilepsy patients. Whether and how much 7T MRI further improves presurgical diagnosis compared to standard of care 3T MRI remains to be established. We investigate the added value 7T MRI offers in surgical candidates with remaining clinical uncertainty after 3T MRI.

METHODS

7T brain MRI was obtained on sequential patients with drug-resistant focal epilepsy undergoing presurgical evaluation at a comprehensive epilepsy center, including patients with and without suspected lesions on standard 3T MRI. Clinical information and 3T images informed the interpretation of 7T images. Detection of a new lesion on 7T or better characterization of a suspected lesion was considered to add value to the presurgical workup.

RESULTS

Interpretable 7T MRI was acquired in 19 patients. 7T MRI identified a lesion relevant to the seizures in three of eight patients (38%) without a lesion on 3T MRI; no lesion in 7/11 patients (64%) with at least one suspected lesion on 3T MRI, contributing to the final classification of all seven as nonlesional; and confirmed and better characterized the lesion suspected at 3T MR in the remaining 4/11 patients.

CONCLUSIONS

7T MRI detected new lesions in over a third of 3T MRI nonlesional patients, confirmed and better characterized a 3T suspected lesion in one third of patients, and helped exclude a 3T suspected lesion in the remainder. Our initial experience suggests that 7T MRI adds value to surgical planning by improving detection and characterization of suspected brain lesions in drug-resistant focal epilepsy patients.

Comparison and Reliability of Hippocampal Subfield Segmentations Within FreeSurfer Utilizing T1- and T2-Weighted Multispectral MRI Data

The accurate segmentation of in vivo magnetic resonance imaging (MRI) data is a crucial prerequisite for the reliable assessment of disease progression, patient stratification or the establishment of putative imaging biomarkers. This is especially important for the hippocampal formation, a brain area involved in memory formation and often affected by neurodegenerative or psychiatric diseases. FreeSurfer, a widely used automated segmentation software, offers hippocampal subfield delineation with multiple input options. While a single T1-weighted (T1) sequence is regularly used by most studies, it is also possible and advised to use a high-resolution T2-weighted (T2H) sequence or multispectral information. In this investigation it was determined whether there are differences in volume estimations depending on the input images and which combination of these deliver the most reliable results in each hippocampal subfield. 41 healthy participants (age = 25.2 years ± 4.2 SD) underwent two structural MRIs at three Tesla (time between scans: 23 days ± 11 SD) using three different structural MRI sequences, to test five different input configurations (T1, T2, T2H, T1 and T2, and T1 and T2H). We compared the different processing pipelines in a cross-sectional manner and assessed reliability using test-retest variability (%TRV) and the dice coefficient. Our analyses showed pronounced significant differences and large effect sizes between the processing pipelines in several subfields, such as the molecular layer (head), CA1 (head), hippocampal fissure, CA3 (head and body), fimbria and CA4 (head). The longitudinal analysis revealed that T1 and multispectral analysis (T1 and T2H) showed overall higher reliability across all subfields than T2H alone. However, the specific subfields had a substantial influence on the performance of segmentation results, regardless of the processing pipeline. Although T1 showed good test-retest metrics, results must be interpreted with caution, as a standard T1 sequence relies heavily on prior information of the atlas and does not take the actual fine structures of the hippocampus into account. For the most accurate segmentation, we advise the use of multispectral information by using a combination of T1 and high-resolution T2-weighted sequences or a T2 high-resolution sequence alone.

High-resolution Structural Magnetic Resonance Imaging and Quantitative Susceptibility Mapping

High-resolution 7-T imaging and quantitative susceptibility mapping produce greater anatomic detail compared with conventional strengths because of improvements in signal/noise ratio and contrast. The exquisite anatomic details of deep structures, including delineation of microscopic architecture using advanced techniques such as quantitative susceptibility mapping, allows improved detection of abnormal findings thought to be imperceptible on clinical strengths. This article reviews caveats and techniques for translating sequences commonly used on 1.5 or 3 T to high-resolution 7-T imaging. It discusses for several broad disease categories how high-resolution 7-T imaging can advance the understanding of various diseases, improve diagnosis, and guide management.

Vascular Risk Factors of Hippocampal Subfield Volumes in Persons without Dementia: The Medea 7T Study

BACKGROUND

Vascular risk factors have been associated with risk of Alzheimer's disease (AD) and volume loss of the hippocampus, but the associations with subfields of the hippocampus are understudied. Knowing if vascular risk factors contribute to hippocampal subfield atrophy may improve our understanding of vascular contributions to neurodegenerative diseases.

OBJECTIVE

To investigate the associations between age, sex, and vascular risk factors with hippocampal subfields volumes on 7T MRI in older persons without dementia.

METHODS

From the Medea 7T study, 283 participants (67±9 years, 68% men) without dementia had 7T brain MRI and hippocampal subfield segmentation. Subfields were automatically segmented on the 3D T2-weighted 7T images with ASHS software. Using linear mixed models, we estimated adjusted associations of age, sex, and vascular risk factors with z-scores of volumes of the entorhinal cortex (ERC), subiculum (SUB), Cornu Ammonis (CA)1, CA2, CA3, CA4, and dentate gyrus (DG), and tail as multivariate correlated outcomes.

RESULTS

Increasing age was associated with smaller volumes in all subfields, except CA4/DG. Current smoking was associated with smaller ERC and SUB volumes; moderate alcohol use with smaller CA1 and CA4/DG, obesity with smaller volumes of ERC, SUB, CA2, CA3, and tail; and diabetes mellitus with smaller SUB volume. Sex, former smoking, and hypertension were not associated with subfield volumes. When formally tested, no risk factor affected the subfield volumes differentially.

