The influence of manual segmentation strategies and different phases selection on machine learning-based computed tomography in renal tumors: a systematic review and meta-analysis.

BACKGROUND: Delineating the region/volume of interest (ROI/VOI) and selecting the phases are of importance in developing machine learning (ML). The results will change when choosing different methods of drawing the ROI/VOI and selecting different phases. However, there is no related standard for delineating the ROI/VOI and selecting the phases in renal tumors to develop ML based on computed tomography (CT). METHODS: The PubMed and Web of Science were searched for related studies published until March 1, 2023. Inclusion criteria were studies that developed ML models in renal tumors from CT images. And the binary diagnostic accuracy data were extracted to obtain the outcomes, such as sensitivity (SE), specificity (SP), accuracy (ACC), and area under the curve (AUC). RESULTS: Twenty-three papers were included in the meta-analysis with a pooled SE of 87% (95% CI 85-88%), SP of 82% (95% CI 79-85%), and AUC of 91% (95% CI 89-93%) in phases; a pooled SE of 82% (95% CI 80-84%), SP of 85% (95% CI 83-86%), and AUC of 90% (95% CI 88-93%) in phases combined with delineating strategies, respectively. In all different combinations, the contour-focused and single phase produce the highest AUC of 93% (95% CI 90-95%). In subgroup analyses (sample size, year of publication, and geographical distribution), the performance was acceptable on phases and phases combined strategies. CONCLUSIONS: To explore the effect of manual segmentation strategies and different phases selection on ML-based CT, we find that the method of single phase (CMP or NP) combined with contour-focused was considered a better strategy compared to the other strategies.

A preliminary choroid plexus volumetric study in individuals with psychosis.

The choroid plexus (ChP) is part of the blood-cerebrospinal fluid barrier, regulating brain homeostasis and the brain's response to peripheral events. Its upregulation and enlargement are considered essential in psychosis. However, the timing of the ChP enlargement has not been established. This study introduces a novel magnetic resonance imaging-based segmentation method to examine ChP volumes in two cohorts of individuals with psychosis. The first sample consists of 41 individuals with early course psychosis (mean duration of illness = 1.78 years) and 30 healthy individuals. The second sample consists of 30 individuals with chronic psychosis (mean duration of illness = 7.96 years) and 34 healthy individuals. We utilized manual segmentation to measure ChP volumes. We applied ANCOVAs to compare normalized ChP volumes between groups and partial correlations to investigate the relationship between ChP, LV volumes, and clinical characteristics. Our segmentation demonstrated good reliability (.87). We further showed a significant ChP volume increase in early psychosis (left: p < .00010, right: p < .00010) and a significant positive correlation between higher ChP and higher LV volumes in chronic psychosis (left: r = .54, p = .0030, right: r = .68; p < .0010). Our study suggests that ChP enlargement may be a marker of acute response around disease onset. It might also play a modulatory role in the chronic enlargement of lateral ventricles, often reported in psychosis. Future longitudinal studies should investigate the dynamics of ChP enlargement as a promising marker for novel therapeutic strategies.

Is Hippocampal Volume a Relevant Early Marker of Dementia?

OBJECTIVE: Hippocampal volume (HV) is a key imaging marker to improve Alzheimer's disease risk prediction. However, longitudinal studies are rare, and hippocampus may also be implicated in the subtle aging-related cognitive decline observed in dementia-free individuals. Our aim was to determine whether HV, measured by manual or automatic segmentation, is associated with dementia risk and cognitive decline in participants with and without incident dementia. METHODS: At baseline, 510 dementia-free participants from the French longitudinal ESPRIT cohort underwent magnetic resonance imaging. HV was measured by manual and by automatic segmentation (FreeSurfer 6.0). The presence of dementia and cognitive functions were investigated at each follow-up (2, 4, 7, 10, 12, and 15 years). Cox proportional hazards models and linear mixed models were used to assess the association of HV with dementia risk and with cognitive decline, respectively. RESULTS: During the 15-years follow-up, 42 participants developed dementia. Reduced HV (regardless of the measurement method) was significantly associated with higher dementia risk and cognitive decline in the whole sample. However, only the automatically measured HV was associated with cognitive decline in dementia-free participants. CONCLUSION: These results suggest that HV can be used to predict the long-term risk of dementia but also cognitive decline in a dementia-free population. This raises the question of the relevance of HV measurement as an early marker of dementia in the general population.

