Test-retest of automated segmentation with different motion correction strategies: A comparison of prospective versus retrospective methods.
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ABSTRACT:
SUBMITTER: Kecskemeti SR
PROVIDER: S-EPMC7056555 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A test-retest study of FreeSurfer derived cortical thickness, cortical surface area, and cortical volume, as well as quantitative R1 relaxometry assessed on the midpoint of the cortex, was performed on a cohort of pediatric subjects (6-12 years old) scanned without sedation using SNARE-MPnRAGE (self navigated retrospective motion corrected magnetization prepared with n rapid gradient echoes) imaging. Reliability was assessed with coefficients of variation (CoVs) and intraclass correlation coefficients (ICCs) and statistical tests were used to determine differences with and without SNARE motion correction. Comparison of the test-retest measures of SNARE-MPnRAGE with prospectively motion corrected PROMO MPRAGE were also performed. When SNARE motion correction was used all parameters had statistically significant improvements and demonstrated high reliability. Reliability varied depending on parameter, region, and measurement type (vertex or region of interest). For mean thickness/surface area/volume/mean R1 across the regions of FreeSurfer's DK Atlas, the mean CoVs (% x100) were (1.2/1.6/1.9/0.9) and the mean ICCs were (0.88/0.96/0.94/0.83). When assessed on a per-vertex basis, the CoVs and ICCs for thickness/R1 had mean values of (2.9/1.9) and (0.82/0.68) across the regions of the DK Atlas. Retrospectively motion corrected MPnRAGE had significantly lower CoVs and higher ICCs for the morphological measures than PROMO MPRAGE. Motion correction effectively removed motion related biases in nearly all regions for R1 and morphometric measures.
| S-EPMC8525331 | biostudies-literature
Project description:IntroductionThe increasing use of large sample sizes for population and personalized medicine requires high-throughput tools for imaging processing that can handle large amounts of data with diverse image modalities, perform a biologically meaningful information reduction, and result in comprehensive quantification. Exploring the reproducibility of these tools reveals the specific strengths and weaknesses that heavily influence the interpretation of results, contributing to transparence in science.MethodsWe tested-retested the reproducibility of MRICloud, a free automated method for whole-brain, multimodal MRI segmentation and quantification, on two public, independent datasets of healthy adults.ResultsThe reproducibility was extremely high for T1-volumetric analysis, high for diffusion tensor images (DTI) (however, regionally variable), and low for resting-state fMRI.ConclusionIn general, the reproducibility of the different modalities was slightly superior to that of widely used software. This analysis serves as a normative reference for planning samples and for the interpretation of structure-based MRI studies.
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Project description:Long acquisition times due to intrinsically low signal-to-noise ratio and the need for highly homogeneous B0 field make MRS particularly susceptible to motion or scanner instability compared with MRI. Motion-induced changes in both localization and shimming (ie B0 homogeneity) degrade MRS data quality. To mitigate the effects of motion three approaches can be employed: (1) subject immobilization, (2) retrospective correction, and (3) prospective real-time correction using internal and/or external tracking methods. Prospective real-time correction methods can simultaneously update localization and the B0 field to improve MRS data quality. While localization errors can be corrected with both internal (navigators) and external (optical camera, NMR probes) tracking methods, the B0 field correction requires internal navigator methods to measure the B0 field inside the imaged volume and the possibility to update the scanner shim hardware in real time. Internal and external tracking can rapidly update the MRS localization with submillimeter and subdegree precision, while scanner frequency and first-order shims of scanner hardware can be updated by internal methods every sequence repetition. These approaches are most well developed for neuroimaging, for which rigid transformation is primarily applicable. Real-time correction greatly improves the stability of MRS acquisition and quantification, as shown in clinical studies on subjects prone to motion, including children and patients with movement disorders, enabling robust measurement of metabolite signals including those with low concentrations, such as gamma-aminobutyric acid and glutathione. Thus, motion correction is recommended for MRS users and calls for tighter integration and wider availability of such methods by MR scanner manufacturers.
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Project description:Fully automated vehicles (AVs) hold promise toward providing numerous societal benefits including reducing road fatalities. However, we are uncertain about how individuals' perceptions will influence their ability to accept and adopt AVs. The 28-item Automated Vehicle User Perception Survey (AVUPS) is a visual analog scale that was previously constructed, with established face and content validity, to assess individuals' perceptions of AVs. In this study, we examined construct validity, via exploratory factor analysis and subsequent Mokken scale analyses. Next, internal consistency was assessed via Cronbach's alpha (α) and 2-week test-retest reliability was assessed via Spearman's rho (ρ) and intraclass correlation coefficient (ICC). The Mokken scale analyses resulted in a refined 20-item AVUPS and three Mokken subscales assessing specific domains of adults' perceptions of AVs: (a) Intention to use; (b) perceived barriers; and (c) well-being. The Mokken scale analysis showed that all item-coefficients of homogeneity (H) exceeded 0.3, indicating that the items reflect a single latent variable. The AVUPS indicated a strong Mokken scale (H scale = 0.51) with excellent internal consistency (α = 0.95) and test-retest reliability (ρ = 0.76, ICC = 0.95). Similarly, the three Mokken subscales ranged from moderate to strong (range H scale = 0.47-0.66) and had excellent internal consistency (range α = 0.84-0.94) and test-retest reliability (range ICC = 0.84-0.93). The AVUPS and three Mokken subscales of AV acceptance were validated in a moderate sample size (N = 312) of adults living in the United States. Two-week test-retest reliability was established using a subset of Amazon Mechanical Turk participants (N = 84). The AVUPS, or any combination of the three subscales, can be used to validly and reliably assess adults' perceptions before and after being exposed to AVs. The AVUPS can be used to quantify adults' acceptance of fully AVs.