CONCLUSION

Several vascular risk factors were associated with smaller volumes of specific hippocampal subfields. However, no statistical evidence was found that subfields were differentially affected by these risk factors.

MRI with ultrahigh field strength and high-performance gradients: challenges and opportunities for clinical neuroimaging at 7 T and beyond

Research in ultrahigh magnetic field strength combined with ultrahigh and ultrafast gradient technology has provided enormous gains in sensitivity, resolution, and contrast for neuroimaging. This article provides an overview of the technical advantages and challenges of performing clinical neuroimaging studies at ultrahigh magnetic field strength combined with ultrahigh and ultrafast gradient technology. Emerging clinical applications of 7-T MRI and state-of-the-art gradient systems equipped with up to 300 mT/m gradient strength are reviewed, and the impact and benefits of such advances to anatomical, structural and functional MRI are discussed in a variety of neurological conditions. Finally, an outlook and future directions for ultrahigh field MRI combined with ultrahigh and ultrafast gradient technology in neuroimaging are examined.

Neuroimaging at 7 T: are we ready for clinical transition?

In the last 20 years, ultra-high field (UHF) magnetic resonance imaging (MRI) has become an outstanding research tool for the study of the human brain, with 90 of these scanners installed today, worldwide. The recent clearances from regulatory bodies in the USA and Europe to 7-T clinical systems have set the ground for a transition from pure research applications to research and clinical use of these systems. As today, UFH neuroimaging is demonstrating clinical value and, given the importance of this topic for both preclinical scientists and clinical neuroradiologists, European Radiology Experimental is launching a thematic series entitled "7-T neuro MRI: from research to clinic", consisting of peer-reviewed articles, invited or spontaneously submitted, on topics selected by the guest editors, describing the state of the art of UHF MRI neuroimaging across different pathologies, as well as related clinical applications. In this editorial, we discuss some of the challenges related to the clinical use of 7-T scanners and the strengths and weaknesses of clinical imaging at UHF.

Stability of hippocampal subfield volumes after trauma and relationship to development of PTSD symptoms

BACKGROUND

The hippocampus plays a central role in post-traumatic stress disorder (PTSD) pathogenesis, and the majority of neuroimaging research on PTSD has studied the hippocampus in its entirety. Although extensive literature demonstrates changes in hippocampal volume are associated with PTSD, fewer studies have probed the relationship between symptoms and the hippocampus' functionally and structurally distinct subfields. We utilized data from a longitudinal study examining post-trauma outcomes to determine whether hippocampal subfield volumes change post-trauma and whether specific subfields are significantly associated with, or prospectively related to, PTSD symptom severity. As a secondary aim, we leveraged our unique study design sample to also investigate reliability of hippocampal subfield volumes using both cross-sectional and longitudinal pipelines available in FreeSurfer v6.0.

METHODS

Two-hundred and fifteen traumatically injured individuals were recruited from an urban Emergency Department. Two-weeks post-injury, participants underwent two consecutive days of neuroimaging (time 1: T1, and time 2: T2) with magnetic resonance imaging (MRI) and completed self-report assessments. Six-months later (time 3: T3), participants underwent an additional scan and were administered a structured interview assessing PTSD symptoms. First, we calculated reliability of hippocampal measurements at T1 and T2 (automatically segmented with FreeSurfer v6.0). We then examined the prospective (T1 subfields) and cross-sectional (T3 subfields) relationship between volumes and PTSD. Finally, we tested whether change in subfield volumes between T1 and T3 explained PTSD symptom variability.

RESULTS

After controlling for sex, age, and total brain volume, none of the subfield volumes (T1) were prospectively related to T3 PTSD symptoms nor were subfield volumes (T3) associated with current PTSD symptoms (T3). Tl - T2 reliability of all hippocampal subfields ranged from good to excellent (intraclass correlation coefficient (ICC) values > 0.83), with poorer reliability in the hippocampal fissure.

CONCLUSION

Our study was a novel examination of the prospective relationship between hippocampal subfield volumes in relation to PTSD in a large trauma-exposed urban sample. There was no significant relationship between subfield volumes and PTSD symptoms, however, we confirmed FreeSurfer v6.0 hippocampal subfield segmentation is reliable when applied to a traumatically-injured sample, using both cross-sectional and longitudinal analysis pipelines. Although hippocampal subfield volumes may be an important marker of individual variability in PTSD, findings are likely conditional on the timing of the measurements (e.g. acute or chronic post-trauma periods) and analysis strategy (e.g. cross-sectional or prospective).

Volumetric glutamate imaging (GluCEST) using 7T MRI can lateralize nonlesional temporal lobe epilepsy: A preliminary study

INTRODUCTION

Drug-resistant epilepsy patients show worse outcomes after resection when standard neuroimaging is nonlesional, which occurs in one-third of patients. In prior work, we employed 2-D glutamate imaging, Glutamate Chemical Exchange Saturation Transfer (GluCEST), to lateralize seizure onset in nonlesional temporal lobe epilepsy (TLE) based on increased ipsilateral GluCEST signal in the total hippocampus and hippocampal head. We present a significant advancement to single-slice GluCEST imaging, allowing for three-dimensional analysis of brain glutamate networks.

METHODS

The study population consisted of four MRI-negative, nonlesional TLE patients (two male, two female) with electrographically identified left temporal onset seizures. Imaging was conducted on a Siemens 7T MRI scanner using the CEST method for glutamate, while the advanced normalization tools (ANTs) pipeline and the Automated Segmentation of the Hippocampal Subfields (ASHS) method were employed for image analysis.