Automatic Segmentation of Parkinson Disease Therapeutic Targets Using Nonlinear Registration and Clinical MR Imaging: Comparison of Methodology, Presence of Disease, and Quality Control.

INTRODUCTION: Accurate and precise delineation of the globus pallidus pars interna (GPi) and subthalamic nucleus (STN) is critical for the clinical treatment and research of Parkinson's disease (PD). Automated segmentation is a developing technology which addresses limitations of visualizing deep nuclei on MR imaging and standardizing their definition in research applications. We sought to compare manual segmentation with three workflows for template-to-patient nonlinear registration providing atlas-based automatic segmentation of deep nuclei. METHODS: Bilateral GPi, STN, and red nucleus (RN) were segmented for 20 PD and 20 healthy control (HC) subjects using 3T MRIs acquired for clinical purposes. The automated workflows used were an option available in clinical practice and two common research protocols. Quality control (QC) was performed on registered templates via visual inspection of readily discernible brain structures. Manual segmentation using T1, proton density, and T2 sequences was used as "ground truth" data for comparison. Dice similarity coefficient (DSC) was used to assess agreement between segmented nuclei. Further analysis was done to compare the influences of disease state and QC classifications on DSC. RESULTS: Automated segmentation workflows (CIT-S, CRV-AB, and DIST-S) had the highest DSC for the RN and lowest for the STN. Manual segmentations outperformed automated segmentation for all workflows and nuclei; however, for 3/9 workflows (CIT-S STN, CRV-AB STN, and CRV-AB GPi) the differences were not statically significant. HC and PD only showed significant differences in 1/9 comparisons (DIST-S GPi). QC classification only demonstrated significantly higher DSC in 2/9 comparisons (CRV-AB RN and GPi). CONCLUSION: Manual segmentations generally performed better than automated segmentations. Disease state does not appear to have a significant effect on the quality of automated segmentations via nonlinear template-to-patient registration. Notably, visual inspection of template registration is a poor indicator of the accuracy of deep nuclei segmentation. As automatic segmentation methods continue to evolve, efficient and reliable QC methods will be necessary to support safe and effective integration into clinical workflows.

PILLAR: ParaspInaL muscLe segmentAtion pRoject - a comprehensive online resource to guide manual segmentation of paraspinal muscles from magnetic resonance imaging.

BACKGROUND: There is an increasing interest in assessing paraspinal morphology and composition in relation to low back pain (LBP). However, variations in methods and segmentation protocols contribute to the inconsistent findings in the literature. We present an on-line resource, the ParaspInaL muscLe segmentAtion pRoject (PILLAR, https://projectpillar.github.io/ ), to provide a detailed description and visual guide of a segmentation protocol by using the publicly available ITK-SNAP software and discuss related challenges when performing paraspinal lumbar muscles segmentations from magnetic resonance imaging (MRI). METHODS: T2-weighted and corresponding fat-water IDEAL axial MRI from 3 males and 3 females (2 chronic LBP and 1 control for each sex) were used to demonstrate our segmentation protocol for each lumbar paraspinal muscle (erector spinae, lumbar multifidus, quadratus lumborum and psoas) and lumbar spinal level (L1-L5). RESULTS: Proper segmentation requires an understanding of the anatomy of paraspinal lumbar muscles and the variations in paraspinal muscle morphology and composition due to age, sex, and the presence of LBP or related spinal pathologies. Other challenges in segmentation includes the presence and variations of intramuscular and epimuscular fat, and side-to-side asymmetry. CONCLUSION: The growing interest to assess the lumbar musculature and its role in the development and recurrence of LBP prompted the need for comprehensive and easy-to-follow resources, such as the PILLAR project to reduce inconsistencies in segmentation protocols. Standardizing manual muscle measurements from MRI will facilitate comparisons between studies while the field is progressively moving towards the automatization of paraspinal muscle measurements for large cohort studies.

Intra-operator Repeatability of Manual Segmentations of the Hip Muscles on Clinical Magnetic Resonance Images.