| S-EPMC7868437 | biostudies-literature
Project description:PurposeManagement of vestibular schwannoma (VS) is based on tumour size as observed on T1 MRI scans with contrast agent injection. The current clinical practice is to measure the diameter of the tumour in its largest dimension. It has been shown that volumetric measurement is more accurate and more reliable as a measure of VS size. The reference approach to achieve such volumetry is to manually segment the tumour, which is a time intensive task. We suggest that semi-automated segmentation may be a clinically applicable solution to this problem and that it could replace linear measurements as the clinical standard.MethodsUsing high-quality software available for academic purposes, we ran a comparative study of manual versus semi-automated segmentation of VS on MRI with 5 clinicians and scientists. We gathered both quantitative and qualitative data to compare the two approaches; including segmentation time, segmentation effort and segmentation accuracy.ResultsWe found that the selected semi-automated segmentation approach is significantly faster (167 s vs 479 s, [Formula: see text]), less temporally and physically demanding and has approximately equal performance when compared with manual segmentation, with some improvements in accuracy. There were some limitations, including algorithmic unpredictability and error, which produced more frustration and increased mental effort in comparison with manual segmentation.ConclusionWe suggest that semi-automated segmentation could be applied clinically for volumetric measurement of VS on MRI. In future, the generic software could be refined for use specifically for VS segmentation, thereby improving accuracy.
| S-EPMC7419453 | biostudies-literature
Project description:Accurate and reproducible automated segmentation of human hippocampal subfields is of interest to study their roles in cognitive functions and disease processes. Multispectral structural MRI methods have been proposed to improve automated hippocampal subfield segmentation accuracy, but the reproducibility in a multicentric setting is, to date, not well characterized. Here, we assessed test-retest reproducibility of FreeSurfer 6.0 hippocampal subfield segmentations using multispectral MRI analysis pipelines (22 healthy subjects scanned twice, a week apart, at four 3T MRI sites). The harmonized MRI protocol included two 3D-T1, a 3D-FLAIR, and a high-resolution 2D-T2. After within-session T1 averaging, subfield volumes were segmented using three pipelines with different multispectral data: two longitudinal ("long_T1s" and "long_T1s_FLAIR") and one cross-sectional ("long_T1s_FLAIR_crossT2"). Volume reproducibility was quantified in magnitude (reproducibility error-RE) and space (DICE coefficient). RE was lower in all hippocampal subfields, except for hippocampal fissure, using the longitudinal pipelines compared to long_T1s_FLAIR_crossT2 (average RE reduction of 0.4-3.6%). Similarly, the longitudinal pipelines showed a higher spatial reproducibility (1.1-7.8% of DICE improvement) in all hippocampal structures compared to long_T1s_FLAIR_crossT2. Moreover, long_T1s_FLAIR provided a small but significant RE improvement in comparison to long_T1s (p = 0.015), whereas no significant DICE differences were found. In addition, structures with volumes larger than 200 mm3 had better RE (1-2%) and DICE (0.7-0.95) than smaller structures. In summary, our study suggests that the most reproducible hippocampal subfield FreeSurfer segmentations are derived from a longitudinal pipeline using 3D-T1s and 3D-FLAIR. Adapting a longitudinal pipeline to include high-resolution 2D-T2 may lead to further improvements.
| S-EPMC7817563 | biostudies-literature
Project description:We compare three widely used brain volumetry methods available in the software packages FSL, SPM5, and FreeSurfer and evaluate their performance using simulated and real MR brain data sets. We analyze the accuracy of gray and white matter volume measurements and their robustness against changes of image quality using the BrainWeb MRI database. These images are based on "gold-standard" reference brain templates. This allows us to assess between- (same data set, different method) and also within-segmenter (same method, variation of image quality) comparability, for both of which we find pronounced variations in segmentation results for gray and white matter volumes. The calculated volumes deviate up to >10% from the reference values for gray and white matter depending on method and image quality. Sensitivity is best for SPM5, volumetric accuracy for gray and white matter was similar in SPM5 and FSL and better than in FreeSurfer. FSL showed the highest stability for white (<5%), FreeSurfer (6.2%) for gray matter for constant image quality BrainWeb data. Between-segmenter comparisons show discrepancies of up to >20% for the simulated data and 24% on average for the real data sets, whereas within-method performance analysis uncovered volume differences of up to >15%. Since the discrepancies between results reach the same order of magnitude as volume changes observed in disease, these effects limit the usability of the segmentation methods for following volume changes in individual patients over time and should be taken into account during the planning and analysis of brain volume studies.