RESULTS

Volumetric GluCEST imaging was validated in four nonlesional TLE patients showing increased glutamate lateralized to the hippocampus of seizure onset (p = .048, with a difference among ipsilateral to contralateral GluCEST signal percentage ranging from -0.05 to 1.37), as well as increased GluCEST signal in the ipsilateral subiculum (p = .034, with a difference among ipsilateral to contralateral GluCEST signal ranging from 0.13 to 1.57).

CONCLUSIONS

The ability of 3-D, volumetric GluCEST to localize seizure onset down to the hippocampal subfield in nonlesional TLE is an improvement upon our previous 2-D, single-slice GluCEST method. Eventually, we hope to expand volumetric GluCEST to whole-brain glutamate imaging, thus enabling noninvasive analysis of glutamate networks in epilepsy and potentially leading to improved clinical outcomes.

Surface-based hippocampal subfield segmentation

Though it is often termed 'subcortical,' the hippocampus is composed of a folded 'archicortical' sheet contiguous with the neocortex. The human hippocampus varies considerably in its internal folding configuration, creating major challenges in interindividual alignment and parcellation into subfields. In this opinion article, we discuss surface-based methods that aim to explicitly model hippocampal folding, similar to methods used in the neocortex, allowing interindividual alignment in an unfolded or flat-mapped 2D space. Such an approach enables detailed morphological characterization, constrains the problem of subfield segmentation, and provides a way to visualize data without occlusions. We argue that, when applied to magnetic resonance imaging (MRI) data, such methods overcome pitfalls of more conventional manual or registration-based subfield segmentation approaches.

Variations in response to trauma and hippocampal subfield changes

Models of posttraumatic stress disorder (PTSD) suggest that the hippocampus is key to the persistence of traumatic memory. Yet very little is known about the precise changes that take place in this structure, nor their relation with PTSD symptoms. Previous studies have mostly used magnetic resonance imaging (MRI) at low resolutions, making it impossible to identify sensitive anatomical landmarks, or compared groups often unequally matched in terms of traumatic exposure. The present cross-sectional study included 92 individuals who had all been exposed to the terrorist attacks in Paris on November 13, 2015 (53 of whom subsequently developed PTSD) and 56 individuals who had not been exposed. Hippocampal subfield volumes were estimated using cross-validated automatic segmentation of high-resolution MRI images. Results revealed changes in CA1 and CA2-3/dentate gyrus (DG) volumes in individuals with PTSD, but not in resilient (i.e., exposed but without PTSD) individuals, after controlling for potential nuisance variables such as previous traumatic exposure and substance abuse. In line with current models of hippocampal subfield functions, CA1 changes were linked to the uncontrollable re-experiencing of intrusive memories, while CA2-3/DG changes, potentially exacerbated by comorbid depression, fostered the overgeneralization of fear linked to avoidance and hypervigilance behaviors. Additional analyses revealed that CA1 integrity was linked to optimum functioning of the memory control network in resilient individuals. These findings shed new light on potential pathophysiological mechanisms in the hippocampus subtending the development of PTSD and the failure to recover from trauma.

High resolution structural and functional MRI of the hippocampus in young adults with Down syndrome

Down syndrome is the phenotypic consequence of trisomy 21, with clinical presentation including both neurodevelopmental and neurodegenerative components. Although the intellectual disability typically displayed by individuals with Down syndrome is generally global, it also involves disproportionate deficits in hippocampally-mediated cognitive processes. Hippocampal dysfunction may also relate to Alzheimer’s disease-type pathology, which can appear in as early as the first decade of life and becomes universal by age 40. Using 7-tesla MRI of the brain, we present an assessment of the structure and function of the hippocampus in 34 individuals with Down syndrome (mean age 24.5 years ± 6.5) and 27 age- and sex-matched typically developing healthy controls. In addition to increased whole-brain mean cortical thickness and lateral ventricle volumes (P < 1.0 × 10⁻⁴), individuals with Down syndrome showed selective volume reductions in bilateral hippocampal subfields cornu Ammonis field 1, dentate gyrus, and tail (P < 0.005). In the group with Down syndrome, bilateral hippocampi showed widespread reductions in the strength of functional connectivity, predominately to frontal regions (P < 0.02). Age was not related to hippocampal volumes or functional connectivity measures in either group, but both groups showed similar relationships of age to whole-brain volume measures (P < 0.05). Finally, we performed an exploratory analysis of a subgroup of individuals with Down syndrome with both imaging and neuropsychological assessments. This analysis indicated that measures of spatial memory were related to mean cortical thickness, total grey matter volume and right hemisphere hippocampal subfield volumes (P < 0.02). This work provides a first demonstration of the usefulness of high-field MRI to detect subtle differences in structure and function of the hippocampus in individuals with Down syndrome, and suggests the potential for development of MRI-derived measures as surrogate markers of drug efficacy in pharmacological studies designed to investigate enhancement of cognitive function.

Recent Advances in Neuroimaging of Epilepsy

Human neuroimaging has had a major impact on the biological understanding of epilepsy and the relationship between pathophysiology, seizure management, and outcomes. This review highlights notable recent advancements in hardware, sequences, methods, analyses, and applications of human neuroimaging techniques utilized to assess epilepsy. These structural, functional, and metabolic assessments include magnetic resonance imaging (MRI), positron emission tomography (PET), and magnetoencephalography (MEG). Advancements that highlight non-invasive neuroimaging techniques used to study the whole brain are emphasized due to the advantages these provide in clinical and research applications. Thus, topics range across presurgical evaluations, understanding of epilepsy as a network disorder, and the interactions between epilepsy and comorbidities. New techniques and approaches are discussed which are expected to emerge into the mainstream within the next decade and impact our understanding of epilepsies. Further, an increasing breadth of investigations includes the interplay between epilepsy, mental health comorbidities, and aberrant brain networks. In the final section of this review, we focus on neuroimaging studies that assess bidirectional relationships between mental health comorbidities and epilepsy as a model for better understanding of the commonalities between both conditions.