The manual segmentation of muscles on magnetic resonance images is the gold standard procedure to reconstruct muscle volumes from medical imaging data and extract critical information for clinical and research purposes. (Semi)automatic methods have been proposed to expedite the otherwise lengthy process. These, however, rely on manual segmentations. Nonetheless, the repeatability of manual muscle volume segmentations performed on clinical MRI data has not been thoroughly assessed. When conducted, volumetric assessments often disregard the hip muscles. Therefore, one trained operator performed repeated manual segmentations (n = 3) of the iliopsoas (n = 34) and gluteus medius (n = 40) muscles on coronal T1-weighted MRI scans, acquired on 1.5 T scanners on a clinical population of patients elected for hip replacement surgery. Reconstructed muscle volumes were divided in sub-volumes and compared in terms of volume variance (normalized variance of volumes - nVV), shape (Jaccard Index-JI) and surface similarity (maximal Hausdorff distance-HD), to quantify intra-operator repeatability. One-way repeated measures ANOVA (or equivalent) tests with Bonferroni corrections for multiple comparisons were conducted to assess statistical significance. For both muscles, repeated manual segmentations were highly similar to one another (nVV: 2-6%, JI > 0.78, HD < 15 mm). However, shape and surface similarity were significantly lower when muscle extremities were included in the segmentations (e.g., iliopsoas: HD -12.06 to 14.42 mm, P < 0.05). Our findings show that the manual segmentation of hip muscle volumes on clinical MRI scans provides repeatable results over time. Nonetheless, extreme care should be taken in the segmentation of muscle extremities.

Agreement Between Automated and Manual MRI Volumetry in Alzheimer's Disease: A Systematic Review and Meta-Analysis.

BACKGROUND: Automated magnetic resonance imaging (MRI) volumetry is a promising tool to evaluate regional brain volumes in dementia and especially Alzheimer's disease (AD). PURPOSE: To compare automated methods and the gold standard manual segmentation in measuring regional brain volumes on MRI across healthy controls, patients with mild cognitive impairment, and patients with dementia due to AD. STUDY TYPE: Systematic review and meta-analysis. DATA SOURCES: MEDLINE, Embase, and PsycINFO were searched through October 2021. FIELD STRENGTH: 1.0 T, 1.5 T, or 3.0 T. ASSESSMENT: Two review authors independently identified studies for inclusion and extracted data. Methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2). STATISTICAL TESTS: Standardized mean differences (SMD; Hedges' g) were pooled using random-effects meta-analysis with robust variance estimation. Subgroup analyses were undertaken to explore potential sources of heterogeneity. Sensitivity analyses were conducted to examine the impact of the within-study correlation between effect estimates on the meta-analysis results. RESULTS: Seventeen studies provided sufficient data to evaluate the hippocampus, lateral ventricles, and parahippocampal gyrus. The pooled SMD for the hippocampus, lateral ventricles, and parahippocampal gyrus were 0.22 (95% CI -0.50 to 0.93), 0.12 (95% CI -0.13 to 0.37), and -0.48 (95% CI -1.37 to 0.41), respectively. For the hippocampal data, subgroup analyses suggested that the pooled SMD was invariant across clinical diagnosis and field strength. Subgroup analyses could not be conducted on the lateral ventricles data and the parahippocampal gyrus data due to insufficient data. The results were robust to the selected within-study correlation value. DATA CONCLUSION: While automated methods are generally comparable to manual segmentation for measuring hippocampal, lateral ventricle, and parahippocampal gyrus volumes, wide 95% CIs and large heterogeneity suggest that there is substantial uncontrolled variance. Thus, automated methods may be used to measure these regions in patients with AD but should be used with caution. EVIDENCE LEVEL: 3 TECHNICAL EFFICACY: Stage 3.

Towards defining muscular regions of interest from axial magnetic resonance imaging with anatomical cross-reference: a scoping review of lateral hip musculature.

