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Test-retest reliability of freesurfer measurements within and between sites: Effects of visual approval process

Published on Sep 1, 2015in Human Brain Mapping 4.55
· DOI :10.1002/hbm.22856
Zafer Iscan7
Estimated H-index: 7
(HSE: National Research University – Higher School of Economics),
Tony B. Jin3
Estimated H-index: 3
(SBU: Stony Brook University)
+ 17 AuthorsChristine DeLorenzo16
Estimated H-index: 16
(SBU: Stony Brook University)
Cite
Abstract
In the last decade, many studies have used automated processes to analyze magnetic resonance imaging (MRI) data such as cortical thickness, which is one indicator of neuronal health. Due to the convenience of image processing software (e.g., FreeSurfer), standard practice is to rely on automated results without performing visual inspection of intermediate processing. In this work, structural MRIs of 40 healthy controls who were scanned twice were used to determine the test–retest reliability of FreeSurfer-derived cortical measures in four groups of subjects—those 25 that passed visual inspection (approved), those 15 that failed visual inspection (disapproved), a combined group, and a subset of 10 subjects (Travel) whose test and retest scans occurred at different sites. Test–retest correlation (TRC), intraclass correlation coefficient (ICC), and percent difference (PD) were used to measure the reliability in the Destrieux and Desikan–Killiany (DK) atlases. In the approved subjects, reliability of cortical thickness/surface area/volume (DK atlas only) were: TRC (0.82/0.88/0.88), ICC (0.81/0.87/0.88), PD (0.86/1.19/1.39), which represent a significant improvement over these measures when disapproved subjects are included. Travel subjects’ results show that cortical thickness reliability is more sensitive to site differences than the cortical surface area and volume. To determine the effect of visual inspection on sample size required for studies of MRI-derived cortical thickness, the number of subjects required to show group differences was calculated. Significant differences observed across imaging sites, between visually approved/disapproved subjects, and across regions with different sizes suggest that these measures should be used with caution. Hum Brain Mapp 36:3472–3485, 2015. © 2015 Wiley Periodicals, Inc.
  • References (47)
  • Citations (36)
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References47
Newest
Published on Mar 1, 2015in NeuroImage 5.81
Franziskus Liem13
Estimated H-index: 13
(UZH: University of Zurich),
Susan Mérillat12
Estimated H-index: 12
(UZH: University of Zurich)
+ 4 AuthorsLutz Jäncke78
Estimated H-index: 78
Abstract FreeSurfer is a tool to quantify cortical and subcortical brain anatomy automatically and noninvasively. Previous studies have reported reliability and statistical power analyses in relatively small samples or only selected one aspect of brain anatomy. Here, we investigated reliability and statistical power of cortical thickness, surface area, volume, and the volume of subcortical structures in a large sample (N = 189) of healthy elderly subjects (64 + years). Reliability (intraclass co...
Published on Oct 1, 2014in NeuroImage 5.81
Nicholas J. Tustison23
Estimated H-index: 23
(UVA: University of Virginia),
Philip A. Cook23
Estimated H-index: 23
(UPenn: University of Pennsylvania)
+ 8 AuthorsJames C. Gee58
Estimated H-index: 58
(UPenn: University of Pennsylvania)
Abstract Many studies of the human brain have explored the relationship between cortical thickness and cognition, phenotype, or disease. Due to the subjectivity and time requirements in manual measurement of cortical thickness, scientists have relied on robust software tools for automation which facilitate the testing and refinement of neuroscientific hypotheses. The most widely used tool for cortical thickness studies is the publicly available, surface-based FreeSurfer package. Critical to the ...
Published on Jul 1, 2014in Developmental Cognitive Neuroscience 4.92
Kathryn L. Mills16
Estimated H-index: 16
(UCL: University College London),
Christian K. Tamnes31
Estimated H-index: 31
(University of Oslo)
Magnetic resonance imaging (MRI) has allowed the unprecedented capability to measure the human brain in vivo. This technique has paved the way for longitudinal studies exploring brain changes across the entire life span. Results from these studies have given us a glimpse into the remarkably extended and multifaceted development of our brain, converging with evidence from anatomical and histological studies. Ever-evolving techniques and analytical methods provide new avenues to explore and questi...
Published on Jun 18, 2014in The Journal of Neuroscience 6.07
Andreas Berg Storsve13
Estimated H-index: 13
,
Anders M. Fjell55
Estimated H-index: 55
(Oslo University Hospital)
+ 4 AuthorsKristine B. Walhovd55
Estimated H-index: 55
(Oslo University Hospital)
Human cortical thickness and surface area are genetically independent, emerge through different neurobiological events during development, and are sensitive to different clinical conditions. However, the relationship between changes in the two over time is unknown. Additionally, longitudinal studies have almost invariably been restricted to older adults, precluding the delineation of adult life span trajectories of change in cortical structure. In this longitudinal study, we investigated changes...