Clear and Consistent Imaging of Hippocampal Internal Architecture With High Resolution Multiple Image Co-registration and Averaging (HR-MICRA)

Magnetic resonance imaging of hippocampal internal architecture (HIA) at 3T is challenging. HIA is defined by layers of gray and white matter that are less than 1 mm thick in the coronal plane. To visualize HIA, conventional MRI approaches have relied on sequences with high in-plane resolution (≤0.5 mm) but comparatively thick slices (2–5 mm). However, thicker slices are prone to volume averaging effects that result in loss of HIA clarity and blurring of the borders of the hippocampal subfields in up to 61% of slices as has been reported. In this work we describe an approach to hippocampal imaging that provides consistently high HIA clarity using a commonly available sequence and post-processing techniques that is flexible and may be applicable to any MRI platform. We refer to this approach as High Resolution Multiple Image Co-registration and Averaging (HR-MICRA). This approach uses a variable flip angle turbo spin echo sequence to repeatedly acquire a whole brain T2w image volume with high resolution in three dimensions in a relatively short amount of time, and then co-register the volumes to correct for movement and average the repeated scans to improve SNR. We compared the averages of 4, 9, and 16 individual scans in 20 healthy controls using a published HIA clarity rating scale. In the body of the hippocampus, the proportion of slices with good or excellent HIA clarity was 90%, 83%, and 67% for the 16x, 9x, and 4x HR-MICRA images, respectively. Using the 4x HR-MICRA images as a baseline, the 9x HR-MICRA images were 2.6 times and 16x HR-MICRA images were 3.2 times more likely to have high HIA ratings (p < 0.001) across all hippocampal segments (head, body, and tail). The thin slices of the HR-MICRA images allow reformatting in any plane with clear visualization of hippocampal dentation in the sagittal plane. Clear and consistent visualization of HIA will allow application of this technique to future hippocampal structure research, as well as more precise manual or automated segmentation.

UltraHigh Field MR Imaging in Epilepsy

More than one million people in the United States suffer from seizures that are not controlled with antiseizure medications. Targeted interventions such as surgery and deep brain stimulation can confer seizure reduction or even freedom in many of these patients with drug-resistant epilepsy, but success critically depends on identification of epileptogenic zones through MR imaging. Ultrahigh field imaging facilitates improved sensitivity and resolution across many imaging modalities and may facilitate better detection of epileptic markers than is achieved at lower field strengths. The increasing availability and clinical adoption of ultrahigh field scanners play an important role in characterizing drug-resistant epilepsy and planning for its treatment.

A Randomized Controlled Trial on the Effects of a 12-Week High- vs. Low-Intensity Exercise Intervention on Hippocampal Structure and Function in Healthy, Young Adults

Physical exercise affects hippocampal structure and function, but the underlying neural mechanisms and the effects of exercise intensity remain incompletely understood. Therefore, we undertook a comprehensive, multi-modal 3T and 7T MRI randomized controlled trial (Netherlands Trial Register - NL5847) in which we randomized 52 young, non-athletic volunteers to a 12-week low- or high-intensity exercise program. Using state-of-the-art methods, we investigated changes in hippocampal volume, as well as changes in vasculature, neuro-metabolites, and peripheral growth factors as potential underpinnings. Cardiorespiratory fitness improved over time (p < 0.001), but no interaction with exercise intensity was found (p = 0.48). Accordingly, we did not observe significant interactions between exercise condition and time on MRI measures (all p > 0.06). However, we found a significant decrease in right hippocampal volume (p < 0.01), an increase in left hippocampal glutathione (p < 0.01), and a decrease of left hippocampal cerebral blood volume (p = 0.01) over time, regardless of exercise condition. Additional exploratory analyses showed that changes in brain-derived neurotrophic factor (p = 0.01), insulin-like growth-factor (p = 0.03), and dorsal anterior cingulate cortex N-acetyl-aspartate levels (p = 0.01) were positively associated with cardiorespiratory fitness changes. Furthermore, a trend toward a positive association of fitness and gray-matter cerebral blood flow (p = 0.06) was found. Our results do not provide evidence for differential effects between high-intensity (aerobic) and low-intensity (toning) exercise on hippocampal structure and function in young adults. However, we show small but significant effects of exercise on hippocampal volume, neurometabolism and vasculature across exercise conditions. Moreover, our exploratory results suggest that exercise might not specifically only benefit hippocampal structure and function, but rather has a more widespread effect. These findings suggest that, in agreement with previous MRI studies demonstrating moderate to strong effects in elderly and diseased populations, but none to only mild effects in young healthy cohorts, the benefits of exercise on the studied brain measures may be age-dependent and restorative rather than stimulatory. Our study highlights the importance of a multi-modal, whole-brain approach to assess macroscopic and microscopic changes underlying exercise-induced brain changes, to better understand the role of exercise as a potential non-pharmacological intervention.