BACKGROUND: Measures of hip muscle morphology and composition (e.g., muscle size and fatty infiltration) are possible with magnetic resonance imaging (MRI). Standardised protocols or guidelines do not exist for evaluation of hip muscle characteristics, hindering reliable and valid inter-study analysis. This scoping review aimed to collate and synthesise MRI methods for measuring lateral hip muscle size and fatty infiltration to inform the future development of standardised protocols. METHODS: Five electronic databases (Medline, CINAHL, Embase, SportsDISCUS and AMED) were searched. Healthy or musculoskeletal pain populations that used MRI to assess lateral hip muscle size and fatty infiltration were included. Lateral hip muscles of interest included tensor fascia late (TFL), gluteus maximus, gluteus medius, and gluteus minimus. Data on MRI parameters, axial slice location, muscle size and fatty infiltrate measures were collected and analysed. Cross referencing for anatomical locations were made between MRI axial slice and E-12 anatomical plastinate sections. RESULTS: From 2684 identified publications, 78 studies contributed data on volume (n = 31), cross sectional area (CSA) (n = 24), and fatty infiltration (n = 40). Heterogeneity was observed for MRI parameters and anatomical boundaries scrutinizing hip muscle size and fatty infiltration. Seven single level axial slices were identified that provided consistent CSA measurement, including three for both gluteus maximus and TFL, and four for both gluteus medius and minimus. For assessment of fatty infiltration, six axial slice locations were identified including two for TFL, and four for each of the gluteal muscles. CONCLUSIONS: Several consistent anatomical levels were identified for single axial MR slice to facilitate muscle size and fatty infiltration muscle measures at the hip, providing the basis for reliable and accurate data synthesis and improvements in the validity of future between studies analyses. This work establishes the platform for standardised methods for the MRI assessment of lateral hip musculature and will aid in the examination of musculoskeletal conditions around the hip joint. Further studies into whole muscle measures are required to further optimise methodological parameters for hip muscle assessment.

Volumetric White Matter Hyperintensity Ranges Correspond to Fazekas Scores on Brain MRI.

INTRODUCTION: White matter hyperintensity (WMH) is an abnormal T2 signal in the deep and subcortical white matter visualized on MRI associated with hypertension, cerebrovascular disease, and aging. The Fazekas (Fz) scoring system is a commonly used qualitative tool to assess the severity of WMH. While studies have compared Fazekas scores to other scoring methods, the comparison of Fazekas scores and volume of WMH using current semiautomated volumetric techniques has not been studied. METHODS: We reviewed MRI studies acquired at our institution between 2015 and 2017. Relative WMH was scored by one author trained in Fazekas scoring. A board certified neuroradiologist scored them independently for confirmation. Manual segmentations of WMH were completed using 3D Slicer 4.9. A 3D model was formed to quantify WMH in milliliters (mL). ANOVA tests were performed to determine the association of Fazekas scores with corresponding WMH volumes. RESULTS: Among the 198 patients in our study, WMH were visualized in 163 (Fz1: n=66; Fz2: n=49; Fz3: n=48). WMH volumes significantly differed according to Fazekas score (F = 141.1, p<0.001), with increasing WMHV associated with higher Fazekas scores: Fz1, range 0.1-8.3 mL (mean 3.7, SD 2.3); Fz2, range 6.0-17.7 mL (mean 10.8, SD 3.1); Fz3, range 14.2-77.2 mL (mean 35.2, SD 17.9); and Fz3 (excluding 11 outliers above 50 mL), 14.2-47.0 mL (mean 27.1, SD 8.9). CONCLUSION: Fazekas scores correspond with distinct ranges of WMH volume with relatively little overlap, but scores based on volumes are more efficacious. A modified Fazekas from 0-4 should be considered.

Evaluation of interrater reliability of different muscle segmentation techniques in diffusion tensor imaging.

INTRODUCTION: Muscle diffusion tensor imaging (mDTI) is a quantitative MRI technique that can provide information about muscular microstructure and integrity. Ultrasound and DTI studies have shown intramuscular differences, and therefore separation of different muscles for analysis is essential. The commonly used methods to assess DTI metrics in muscles are manual segmentation and tract-based analysis. Recently methods such as volume-based tractography have been applied to optimize muscle architecture estimation, but can also be used to assess DTI metrics. PURPOSE: To evaluate diffusion metrics obtained using three different methods-volume-based tractography, manual segmentation-based analysis and tract-based analysis-with respect to their interrater reliability and their ability to detect intramuscular variance. MATERIALS AND METHODS: 30 volunteers underwent an MRI examination in a 3 T scanner using a 16-channel Torso XL coil. Diffusion-weighted images were acquired to obtain DTI metrics. These metrics were evaluated in six thigh muscles using volume-based tractography, manual segmentation and standard tractography. All three methods were performed by two independent raters to assess interrater reliability by ICC analysis and Bland-Altman plots. Ability to assess intramuscular variance was compared using an ANOVA with muscle as a between-subjects factor. RESULTS: Interrater reliability for all methods was found to be excellent. The highest interrater reliability was found for volume-based tractography (ICC ≥ 0.967). Significant differences for the factor muscle in all examined diffusion parameters were shown in muscles using all methods (main effect p < 0.001). CONCLUSIONS: Diffusion data can be assessed by volume tractography, standard tractography and manual segmentation with high interrater reliability. Each method produces different results for the investigated DTI parameters. Volume-based tractography was superior to conventional manual segmentation and tractography regarding interrater reliability and detection of intramuscular variance, while tract-based analysis showed the lowest coefficients of variation.

