| 1. |
- Eklund, Anders, 1981-, et al.
(författare)
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Cluster failure revisited: Impact of first level design and physiological noise on cluster false positive rates
- 2019
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 40:7, s. 2017-2032
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Tidskriftsartikel (refereegranskat)abstract
- Methodological research rarely generates a broad interest, yet our work on the validity of cluster inference methods for functional magnetic resonance imaging (fMRI) created intense discussion on both the minutia of our approach and its implications for the discipline. In the present work, we take on various critiques of our work and further explore the limitations of our original work. We address issues about the particular event‐related designs we used, considering multiple event types and randomization of events between subjects. We consider the lack of validity found with one‐sample permutation (sign flipping) tests, investigating a number of approaches to improve the false positive control of this widely used procedure. We found that the combination of a two‐sided test and cleaning the data using ICA FIX resulted in nominal false positive rates for all data sets, meaning that data cleaning is not only important for resting state fMRI, but also for task fMRI. Finally, we discuss the implications of our work on the fMRI literature as a whole, estimating that at least 10% of the fMRI studies have used the most problematic cluster inference method (p = .01 cluster defining threshold), and how individual studies can be interpreted in light of our findings. These additional results underscore our original conclusions, on the importance of data sharing and thorough evaluation of statistical methods on realistic null data.
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| 2. |
- Eklund, Anders, 1981-, et al.
(författare)
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Reply to Chen et al.: Parametric methods for cluster inference perform worse for two‐sided t‐tests
- 2019
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 40:5, s. 1689-1691
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- One‐sided t‐tests are commonly used in the neuroimaging field, but two‐sided tests should be the default unless a researcher has a strong reason for using a one‐sided test. Here we extend our previous work on cluster false positive rates, which used one‐sided tests, to two‐sided tests. Briefly, we found that parametric methods perform worse for two‐sided t‐tests, and that nonparametric methods perform equally well for one‐sided and two‐sided tests.
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| 3. |
- de Almeida Martins, João P., et al.
(författare)
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Computing and visualising intra-voxel orientation-specific relaxation–diffusion features in the human brain
- 2021
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 42:2, s. 310-328
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Tidskriftsartikel (refereegranskat)abstract
- Diffusion MRI techniques are used widely to study the characteristics of the human brain connectome in vivo. However, to resolve and characterise white matter (WM) fibres in heterogeneous MRI voxels remains a challenging problem typically approached with signal models that rely on prior information and constraints. We have recently introduced a 5D relaxation–diffusion correlation framework wherein multidimensional diffusion encoding strategies are used to acquire data at multiple echo-times to increase the amount of information encoded into the signal and ease the constraints needed for signal inversion. Nonparametric Monte Carlo inversion of the resulting datasets yields 5D relaxation–diffusion distributions where contributions from different sub-voxel tissue environments are separated with minimal assumptions on their microscopic properties. Here, we build on the 5D correlation approach to derive fibre-specific metrics that can be mapped throughout the imaged brain volume. Distribution components ascribed to fibrous tissues are resolved, and subsequently mapped to a dense mesh of overlapping orientation bins to define a smooth orientation distribution function (ODF). Moreover, relaxation and diffusion measures are correlated to each independent ODF coordinate, thereby allowing the estimation of orientation-specific relaxation rates and diffusivities. The proposed method is tested on a healthy volunteer, where the estimated ODFs were observed to capture major WM tracts, resolve fibre crossings, and, more importantly, inform on the relaxation and diffusion features along with distinct fibre bundles. If combined with fibre-tracking algorithms, the methodology presented in this work has potential for increasing the depth of characterisation of microstructural properties along individual WM pathways.
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| 4. |
- Fu, Jingru, et al.
(författare)
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Fast three-dimensional image generation for healthy brain aging using diffeomorphic registration
- 2023
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 44:4, s. 1289-1308
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Tidskriftsartikel (refereegranskat)abstract
- Predicting brain aging can help in the early detection and prognosis of neurodegenerative diseases. Longitudinal cohorts of healthy subjects scanned through magnetic resonance imaging (MRI) have been essential to understand the structural brain changes due to aging. However, these cohorts suffer from missing data due to logistic issues in the recruitment of subjects. This paper proposes a methodology for filling up missing data in longitudinal cohorts with anatomically plausible images that capture the subject-specific aging process. The proposed methodology is developed within the framework of diffeomorphic registration. First, two novel modules are introduced within Synthmorph, a fast, state-of-the-art deep learning-based diffeomorphic registration method, to simulate the aging process between the first and last available MRI scan for each subject in three-dimensional (3D). The use of image registration also makes the generated images plausible by construction. Second, we used six image similarity measurements to rearrange the generated images to the specific age range. Finally, we estimated the age of every generated image by using the assumption of linear brain decay in healthy subjects. The methodology was evaluated on 2662 T1-weighted MRI scans from 796 healthy participants from 3 different longitudinal cohorts: Alzheimer's Disease Neuroimaging Initiative, Open Access Series of Imaging Studies-3, and Group of Neuropsychological Studies of the Canary Islands (GENIC). In total, we generated 7548 images to simulate the access of a scan per subject every 6 months in these cohorts. We evaluated the quality of the synthetic images using six quantitative measurements and a qualitative assessment by an experienced neuroradiologist with state-of-the-art results. The assumption of linear brain decay was accurate in these cohorts (R2 ∈ [.924,.940]). The experimental results show that the proposed methodology can produce anatomically plausible aging predictions that can be used to enhance longitudinal datasets. Compared to deep learning-based generative methods, diffeomorphic registration is more likely to preserve the anatomy of the different structures of the brain, which makes it more appropriate for its use in clinical applications. The proposed methodology is able to efficiently simulate anatomically plausible 3D MRI scans of brain aging of healthy subjects from two images scanned at two different time points.