FreeSurfer ‐based segmentation of hippocampal subfields: A review of methods and applications, with a novel quality control procedure for ENIGMA studies and other collaborative efforts

Structural hippocampal abnormalities are common in many neurological and psychiatric disorders, and variation in hippocampal measures is related to cognitive performance and other complex phenotypes such as stress sensitivity. Hippocampal subregions are increasingly studied, as automated algorithms have become available for mapping and volume quantification. In the context of the Enhancing Neuro Imaging Genetics through Meta Analysis Consortium, several Disease Working Groups are using the FreeSurfer software to analyze hippocampal subregion (subfield) volumes in patients with neurological and psychiatric conditions along with data from matched controls. In this overview, we explain the algorithm's principles, summarize measurement reliability studies, and demonstrate two additional aspects (subfield autocorrelation and volume/reliability correlation) with illustrative data. We then explain the rationale for a standardized hippocampal subfield segmentation quality control (QC) procedure for improved pipeline harmonization. To guide researchers to make optimal use of the algorithm, we discuss how global size and age effects can be modeled, how QC steps can be incorporated and how subfields may be aggregated into composite volumes. This discussion is based on a synopsis of 162 published neuroimaging studies (01/2013–12/2019) that applied the FreeSurfer hippocampal subfield segmentation in a broad range of domains including cognition and healthy aging, brain development and neurodegeneration, affective disorders, psychosis, stress regulation, neurotoxicity, epilepsy, inflammatory disease, childhood adversity and posttraumatic stress disorder, and candidate and whole genome (epi‐)genetics. Finally, we highlight points where FreeSurfer‐based hippocampal subfield studies may be optimized.

7T Epilepsy Task Force Consensus Recommendations on the Use of 7T MRI in Clinical Practice

Identifying a structural brain lesion on MRI has important implications in epilepsy and is the most important factor that correlates with seizure freedom after surgery in patients with drug-resistant focal onset epilepsy. However, at conventional magnetic field strengths (1.5 and 3T), only approximately 60%-85% of MRI examinations reveal such lesions. Over the last decade, studies have demonstrated the added value of 7T MRI in patients with and without known epileptogenic lesions from 1.5 and/or 3T. However, translation of 7T MRI to clinical practice is still challenging, particularly in centers new to 7T, and there is a need for practical recommendations on targeted use of 7T MRI in the clinical management of patients with epilepsy. The 7T Epilepsy Task Force-an international group representing 21 7T MRI centers with experience from scanning over 2,000 patients with epilepsy-would hereby like to share its experience with the neurology community regarding the appropriate clinical indications, patient selection and preparation, acquisition protocols and setup, technical challenges, and radiologic guidelines for 7T MRI in patients with epilepsy. This article mainly addresses structural imaging; in addition, it presents multiple nonstructural MRI techniques that benefit from 7T and hold promise as future directions in epilepsy. Answering to the increased availability of 7T MRI as an approved tool for diagnostic purposes, this article aims to provide guidance on clinical 7T MRI epilepsy management by giving recommendations on referral, suitable 7T MRI protocols, and image interpretation.

Anatomical Variations, Mimics, and Pitfalls in Imaging of Patients with Epilepsy

Epilepsy is among one of the most common neurologic disorders. The role of magnetic resonance imaging (MRI) in the diagnosis and management of patients with epilepsy is well established, and most patients with epilepsy are likely to undergo at least one or more MRI examinations in the course of their disease. Recent advances in high-field MRI have enabled high resolution in vivo visualization of small and intricate anatomic structures that are of great importance in the assessment of seizure disorders. Familiarity with normal anatomic variations is essential in the accurate diagnosis and image interpretation, as these variations may be mistaken for epileptogenic foci, leading to unnecessary follow-up imaging, or worse, unnecessary treatment. After a brief overview of normal imaging anatomy of the mesial temporal lobe, this article will review a few important common and uncommon anatomic variations, mimics, and pitfalls that may be encountered in the imaging evaluation of patients with epilepsy.

Volume increase in the dentate gyrus after electroconvulsive therapy in depressed patients as measured with 7T

Electroconvulsive therapy (ECT) is the most effective treatment for depression, yet its working mechanism remains unclear. In the animal analog of ECT, neurogenesis in the dentate gyrus (DG) of the hippocampus is observed. In humans, volume increase of the hippocampus has been reported, but accurately measuring the volume of subfields is limited with common MRI protocols. If the volume increase of the hippocampus in humans is attributable to neurogenesis, it is expected to be exclusively present in the DG, whereas other processes (angiogenesis, synaptogenesis) also affect other subfields. Therefore, we acquired an optimized MRI scan at 7-tesla field strength allowing sensitive investigation of hippocampal subfields. A further increase in sensitivity of the within-subjects measurements is gained by automatic placement of the field of view. Patients receive two MRI scans: at baseline and after ten bilateral ECT sessions (corresponding to a 5-week interval). Matched controls are also scanned twice, with a similar 5-week interval. A total of 31 participants (23 patients, 8 controls) completed the study. A large and significant increase in DG volume was observed after ECT (M = 75.44 mm³, std error = 9.65, p < 0.001), while other hippocampal subfields were unaffected. We note that possible type II errors may be present due to the small sample size. In controls no changes in volume were found. Furthermore, an increase in DG volume was related to a decrease in depression scores, and baseline DG volume predicted clinical response. These findings suggest that the volume change of the DG is related to the antidepressant properties of ECT, and may reflect neurogenesis.