Optimization and comparative evaluation of nonlinear deformation algorithms for atlas-based segmentation of DBS target nuclei.

Nonlinear registration of individual brain MRI scans to standard brain templates is common practice in neuroimaging and multiple registration algorithms have been developed and refined over the last 20 years. However, little has been done to quantitatively compare the available algorithms and much of that work has exclusively focused on cortical structures given their importance in the fMRI literature. In contrast, for clinical applications such as functional neurosurgery and deep brain stimulation (DBS), proper alignment of subcortical structures between template and individual space is important. This allows for atlas-based segmentations of anatomical DBS targets such as the subthalamic nucleus (STN) and internal pallidum (GPi). Here, we systematically evaluated the performance of six modern and established algorithms on subcortical normalization and segmentation results by calculating over 11,000 nonlinear warps in over 100 subjects. For each algorithm, we evaluated its performance using T1-or T2-weighted acquisitions alone or a combination of T1-, T2-and PD-weighted acquisitions in parallel. Furthermore, we present optimized parameters for the best performing algorithms. We tested each algorithm on two datasets, a state-of-the-art MRI cohort of young subjects and a cohort of subjects age- and MR-quality-matched to a typical DBS Parkinson's Disease cohort. Our final pipeline is able to segment DBS targets with precision comparable to manual expert segmentations in both cohorts. Although the present study focuses on the two prominent DBS targets, STN and GPi, these methods may extend to other small subcortical structures like thalamic nuclei or the nucleus accumbens.

Gadolinium effect on thalamus and whole brain tissue segmentation.

PURPOSE: Gadolinium-based contrast agent (GBCA) effect on automated segmentation algorithms of subcortical gray matter (GM) is not fully known. The aim of this study is to determine gadolinium effect on the segmentation of the thalamus and whole brain tissue using different automated segmentation techniques. METHODS: Eighty-four multiple sclerosis (MS) patients underwent an MRI acquisition of two 3DT1-weighted sequences with and without gadolinium injection among which 10 were excluded after image quality check. Manual thalamic segmentation considered as gold standard was performed on unenhanced T1 images. volBrain and FSL-Anat were used to automatically segment the thalamus on both enhanced and unenhanced T1 and the degree of similitude (DICE) values were compared between manual and automatic segmentations. Whole brain tissue segmentation (GM, white matter (WM), and lateral ventricles (LV)) was also performed using SIENAX. A paired samples t test was applied to test the significance of DICE value differences between the thalamic manual and automatic segmentations of both enhanced and unenhanced T1 images. RESULTS: Significant differences (FSL-Anat 1.474% p < 0.001 and volBrain 1.990% p < 0.001) in DICE between thalamic manual and automatic segmentations on both enhanced and unenhanced images were observed. Automatic tissue segmentation showed a mean DICE of 81.5%, with LV having the lowest DICE value (74.2%). When compared to tissue segmentations, automatic thalamic segmentations by FSL-Anat or volBrain demonstrated a higher degree of similitude (FSL-Anat = 91.7% and volBrain = 90.7%). CONCLUSION: Gadolinium has a significant effect on subcortical GM segmentation. Although significant, the observed subtle changes could be considered acceptable when used for region-based analysis in perfusion or diffusion imaging.

Towards defining muscular regions of interest from axial magnetic resonance imaging with anatomical cross-reference: part II - cervical spine musculature.