| S-EPMC6870639 | biostudies-literature
Project description:PurposePatient motion during PET acquisition may affect measured time-activity curves, thereby reducing accuracy of tracer kinetic analyses. The aim of the present study was to evaluate different off-line frame-by-frame methods to correct patient motion, which is of particular interest when no optical motion tracking system is available or when older data sets have to be reanalysed.MethodsFour different motion correction methods were evaluated. In the first method attenuation-corrected frames were realigned with the summed image of the first 3 min. The second method was identical, except that non-attenuation-corrected images were used. In the third and fourth methods non-attenuation-corrected images were realigned with standard and cupped transmission images, respectively. Two simulation studies were performed, based on [11C]flumazenil and (R)-[11C]PK11195 data sets, respectively. For both simulation studies different types (rotational, translational) and degrees of motion were added. Simulated PET scans were corrected for motion using all correction methods. The optimal method derived from these simulation studies was used to evaluate two (one with and one without visible movement) clinical data sets of [11C]flumazenil, (R)-[11C]PK11195 and [11C]PIB. For these clinical data sets, the volume of distribution (VT) was derived using Logan analysis and values were compared before and after motion correction.ResultsFor both [11C]flumazenil and (R)-[11C]PK11195 simulation studies, optimal results were obtained when realignment was based on non-attenuation-corrected images. For the clinical data sets motion disappeared visually after motion correction. Regional differences of up to 433% in VT before and after motion correction were found for scans with visible movement. On the other hand, when no visual motion was present in the original data set, overall differences in VT before and after motion correction were <1.5 ± 1.3%.ConclusionFrame-by-frame motion correction using non-attenuation-corrected images improves the accuracy of tracer kinetic analysis compared to non-motion-corrected data. Electronic supplementary material The online version of this article (doi:10.1007/s00259-009-1193-y) contains supplementary material, which is available to authorised users.
| S-EPMC2779434 | biostudies-literature
Project description:Visibility graphs provide a novel approach for analysing time-series data. Graph theoretical analysis of visibility graphs can provide new features for data mining applications in fMRI. However, visibility graphs features have not been used widely in the field of neuroscience. This is likely due to a lack of understanding of their robustness in the presence of noise (e.g., motion) and their test-retest reliability. In this study, we investigated visibility graph properties of fMRI data in the human connectome project (N = 1010) and tested their sensitivity to motion and test-retest reliability. We also characterised the strength of connectivity obtained using degree synchrony of visibility graphs. We found that strong correlation (r > 0.5) between visibility graph properties, such as the number of communities and average degrees, and motion in the fMRI data. The test-retest reliability (Intraclass correlation coefficient (ICC)) of graph theoretical features was high for the average degrees (0.74, 95% CI = [0.73, 0.75]), and moderate for clustering coefficient (0.43, 95% CI = [0.41, 0.44]) and average path length (0.41, 95% CI = [0.38, 0.44]). Functional connectivity between brain regions was measured by correlating the visibility graph degrees. However, the strength of correlation was found to be moderate to low (r < 0.35). These findings suggest that even small movement in fMRI data can strongly influence robustness and reliability of visibility graph features, thus, requiring robust motion correction strategies prior to data analysis. Further studies are necessary for better understanding of the potential application of visibility graph features in fMRI.
| S-EPMC11021232 | biostudies-literature
Project description:Objective:To study the automated segmentation of retinal layers using spectral domain optical coherence tomography (OCT) and the impact of manual correction over segmentation mistakes. Methods:This was a retrospective, cross-sectional, comparative study that compared the automated segmentation of macular thickness using Spectralis™ OCT technology (Heidelberg Engineering, Heidelberg, Germany) versus manual segmentation in eyes with no macular changes, macular cystoid edema (CME), and choroidal neovascularization (CNV). Automated segmentation of macular thickness was manually corrected by two independent examiners and reanalyzed by them together in case of disagreement. Results:In total, 306 eyes of 254 consecutive patients were evaluated. No statistically significant differences were noted between automated and manual macular thickness measurements in patients with normal maculas, while a statistically significant difference was found in central thickness in patients with CNV and with CME. Segmentation mistakes in macular OCTs were present in 5.3% (5 of 95) in the normal macula group, 16.4% (23 of 140) in the CME group, and 66.2% (47 of 71) in CNV group. The difference between automated and manual macular thickness was higher than 10% in 1.4% (2 of 140) in the CME group and in 28.17% (20 of 71) in the CNV group. Only one case in the normal group had a higher than 10% segmentation error (1 of 95). Conclusion:The evaluation of automated segmented OCT images revealed appropriate delimitation of macular thickness in patients with no macular changes or with CME, since the frequency and magnitude of the segmentation mistakes had low impact over clinical evaluation of the images. Conversely, automated macular thickness segmentation in patients with CNV showed a high frequency and magnitude of mistakes, with potential impact on clinical analysis.
| S-EPMC7020356 | biostudies-literature