Structural Covariance Changes of Anterior and Posterior Hippocampus During Musical Training in Young Adults

Musical training can induce the functional and structural changes of the hippocampus. The hippocampus is not a homogeneous structure which can be divided into anterior and posterior parts along its longitudinal axis, and the whole-brain structural covariances of anterior (aHC) and posterior hippocampus (pHC) show distinct patterns in young adults. However, little is known about whether the anterior and posterior hippocampal structural covariances change after long-term musical training. Here, we investigated the musical training-induced changes of the whole-brain structural covariances of bilateral aHC and pHC in a longitudinal designed experiment with two groups (training group and control group) across three time points [the beginning (TP1) and the end (TP2) of 24 weeks of training, and 12 weeks after training (TP3)]. Using seed partial least square, we identified two significant patterns of structural covariance of the aHC and pHC. The first showed common structural covariance of the aHC and pHC. The second pattern revealed distinct structural covariance of the two regions and reflected the changes of structural covariance of the left pHC in the training group across three time points: the left pHC showed significant structural covariance with bilateral hippocampus and parahippocampal gyrus, left calcarine sulcus only at TP1 and TP3. Furthermore, the integrity of distinct structural networks of aHC and pHC in the second pattern significantly increased in the training group. Our findings suggest that musical training could change the organization of structural whole-brain covariance for left pHC and enhance the degree of the structural covariance network differentiation of the aHC and pHC in young adults.

CAST: A multi-scale convolutional neural network based automated hippocampal subfield segmentation toolbox

In this study, we developed a multi-scale Convolutional neural network based Automated hippocampal subfield Segmentation Toolbox (CAST) for automated segmentation of hippocampal subfields. Although training CAST required approximately three days on a single workstation with a high-quality GPU card, CAST can segment a new subject in less than 1 ​min even with GPU acceleration disabled, thus this method is more time efficient than current automated methods and manual segmentation. This toolbox is highly flexible with either a single modality or multiple modalities and can be easily set up to be trained with a researcher's unique data. A 3D multi-scale deep convolutional neural network is the key algorithm used in the toolbox. The main merit of multi-scale images is the capability to capture more global structural information from down-sampled images without dramatically increasing memory and computational burden. The original images capture more local information to refine the boundary between subfields. Residual learning is applied to alleviate the vanishing gradient problem and improve the performance with a deeper network. We applied CAST with the same settings on two datasets, one 7T dataset (the UMC dataset) with only the T2 image and one 3T dataset (the MNI dataset) with both T1 and T2 images available. The segmentation accuracy of both CAST and the state-of-the-art automated method ASHS, in terms of the dice similarity coefficient (DSC), were comparable. CAST significantly improved the reliability of segmenting small subfields, such as CA2, CA3, and the entorhinal cortex (ERC), in terms of the intraclass correlation coefficient (ICC). Both ASHS and manual segmentation process some subfields (e.g. CA2 and ERC) with high DSC values but low ICC values, consequently increasing the difficulty of judging segmentation quality. CAST produces very consistent DSC and ICC values, with a maximal discrepancy of 0.01 (DSC-ICC) across all subfields. The pre-trained model, source code, and settings for the CAST toolbox are publicly available.

Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using multi-contrast MRI

The volumetric and morphometric examination of hippocampus formation subfields in a longitudinal manner using in vivo MRI could lead to more sensitive biomarkers for neuropsychiatric disorders and diseases including Alzheimer's disease, as the anatomical subregions are functionally specialised. Longitudinal processing allows for increased sensitivity due to reduced confounds of inter-subject variability and higher effect-sensitivity than cross-sectional designs. We examined the performance of a new longitudinal pipeline (Longitudinal Automatic Segmentation of Hippocampus Subfields [LASHiS]) against three freely available, published approaches. LASHiS automatically segments hippocampus formation subfields by propagating labels from cross-sectionally labelled time point scans using joint-label fusion to a non-linearly realigned 'single subject template', where image segmentation occurs free of bias to any individual time point. Our pipeline measures tissue characteristics available in in vivo high-resolution MRI scans, at both clinical (3 ​T) and ultra-high field strength (7 ​T) and differs from previous longitudinal segmentation pipelines in that it leverages multi-contrast information in the segmentation process. LASHiS produces robust and reliable automatic multi-contrast segmentations of hippocampus formation subfields, as measured by higher volume similarity coefficients and Dice coefficients for test-retest reliability and robust longitudinal Bayesian Linear Mixed Effects results at 7 ​T, while showing sound results at 3 ​T. All code for this project including the automatic pipeline is available at https://github.com/CAIsr/LASHiS.

Automated Multi-Atlas Segmentation of Hippocampal and Extrahippocampal Subregions in Alzheimer's Disease at 3T and 7T: What Atlas Composition Works Best?

BACKGROUND

Multi-atlas segmentation, a popular technique implemented in the Automated Segmentation of Hippocampal Subfields (ASHS) software, utilizes multiple expert-labelled images ("atlases") to delineate medial temporal lobe substructures. This multi-atlas method is increasingly being employed in early Alzheimer's disease (AD) research, it is therefore becoming important to know how the construction of the atlas set in terms of proportions of controls and patients with mild cognitive impairment (MCI) and/or AD affects segmentation accuracy.

OBJECTIVE

To evaluate whether the proportion of controls in the training sets affects the segmentation accuracy of both controls and patients with MCI and/or early AD at 3T and 7T.

METHODS

We performed cross-validation experiments varying the proportion of control subjects in the training set, ranging from a patient-only to a control-only set. Segmentation accuracy of the test set was evaluated by the Dice similarity coeffiecient (DSC). A two-stage statistical analysis was applied to determine whether atlas composition is linked to segmentation accuracy in control subjects and patients, for 3T and 7T.

RESULTS

The different atlas compositions did not significantly affect segmentation accuracy at 3T and for patients at 7T. For controls at 7T, including more control subjects in the training set significantly improves the segmentation accuracy, but only marginally, with the maximum of 0.0003 DSC improvement per percent increment of control subject in the training set.

CONCLUSION

ASHS is robust in this study, and the results indicate that future studies investigating hippocampal subfields in early AD populations can be flexible in the selection of their atlas compositions.