BACKGROUND: It has been suggested that the quantification of paravertebral muscle composition and morphology (e.g. size/shape/structure) with magnetic resonance imaging (MRI) has diagnostic, prognostic, and therapeutic potential in contributing to overall musculoskeletal health. If this is to be realised, then consensus towards standardised MRI methods for measuring muscular size/shape/structure are crucial to allow the translation of such measurements towards management of, and hopefully improved health for, those with some musculoskeletal conditions. Following on from an original paper detailing methods for measuring muscles traversing the lumbar spine, we propose new methods based on anatomical cross-reference that strive towards standardising MRI-based quantification of anterior and posterior cervical spine muscle composition. METHODS: In this descriptive technical advance paper we expand our methods from the lumbar spine by providing a detailed examination of regional cervical spine muscle morphology, followed by a comprehensive description of the proposed technique defining muscle ROI from axial MRI. Cross-referencing cervical musculature and vertebral anatomy includes an innovative comparison between axial E12 sheet-plastinates derived from cadaveric material to a series of axial MRIs detailing commonly used sequences. These images are shown at different cervical levels to illustrate differences in regional morphology. The method for defining ROI for both anterior (scalenes group, sternocleidomastoid, longus colli, longus capitis) and posterior (multifidus, semispinalis cervicis, semispinalis capitis, splenius capitis) cervical muscles is then described and discussed in relation to existing literature. RESULTS: A series of steps towards standardising the quantification of cervical spine muscle quality are described, with concentration on the measurement of muscle volume and fatty infiltration (MFI). We offer recommendations for imaging parameters that should additionally inform a priori decisions when planning investigations of cervical muscle tissues with MRI. CONCLUSIONS: The proposed method provides an option rather than a final position for quantifying cervical spine muscle composition and morphology using MRI. We intend to stimulate discussion towards establishing measurement consensus whereby data-pooling and meaningful comparisons between imaging studies (primarily MRI) investigating cervical muscle quality becomes available and the norm.

Development of a histologically validated segmentation protocol for the hippocampal body.

BACKGROUND: Recent findings have demonstrated that hippocampal subfields can be selectively affected in different disease states, which has led to efforts to segment the human hippocampus with in vivo magnetic resonance imaging (MRI). However, no studies have examined the histological accuracy of subfield segmentation protocols. The presence of MRI-visible anatomical landmarks with known correspondence to histology represents a fundamental prerequisite for in vivo hippocampal subfield segmentation. In the present study, we aimed to: 1) develop a novel method for hippocampal body segmentation, based on two MRI-visible anatomical landmarks (stratum lacunosum moleculare [SLM] & dentate gyrus [DG]), and assess its accuracy in comparison to the gold standard direct histological measurements; 2) quantify the accuracy of two published segmentation strategies in comparison to the histological gold standard; and 3) apply the novel method to ex vivo MRI and correlate the results with histology. METHODS: Ultra-high resolution ex vivo MRI was performed on six whole cadaveric hippocampal specimens, which were then divided into 22 blocks and histologically processed. The hippocampal bodies were segmented into subfields based on histological criteria and subfield boundaries and areas were directly measured. A novel method was developed using mean percentage of the total SLM distance to define subfield boundaries. Boundary distances and subfield areas on histology were then determined using the novel method and compared to the gold standard histological measurements. The novel method was then used to determine ex vivo MRI measures of subfield boundaries and areas, which were compared to histological measurements. RESULTS: For direct histological measurements, the mean percentages of total SLM distance were: Subiculum/CA1 = 9.7%, CA1/CA2 = 78.4%, CA2/CA3 = 97.5%. When applied to histology, the novel method provided accurate measures for CA1/CA2 (ICC = 0.93) and CA2/CA3 (ICC = 0.97) boundaries, but not for the Subiculum/CA1 (ICC = -0.04) boundary. Accuracy was poorer using previous techniques for CA1/CA2 (maximum ICC = 0.85) and CA2/CA3 (maximum ICC = 0.88), with the previously reported techniques also performing poorly in defining the Subiculum/CA1 boundary (maximum ICC = 0.00). Ex vivo MRI measurements using the novel method were linearly related to direct measurements of SLM length (r2 = 0.58), CA1/CA2 boundary (r2 = 0.39) and CA2/CA3 boundary (r2 = 0.47), but not for Subiculum/CA1 boundary (r2 = 0.01). Subfield areas measured with the novel method on histology and ex vivo MRI were linearly related to gold standard histological measures for CA1, CA2, and CA3/CA4/DG. CONCLUSIONS: In this initial proof of concept study, we used ex vivo MRI and histology of cadaveric hippocampi to develop a novel segmentation protocol for the hippocampal body. The novel method utilized two anatomical landmarks, SLM & DG, and provided accurate measurements of CA1, CA2, and CA3/CA4/DG subfields in comparison to the gold standard histological measurements. The relationships demonstrated between histology and ex vivo MRI supports the potential feasibility of applying this method to in vivo MRI studies.

Manually defining regions of interest when quantifying paravertebral muscles fatty infiltration from axial magnetic resonance imaging: a proposed method for the lumbar spine with anatomical cross-reference.