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| 5. |
- Leutritz, Tobias, et al.
(författare)
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Multi-parameter mapping (MPM) of relaxation (R1, R2*), proton density (PD) and magnetization transfer saturation (MT) at 3T: a multi-center dual-vendor reproducibility and repeatability study
- 2020
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 41:15, s. 4232-4247
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Tidskriftsartikel (refereegranskat)abstract
- Multicenter clinical and quantitative magnetic resonance imaging (qMRI) studies require a high degree of reproducibility across different sites and scanner manufacturers, as well as time points. We therefore implemented a multiparameter mapping (MPM) protocol based on vendor's product sequences and demonstrate its repeatability and reproducibility for whole‐brain coverage. Within ~20 min, four MPM metrics (magnetization transfer saturation [MT], proton density [PD], longitudinal [R1], and effective transverse [R2*] relaxation rates) were measured using an optimized 1 mm isotropic resolution protocol on six 3 T MRI scanners from two different vendors. The same five healthy participants underwent two scanning sessions, on the same scanner, at each site. MPM metrics were calculated using the hMRI‐toolbox. To account for different MT pulses used by each vendor, we linearly scaled the MT values to harmonize them across vendors. To determine longitudinal repeatability and inter‐site comparability, the intra‐site (i.e., scan‐rescan experiment) coefficient of variation (CoV), inter‐site CoV, and bias across sites were estimated. For MT, R1, and PD, the intra‐ and inter‐site CoV was between 4 and 10% across sites and scan time points for intracranial gray and white matter. A higher intra‐site CoV (16%) was observed in R2* maps. The inter‐site bias was below 5% for all parameters. In conclusion, the MPM protocol yielded reliable quantitative maps at high resolution with a short acquisition time. The high reproducibility of MPM metrics across sites and scan time points combined with its tissue microstructure sensitivity facilitates longitudinal multicenter imaging studies targeting microstructural changes, for example, as a quantitative MRI biomarker for interventional clinical trials.
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| 6. |
- Steinbart, David, et al.
(författare)
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Automatic and manual segmentation of the piriform cortex: Method development and validation in patients with temporal lobe epilepsy and Alzheimer's disease.
- 2023
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Ingår i: Human brain mapping. - 1065-9471 .- 1097-0193. ; 44:8, s. 3196-3209
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Tidskriftsartikel (refereegranskat)abstract
- The piriform cortex (PC) is located at the junction of the temporal and frontal lobes. It is involved physiologically in olfaction as well as memory and plays an important role in epilepsy. Its study at scale is held back by the absence of automatic segmentation methods on MRI. We devised a manual segmentation protocol for PC volumes, integrated those manually derived images into the Hammers Atlas Database (n=30) and used an extensively validated method (multi-atlas propagation with enhanced registration, MAPER) for automatic PC segmentation. We applied automated PC volumetry to patients with unilateral temporal lobe epilepsy with hippocampal sclerosis (TLE; n=174 including n=58 controls) and to the Alzheimer's Disease Neuroimaging Initiative cohort (ADNI; n=151, of whom with mild cognitive impairment (MCI), n=71; Alzheimer's disease (AD), n=33; controls, n=47). In controls, mean PC volume was 485mm3 on the right and 461mm3 on the left. Automatic and manual segmentations overlapped with a Jaccard coefficient (intersection/union) of ~0.5 and a mean absolute volume difference of ~22mm3 in healthy controls, ~0.40/ ~28mm3 in patients with TLE, and~0.34/~29mm3 in patients with AD. In patients with TLE, PC atrophy lateralised to the side of hippocampal sclerosis (p<.001). In patients with MCI and AD, PC volumes were lower than those of controls bilaterally (p<.001). Overall, we have validated automatic PC volumetry in healthy controls and two types of pathology. The novel finding of early atrophy of PC at the stage of MCI possibly adds a novel biomarker. PC volumetry can now be applied at scale.
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| 7. |
- Coelho, Santiago, et al.
(författare)
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Assessment of precision and accuracy of brain white matter microstructure using combined diffusion MRI and relaxometry
- 2024
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Ingår i: Human Brain Mapping. - 1065-9471. ; 45:9
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Tidskriftsartikel (refereegranskat)abstract
- Joint modeling of diffusion and relaxation has seen growing interest due to its potential to provide complementary information about tissue microstructure. For brain white matter (WM), we designed an optimal diffusion-relaxometry MRI protocol that samples multiple b-values, B-tensor shapes, and echo times (TE). This variable-TE protocol (27 min) has as subsets a fixed-TE protocol (15 min) and a two-shell dMRI protocol (7 min), both characterizing diffusion only. We assessed the sensitivity, specificity, and reproducibility of these protocols with synthetic experiments and in six healthy volunteers. Compared with the fixed-TE protocol, the variable-TE protocol enables estimation of the free water fraction while also capturing compartmental (Formula presented.) relaxation times. Jointly measuring diffusion and relaxation offers increased sensitivity and specificity to microstructure parameters in brain WM with voxelwise coefficients of variation below 10%.
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