Dissociation of the Perirhinal Cortex and Hippocampus During Discriminative Learning of Similar Objects

Discriminative learning is a paradigm that has been used in animal studies, in which memory of a stimulus is enhanced when it is presented with a similar stimulus rather than with a different one. Human studies have shown that through discriminative learning of similar objects, both item memory and contextual memories are enhanced. However, the underlying neural mechanisms for it are unclear. The hippocampus and perirhinal cortex (PRC) are two possible regions involved in discriminating similar stimuli and forming distinctive memory representations. In this study, 28 participants (15 males) were scanned using high-resolution fMRI when a picture (e.g., a dog) was paired with the same picture, with a similar picture of the same concept (e.g., another dog), or with a picture of a different concept (e.g., a cat). Then, after intervals of 20 min and 1 week, the participants were asked to perform an old/new recognition task, followed by a contextual judgment. The results showed that during encoding, there was stronger activation in the PRC for the "similar" than for the "same" and "different" conditions and it predicted subsequent item memory for the "similar" condition. The hippocampal activation decreased for the "same" versus the "different" condition and the DG/CA3 activation predicted subsequent contextual memory for the "similar" condition. These results suggested that the PRC and hippocampus are functionally dissociated in encoding simultaneously presented objects and predicting subsequent item and contextual memories after discriminative learning.SIGNIFICANCE STATEMENT How the brain separates similar input into nonoverlapping representations and forms distinct memory for them is a fundamental question for the neuroscience of memory. By discriminative learning of similar (vs different) objects, both item and contextual memories are enhanced. This study found functional dissociations between perirhinal cortex (PRC) and hippocampus in discriminating pairs of similar and different objects and in predicting subsequent memory of similar objects in their item and contextual aspects. The results provided clear evidence on the neural mechanisms of discriminative learning and highlighted the importance of the PRC and hippocampus in processing different types of object information when the objects were simultaneously presented.

Volumetric comparison of hippocampal subfields extracted from 4-minute accelerated vs. 8-minute high-resolution T2-weighted 3T MRI scans

The hippocampus has been widely studied using neuroimaging, as it plays an important role in memory and learning. However, hippocampal subfield information is difficult to capture by standard magnetic resonance imaging (MRI) techniques. To facilitate morphometric study of hippocampal subfields, ADNI introduced a high resolution (0.4 mm in plane) T2-weighted turbo spin-echo sequence that requires 8 min. With acceleration, the protocol can be acquired in 4 min. We performed a comparative study of hippocampal subfield volumes using standard and accelerated protocols on a Siemens Prisma 3T MRI in an independent sample of older adults that included 10 cognitively normal controls, 9 individuals with subjective cognitive decline, 10 with mild cognitive impairment, and 6 with a clinical diagnosis of Alzheimer's disease (AD). The Automatic Segmentation of Hippocampal Subfields (ASHS) software was used to segment 9 primary labeled regions including hippocampal subfields and neighboring cortical regions. Intraclass correlation coefficients were computed for reliability tests between 4 and 8 min scans within and across the four groups. Pairwise group analyses were performed, covaried for age, sex and total intracranial volume, to determine whether the patterns of group differences were similar using 4 vs. 8 min scans. The 4 and 8 min protocols, analyzed by ASHS segmentation, yielded similar volumetric estimates for hippocampal subfields as well as comparable patterns of differences between study groups. The accelerated protocol can provide reliable imaging data for investigation of hippocampal subfields in AD-related MRI studies and the decreased scan time may result in less vulnerability to motion.

Hippocampal subfield segmentation in temporal lobe epilepsy: Relation to outcomes

Objective

To investigate the clinical and surgical outcome correlates of preoperative hippocampal subfield volumes in patients with refractory temporal lobe epilepsy (TLE) using a new magnetic resonance imaging (MRI) multisequence segmentation technique.

Methods

We recruited 106 patients with TLE and hippocampal sclerosis (HS) who underwent conventional T1‐weighted and T2 short TI inversion recovery MRI. An automated hippocampal segmentation algorithm was used to identify twelve subfields in each hippocampus. A total of 76 patients underwent amygdalohippocampectomy and postoperative seizure outcome assessment using the standardized ILAE classification. Semiquantitative hippocampal internal architecture (HIA) ratings were correlated with hippocampal subfield volumes.

Results

Patients with left TLE had smaller volumes of the contralateral presubiculum and hippocampus‐amygdala transition area compared to those with right TLE. Patients with right TLE had reduced contralateral hippocampal tail volumes and improved outcomes. In all patients, there were no significant relationships between hippocampal subfield volumes and clinical variables such as duration and age at onset of epilepsy. There were no significant differences in any hippocampal subfield volumes between patients who were rendered seizure free and those with persistent postoperative seizure symptoms. Ipsilateral but not contralateral HIA ratings were significantly correlated with gross hippocampal and subfield volumes.

Conclusions

Our results suggest that ipsilateral hippocampal subfield volumes are not related to the chronicity/severity of TLE. We did not find any hippocampal subfield volume or HIA rating differences in patients with optimal and unfavorable outcomes. In patients with TLE and HS, sophisticated analysis of hippocampal architecture on MRI may have limited value for prediction of postoperative outcome.