BACKGROUND: There is increasing interest in paravertebral muscle composition as a potential prognostic and diagnostic element in lumbar spine health. As a consequence, it is becoming popular to use magnetic resonance imaging (MRI) to examine muscle volume and fatty infiltration in lumbar paravertebral muscles to assess both age-related change and their clinical relevance in low back pain (LBP). A variety of imaging methods exist for both measuring key variables (fat, muscle) and for defining regions of interest, making pooled comparisons between studies difficult and rendering post-production analysis of MRIs confusing. We therefore propose and define a method as an option for use as a standardized MRI procedure for measuring lumbar paravertebral muscle composition, and to stimulate discussion towards establishing consensus for the analysis of skeletal muscle composition amongst clinician researchers. METHOD: In this descriptive methodological study we explain our method by providing an examination of regional lumbar morphology, followed by a detailed description of the proposed technique. Identification of paravertebral muscles and vertebral anatomy includes axial E12 sheet-plastinates from cadaveric material, combined with a series of axial MRIs that encompass sequencing commonly used for investigations of muscle quality (fat-water DIXON, T1-, and T2-weighted) to illustrate regional morphology; these images are shown for L1 and L4 levels to highlight differences in regional morphology. The method for defining regions of interest (ROI) for multifidus (MF), and erector spinae (ES) is then described. RESULTS: Our method for defining ROIs for lumbar paravertebral muscles on axial MRIs is outlined and discussed in relation to existing literature. The method provides a foundation for standardising the quantification of muscle quality that particularly centres on examining fatty infiltration and composition. We provide recommendations relating to imaging parameters that should additionally inform a priori decisions when planning studies examining lumbar muscle tissues with MRI. CONCLUSIONS: We intend this method to provide a platform towards developing and delivering meaningful comparisons between MRI data on lumbar paravertebral muscle quality.

Test-retest reliability of rapid whole body and compartmental fat volume quantification on a widebore 3T MR system in normal-weight, overweight, and obese subjects.

PURPOSE: To measure the test-retest reliability of rapid (<15 min) whole body and visceral fat volume quantification in normal and obese subjects on a widebore 3T MR system and compare it with conventional manual segmentation. MATERIALS AND METHODS: Thirty participants (body mass index [BMI] 20.1-48.6 kg/m2 ) underwent two whole-body magnetic resonance imaging (MRI) examinations on a widebore 3T machine using a 2-point Dixon technique. Phase sensitive reconstruction and intensity inhomogeneity correction produced quantitative datasets of total adipose tissue (TAT), abdominal subcutaneous adipose tissue (ASAT), and visceral adipose tissue (VAT). The quantification was performed automatically using nonrigid atlas-based segmentation and compared with manual segmentation (SliceOmatic). RESULTS: The mean TAT was 31.74 L with a coefficient of variation (CV) of 0.79% and a coefficient of repeatability (CR) of 0.49 L. The ASAT was 7.92 L with a CV of 2.98% and a CR of 0.46 L. There was no significant difference in the semiautomated and manually segmented VAT (P = 0.73) but there were differences in the reliability of the two techniques. The mean semiautomated VAT was 2.56 L, CV 1.8%, and CR 0.09 L compared to the mean manually segmented VAT of 3.12 L, where the CV was 6.3% and the CR was 0.39 L. CONCLUSION: Rapid semiautomated whole body and compartmental fat volume quantification can be derived from a widebore 3T system, for a range of body sizes including obese patients, with "almost perfect" test-retest reliability. J. Magn. Reson. Imaging 2016;44:1464-1473.

Effects of age and Alzheimer's disease on hippocampal subfields: comparison between manual and FreeSurfer volumetry.

Growing interest has developed in hippocampal subfield volumetry over the past few years and an increasing number of studies use the automatic segmentation algorithm implemented in FreeSurfer. However, this approach has not been validated on standard resolution T1-weighted magnetic resonance (MR) as used in most studies. We aimed at comparing hippocampal subfield segmentation using FreeSurfer on standard T1-weighted images versus manual delineation on dedicated high-resolution hippocampal scans. Hippocampal subfields were segmented in 133 individuals including 98 cognitively normal controls aged 19-84 years, 17 mild cognitive impairment and 18 Alzheimer's disease (AD) patients using both methods. Intraclass correlation coefficients (ICC) and Bland-Altman plots were computed to assess the consistency between both methods, and the effects of age and diagnosis were assessed from both measures. Low to moderate ICC (0.31-0.74) were found for the subiculum and other subfields as well as for the whole hippocampus, and the correlations were very low for cornu ammonis (CA)1 (<0.1). FreeSurfer CA1 volume estimates were found to be much lower than those obtained from manual segmentation, and this bias was proportional to the volume of this structure so that no effect of age or AD could be detected on FreeSurfer CA1 volumes. This study points to the differences in the anatomic definition of the subfields between FreeSurfer and manual delineation, especially for CA1, and provides clue for improvement of this automatic technique for potential clinical application on standard T1-weighted MR.