Published on Dec 1, 2013in American Journal of Psychiatry 13.65
Philip van Eijndhoven11
Estimated H-index: 11
,
Guido van Wingen34
Estimated H-index: 34
+ 5 AuthorsIndira Tendolkar36
Estimated H-index: 36
ObjectiveImpaired mood regulation is a key deficit of major depressive disorder that is primarily mediated by an interaction between the paralimbic cortex (i.e., orbitofrontal, cingulate, insular, parahippocampal, and temporopolar cortices) and limbic regions. The authors investigated whether depressed patients and healthy comparison subjects have differences in cortical thickness in the paralimbic cortex and whether potential differences are evident only during a depressive state or are trait r...
Published on Dec 1, 2013in NeuroImage 5.81
Jorge Jovicich23
Estimated H-index: 23
(University of Trento),
Moira Marizzoni11
Estimated H-index: 11
+ 24 AuthorsFlavio Nobili47
Estimated H-index: 47
(UniGe: University of Genoa)
Abstract Large-scale longitudinal multi-site MRI brain morphometry studies are becoming increasingly crucial to characterize both normal and clinical population groups using fully automated segmentation tools. The test–retest reproducibility of morphometry data acquired across multiple scanning sessions, and for different MR vendors, is an important reliability indicator since it defines the sensitivity of a protocol to detect longitudinal effects in a consortium. There is very limited knowledge...
Published on Jan 24, 2013in PLOS ONE 2.78
Javier Pagonabarraga29
Estimated H-index: 29
(Autonomous University of Barcelona),
Idoia Corcuera-Solano2
Estimated H-index: 2
+ 6 AuthorsBeatriz Gómez-Ansón22
Estimated H-index: 22
Background Dementia is a frequent and devastating complication in Parkinson’s disease (PD). There is an intensive search for biomarkers that may predict the progression from normal cognition (PD-NC) to dementia (PDD) in PD. Mild cognitive impairment in PD (PD-MCI) seems to represent a transitional state between PD-NC and PDD. Few studies have explored the structural changes that differentiate PD-NC from PD-MCI and PDD patients.
Published on Sep 18, 2012in PLOS ONE 2.78
Lucas D. Eggert4
Estimated H-index: 4
(University of Osnabrück),
Jens Sommer23
Estimated H-index: 23
+ 2 AuthorsCarsten Konrad41
Estimated H-index: 41
Automated gray matter segmentation of magnetic resonance imaging data is essential for morphometric analyses of the brain, particularly when large sample sizes are investigated. However, although detection of small structural brain differences may fundamentally depend on the method used, both accuracy and reliability of different automated segmentation algorithms have rarely been compared. Here, performance of the segmentation algorithms provided by SPM8, VBM8, FSL and FreeSurfer was quantified ...
Published on Jul 1, 2012in NeuroImage 5.81
Martin Reuter53
Estimated H-index: 53
(MIT: Massachusetts Institute of Technology),
Nicholas J. Schmansky6
Estimated H-index: 6
(Harvard University)
+ 1 AuthorsBruce Fischl92
Estimated H-index: 92
(MIT: Massachusetts Institute of Technology)
Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders. Furthermore, there is a growing appreciation of the potential utility of longitudinally acquired structural images and reliable image processing to evaluate disease modifying therapies. Challenges have been related to the variability that is inherent in the available cross-sectional processing tools, to the introduction of bias in longitudinal processing and to poten...
Published on Jun 1, 2012in Psychiatry Research-neuroimaging 2.21
Pei-Chi Tu15
Estimated H-index: 15
(NYMU: National Yang-Ming University),
Li-Fen Chen19
Estimated H-index: 19
(NYMU: National Yang-Ming University)
+ 3 AuthorsTung-Ping Su32
Estimated H-index: 32
(NYMU: National Yang-Ming University)
Abstract This study uses surfaced-based morphometry to investigate cortical thinning and its functional correlates in patients with major depressive disorder (MDD). Subjects with MDD ( N =36) and healthy control subjects ( N =36) were enrolled in the study. Each subject received T1 structural magnetic resonance imaging (MRI), clinical evaluations, and neuropsychological examinations of executive functions with the Color Trail Test (CTT) and the Wisconsin Card Sorting Test (WCST). This study used...
Cited By36
Newest
Published on Jan 28, 2019in BMC Bioinformatics 2.51
Shadia Mikhael2
Estimated H-index: 2
(Edin.: University of Edinburgh),
Cyril Pernet30
Estimated H-index: 30
(Edin.: University of Edinburgh)
Background Cortical parcellation is an essential neuroimaging tool for identifying and characterizing morphometric and connectivity brain changes occurring with age and disease. A variety of software packages have been developed for parcellating the brain’s cortical surface into a variable number of regions but interpackage differences can undermine reproducibility. Using a ground truth dataset (Edinburgh_NIH10), we investigated such differences for grey matter thickness (GMth), grey matter volu...
Published on Jun 20, 2019in bioRxiv
Iván Vila Álvarez10
Estimated H-index: 10
(University of Oxford),
Andrew Parker41
Estimated H-index: 41
(University of Oxford),
Holly Bridge26
Estimated H-index: 26
(University of Oxford)
Studies of changes in cerebral neocortical thickness often rely on small control samples for comparison with specific populations with abnormal visual systems. We present a normative dataset for FreeSurfer-derived cortical thickness across 25 human visual areas derived from 960 participants in the Human Connectome Project. Cortical thickness varies systematically across visual areas, in broad agreement with canonical visual system hierarchies in the dorsal and ventral pathways. In addition, cort...