Key clinical benefits of neuroimaging at 7T

The growing interest in ultra-high field MRI, with more than 35.000 MR examinations already performed at 7T, is related to improved clinical results with regard to morphological as well as functional and metabolic capabilities. Since the signal-to-noise ratio increases with the field strength of the MR scanner, the most evident application at 7T is to gain higher spatial resolution in the brain compared to 3T. Of specific clinical interest for neuro applications is the cerebral cortex at 7T, for the detection of changes in cortical structure, like the visualization of cortical microinfarcts and cortical plaques in Multiple Sclerosis. In imaging of the hippocampus, even subfields of the internal hippocampal anatomy and pathology may be visualized with excellent spatial resolution. Using Susceptibility Weighted Imaging, the plaque-vessel relationship and iron accumulations in Multiple Sclerosis can be visualized, which may provide a prognostic factor of disease. Vascular imaging is a highly promising field for 7T which is dealt with in a separate dedicated article in this special issue. The static and dynamic blood oxygenation level-dependent contrast also increases with the field strength, which significantly improves the accuracy of pre-surgical evaluation of vital brain areas before tumor removal. Improvement in acquisition and hardware technology have also resulted in an increasing number of MR spectroscopic imaging studies in patients at 7T. More recent parallel imaging and short-TR acquisition approaches have overcome the limitations of scan time and spatial resolution, thereby allowing imaging matrix sizes of up to 128×128. The benefits of these acquisition approaches for investigation of brain tumors and Multiple Sclerosis have been shown recently. Together, these possibilities demonstrate the feasibility and advantages of conducting routine diagnostic imaging and clinical research at 7T.

Mapping the structural and functional network architecture of the medial temporal lobe using 7T MRI

Medial temporal lobe (MTL) subregions play integral roles in memory function and are differentially affected in various neurological and psychiatric disorders. The ability to structurally and functionally characterize these subregions may be important to understanding MTL physiology and diagnosing diseases involving the MTL. In this study, we characterized network architecture of the MTL in healthy subjects (n = 31) using both resting state functional MRI and MTL-focused T2-weighted structural MRI at 7 tesla. Ten MTL subregions per hemisphere, including hippocampal subfields and cortical regions of the parahippocampal gyrus, were segmented for each subject using a multi-atlas algorithm. Both structural covariance matrices from correlations of subregion volumes across subjects, and functional connectivity matrices from correlations between subregion BOLD time series were generated. We found a moderate structural and strong functional inter-hemispheric symmetry. Several bilateral hippocampal subregions (CA1, dentate gyrus, and subiculum) emerged as functional network hubs. We also observed that the structural and functional networks naturally separated into two modules closely corresponding to (a) bilateral hippocampal formations, and (b) bilateral extra-hippocampal structures. Finally, we found a significant correlation in structural and functional connectivity (r = 0.25). Our findings represent a comprehensive analysis of network topology of the MTL at the subregion level. We share our data, methods, and findings as a reference for imaging methods and disease-based research.

Systematic comparison of different techniques to measure hippocampal subfield volumes in ADNI2

Objective

Subfield-specific measurements provide superior information in the early stages of neurodegenerative diseases compared to global hippocampal measurements. The overall goal was to systematically compare the performance of five representative manual and automated T1 and T2 based subfield labeling techniques in a sub-set of the ADNI2 population.

Methods

The high resolution T2 weighted hippocampal images (T2-HighRes) and the corresponding T1 images from 106 ADNI2 subjects (41 controls, 57 MCI, 8 AD) were processed as follows. A. T1-based: 1. Freesurfer + Large-Diffeomorphic-Metric-Mapping in combination with shape analysis. 2. FreeSurfer 5.1 subfields using in-vivo atlas. B. T2-HighRes: 1. Model-based subfield segmentation using ex-vivo atlas (FreeSurfer 6.0). 2. T2-based automated multi-atlas segmentation combined with similarity-weighted voting (ASHS). 3. Manual subfield parcellation. Multiple regression analyses were used to calculate effect sizes (ES) for group, amyloid positivity in controls, and associations with cognitive/memory performance for each approach.

Results

Subfield volumetry was better than whole hippocampal volumetry for the detection of the mild atrophy differences between controls and MCI (ES: 0.27 vs 0.11). T2-HighRes approaches outperformed T1 approaches for the detection of early stage atrophy (ES: 0.27 vs.0.10), amyloid positivity (ES: 0.11 vs 0.04), and cognitive associations (ES: 0.22 vs 0.19).

Conclusions

T2-HighRes subfield approaches outperformed whole hippocampus and T1 subfield approaches. None of the different T2-HghRes methods tested had a clear advantage over the other methods. Each has strengths and weaknesses that need to be taken into account when deciding which one to use to get the best results from subfield volumetry.

Segmenting hippocampal subfields from 3T MRI with multi-modality images

Hippocampal subfields play important roles in many brain activities. However, due to the small structural size, low signal contrast, and insufficient image resolution of 3T MR, automatic hippocampal subfields segmentation is less explored. In this paper, we propose an automatic learning-based hippocampal subfields segmentation method using 3T multi-modality MR images, including structural MRI (T1, T2) and resting state fMRI (rs-fMRI). The appearance features and relationship features are both extracted to capture the appearance patterns in structural MR images and also the connectivity patterns in rs-fMRI, respectively. In the training stage, these extracted features are adopted to train a structured random forest classifier, which is further iteratively refined in an auto-context model by adopting the context features and the updated relationship features. In the testing stage, the extracted features are fed into the trained classifiers to predict the segmentation for each hippocampal subfield, and the predicted segmentation is iteratively refined by the trained auto-context model. To our best knowledge, this is the first work that addresses the challenging automatic hippocampal subfields segmentation using relationship features from rs-fMRI, which is designed to capture the connectivity patterns of different hippocampal subfields. The proposed method is validated on two datasets and the segmentation results are quantitatively compared with manual labels using the leave-one-out strategy, which shows the effectiveness of our method. From experiments, we find a) multi-modality features can significantly increase subfields segmentation performance compared to those only using one modality; b) automatic segmentation results using 3T multi-modality MR images could be partially comparable to those using 7T T1 MRI.