Volumetric alterations in the nucleus accumbens and caudate nucleus in bulimia nervosa: a structural magnetic resonance imaging study.

OBJECTIVE: Bulimia nervosa (BN) is an eating disorder characterized by recurrent episodes of binge eating and inappropriate compensatory behaviors (such as purging, fasting, or excessive exercise) to prevent weight gain. BN has been associated with deficits in inhibitory control processes. The basal ganglia specifically, the nucleus accumbens (NAc) and the caudate nucleus (CN) are part of the frontostriatal circuits involved in inhibitory control. The main goal of this study was to investigate the presence of morphological alterations in the NAc and the CN in a sample of patients diagnosed with BN. METHOD: Forty-one female participants, 21 diagnosed with BN and 20 healthy matched controls (HC), underwent a structural magnetic resonance imaging (MRI) acquisition and clinical assessment. The NAc and the CN were manually segmented using the software Slicer 3D. RESULTS: The results reveal a significant volumetric decrease in the CN and a preserved NAc volume in BN compared to the control group. DISCUSSION: These findings suggest a contributory role of the caudate nucleus part of the dorsal striatum in the psychopathology of BN.

The EADC-ADNI Harmonized Protocol for manual hippocampal segmentation on magnetic resonance: evidence of validity.

BACKGROUND: An international Delphi panel has defined a harmonized protocol (HarP) for the manual segmentation of the hippocampus on MR. The aim of this study is to study the concurrent validity of the HarP toward local protocols, and its major sources of variance. METHODS: Fourteen tracers segmented 10 Alzheimer's Disease Neuroimaging Initiative (ADNI) cases scanned at 1.5 T and 3T following local protocols, qualified for segmentation based on the HarP through a standard web-platform and resegmented following the HarP. The five most accurate tracers followed the HarP to segment 15 ADNI cases acquired at three time points on both 1.5 T and 3T. RESULTS: The agreement among tracers was relatively low with the local protocols (absolute left/right ICC 0.44/0.43) and much higher with the HarP (absolute left/right ICC 0.88/0.89). On the larger set of 15 cases, the HarP agreement within (left/right ICC range: 0.94/0.95 to 0.99/0.99) and among tracers (left/right ICC range: 0.89/0.90) was very high. The volume variance due to different tracers was 0.9% of the total, comparing favorably to variance due to scanner manufacturer (1.2), atrophy rates (3.5), hemispheric asymmetry (3.7), field strength (4.4), and significantly smaller than the variance due to atrophy (33.5%, P < .001), and physiological variability (49.2%, P < .001). CONCLUSIONS: The HarP has high measurement stability compared with local segmentation protocols, and good reproducibility within and among human tracers. Hippocampi segmented with the HarP can be used as a reference for the qualification of human tracers and automated segmentation algorithms.

Delphi definition of the EADC-ADNI Harmonized Protocol for hippocampal segmentation on magnetic resonance.

BACKGROUND: This study aimed to have international experts converge on a harmonized definition of whole hippocampus boundaries and segmentation procedures, to define standard operating procedures for magnetic resonance (MR)-based manual hippocampal segmentation. METHODS: The panel received a questionnaire regarding whole hippocampus boundaries and segmentation procedures. Quantitative information was supplied to allow evidence-based answers. A recursive and anonymous Delphi procedure was used to achieve convergence. Significance of agreement among panelists was assessed by exact probability on Fisher's and binomial tests. RESULTS: Agreement was significant on the inclusion of alveus/fimbria (P = .021), whole hippocampal tail (P = .013), medial border of the body according to visible morphology (P = .0006), and on this combined set of features (P = .001). This definition captures 100% of hippocampal tissue, 100% of Alzheimer's disease-related atrophy, and demonstrated good reliability on preliminary intrarater (0.98) and inter-rater (0.94) estimates. DISCUSSION: Consensus was achieved among international experts with respect to hippocampal segmentation using MR resulting in a harmonized segmentation protocol.