Published on Jun 18, 2018in Brain Imaging and Behavior 3.42
Alejandro D. Meruelo7
Estimated H-index: 7
(UCSD: University of California, San Diego),
Joanna Jacobus25
Estimated H-index: 25
(UCSD: University of California, San Diego)
+ 3 AuthorsSusan F. Tapert63
Estimated H-index: 63
(UCSD: University of California, San Diego)
Academic performance in adolescence strongly influences adult prospects. Intelligence quotient (IQ) has historically been considered a strong predictor of academic performance. Less objectively explored have been morphometric features. We analyzed brain MRI morphometry metrics in early adolescence (age 12–14 years) as quantitative predictors of academic performance over high school using a naive Bayesian classifier approach with n = 170 subjects. Based on the mean GPA, subjects were divided into...
Published on Jan 1, 2019in Frontiers in Human Neuroscience 2.87
Fuchun Lin16
Estimated H-index: 16
,
Guangyao Wu7
Estimated H-index: 7
(WHU: Wuhan University)
+ 1 AuthorsHao Lei30
Estimated H-index: 30
Insula plays an essential role in maintaining the addiction to cigarette smoking and smoking-related alterations on the insular volume and density have been reported in smokers. However, less is known about the effects of chronic cigarette smoking on the insular cortical thickness. In this study, we explored the region-specific changes of insular cortical thickness in heavy smokers and their relations with smoking-related variables. Thirty-seven heavy smokers (29 males; mean age 47.19±7.22 years...
Published on Jun 10, 2019in bioRxiv
Lei Ai3
Estimated H-index: 3
(MIND Institute),
R. Cameron Craddock29
Estimated H-index: 29
(University of Texas at Austin)
+ 4 AuthorsAlexandre R. Franco (Nathan Kline Institute for Psychiatric Research)
New large neuroimaging studies, such as the ABCD and HCP Development studies are adopting a new T1-weighted imaging sequence with volumetric navigators (vNav) in favor of the more traditional 3-Dimensional Magnetization-Prepared Rapid Gradient-Echo Imaging (MPRAGE) sequence. In this study, we used a dataset of children (ages 5-21, N=366) from the Healthy Brian Network Initiative and directly compared the MPRAGE and vNav sequences to determine if the morphometric measurements obtained from both p...
Published on May 1, 2019in Biological Psychiatry 11.50
Elizabeth Bartlett2
Estimated H-index: 2
,
Daniel N. Klein72
Estimated H-index: 72
+ 3 AuthorsGreg Perlman12
Estimated H-index: 12
Abstract Background Evidence supports the notion that early-life stress and trauma impact cortical development and increase vulnerability to depression. However, it remains unclear whether common stressful life events in community-dwelling adolescents have similar consequences for cortical development. Methods A total of 232 adolescent girls (mean age 15.29 ± 0.65 years) were assessed with the Stressful Life Events Schedule (a semistructured interview of stressors in the previous 9 months) and u...
Published on Apr 3, 2019in Psychophysiology 3.38
Lauren Delaparte4
Estimated H-index: 4
(SBU: Stony Brook University),
Elizabeth Bartlett2
Estimated H-index: 2
(SBU: Stony Brook University)
+ 5 AuthorsRoman Kotov36
Estimated H-index: 36
(SBU: Stony Brook University)
Published on Mar 18, 2019in Frontiers in Neuroinformatics 2.68
Andrei Irimia20
Estimated H-index: 20
(SC: University of Southern California),
Alexander S. Maher (SC: University of Southern California)+ 3 AuthorsE Meng Law (SC: University of Southern California)
When properly implemented and processed, anatomic T1-weighted magnetic resonance imaging (MRI) can be ideal for the noninvasive quantification of white matter (WM) and gray matter (GM) in the living human brain. Although MRI is more suitable for distinguishing GM from WM than computed tomography (CT), the growing clinical use of the latter technique has renewed interest in head CT segmentation. Such interest is particularly strong in settings where MRI is unavailable, logistically unfeasible or ...
Published on Jan 1, 2019in NeuroImage 5.81
Martin P. Paulus76
Estimated H-index: 76
(UCSD: University of California, San Diego),
Lindsay M. Squeglia22
Estimated H-index: 22
(MUSC: Medical University of South Carolina)
+ 8 AuthorsHauke Bartsch16
Estimated H-index: 16
(UCSD: University of California, San Diego)
Abstract The adolescent brain undergoes profound structural changes which is influenced by many factors. Screen media activity (SMA; e.g., watching television or videos, playing video games, or using social media) is a common recreational activity in children and adolescents; however, its effect on brain structure is not well understood. A multivariate approach with the first cross-sectional data release from the Adolescent Brain Cognitive Development (ABCD) study was used to test the maturation...