Biology subjects

Kober, T.

Publications and source records attributed to Kober, T..

5 recordsLinked to original sources

bioRxiv2024

Advancing Thalamic Nuclei Segmentation: The Impact of Compressed Sensing and FastSurfer on MRI Processing

The thalamus is a collection of gray matter nuclei that play a crucial role in sensorimotor processing and modulation of cortical activity. Characterizing thalamic nuclei non-invasively with structural MRI is particularly relevant for patient populations with Parkinsons disease, epilepsy, dementia, and schizophrenia. However, severe head motion in these populations poses a significant challenge for in vivo mapping of thalamic nuclei. Recent advancements have leveraged the compressed sensing (CS) framework to accelerate structural MRI acquisition times in MPRAGE sequence variants, while fast segmentation tools like FastSurfer have reduced processing times in neuroimaging research. In this study, we evaluated thalamic nuclei segmentations derived from six different MPRAGE variants with varying degrees of CS acceleration (from about 9 to about 1 minute acquisitions), using both FreeSurfer and FastSurfer for segmentation. Our findings show minimal sequence effects with no systematic bias, and low volume variability across sequences for the whole thalamus and major thalamic nuclei. Notably, CS-accelerated sequences produced less variable volumes compared to non-CS sequences. Additionally, segmentations of thalamic nuclei by FreeSurfer and FastSurfer were highly comparable. We provide first evidence supporting that a good segmentation quality of thalamic nuclei with compressed sensing T1-weighted image acceleration in a clinical 3T MRI system is possible. Our findings encourage future applications of fast T1-weighted MRI to study deep gray matter. CS-accelerated sequences and rapid segmentation methods are promising tools for future studies aiming to characterize thalamic nuclei in vivo at 3T in both healthy individuals and clinical populations.

neuroscience↗

bioRxiv2024

Do you see what I see? Diffusion imaging protocol heterogeneity biases ischemic core volume, location, and clinical associations in acute stroke

PurposeDiffusion-weighted magnetic resonance imaging (DWI) is essential for diagnosing ischemic stroke and identifying targets for emergency revascularization. Apparent diffusion coefficient (ADC) maps derived from DWI are commonly used to locate the infarct core, but they are not strictly quantitative and can vary across platforms and sites due to technical factors. This retrospective study was conducted to examine how differences in ADC map generation, resulting from varied protocols across platforms and sites, affect the determination of infarct core size, location, and related clinical outcomes in acute stroke. MethodsIn this retrospective study, 726 acute anterior circulation stroke patients admitted to the Lausanne University Hospital between May 2018 and January 2021 were selected. DWI data were used to generate ADC maps as they would appear from different protocols: two simulated with low and medium angular resolution (4 and 12 diffusion gradient directions) and one with high angular resolution (20 directions). Using a DEFUSE like criteria and image post-processing, ischemic cores were localized; core volume, location, and associations to National Institutes of Health Stroke Scale (NIHSS) and modified Rankin Scale (mRS) scores were compared between the two imaging sequences. ResultsSignificant differences were observed in the ADC distribution within white matter, particularly in the kurtosis and skewness, with the segmented infarct core volume being higher in protocols with reduced angular resolution compared to the 20-directions data (7.63 ml vs. 3.78 ml). The volumetric differences persisted after correcting for age, sex, and type of intervention. Infarcted voxels locations varied significantly between the two protocols. This variability affected associations between infarct core volume and clinical scores, with lower associations observed for 4-directions data compared to 20-directions data for NIHSS at admission and after 24 hours, and mRS after 3 months, further confirmed by multivariate regression. ConclusionsImaging protocol heterogeneity leads to significant changes in the ADC distribution, ischemic core location, size, and association with clinical scores. Work is needed in standardizing imaging protocols to improve the reliability of ADC as an imaging biomarker in stroke management.protocols to improve the reliability of ADC as an imaging biomarker in stroke management. Key ResultsO_LIOrientation changes in diffusion imaging significantly impact ADC distribution and threshold-based infarct core volume determination, affecting multi-centric studies. C_LIO_LILower number of directions in DWI acquisitions weakens associations between infarct volume measurements and clinical scores. C_LIO_LIFindings emphasize the impact of DWI acquisition protocol heterogeneity and image processing on acute stroke workups. C_LI

neuroscience↗

bioRxiv2023

Hi-Fi fMRI: High-resolution, fast-sampled and sub-second whole-brain functional MRI at 3T in humans

Functional magnetic resonance imaging (fMRI) is a methodological cornerstone of neuroscience. Most studies measure blood-oxygen-level-dependent (BOLD) signal using echo-planar imaging (EPI), Cartesian sampling, and image reconstruction with a one-to-one correspondence between the number of acquired volumes and reconstructed images. However, EPI schemes are subject to trade-offs between spatial and temporal resolutions. We make strides in overcoming these limitations by measuring BOLD with a gradient recalled echo (GRE) with a 3D radial-spiral phyllotaxis trajectory at a high sampling rate (28.49ms) on standard 3T field strength. The framework enables the reconstruction of 3D signal time courses with whole-brain coverage at simultaneously higher nominal spatial (1mm3) and temporal (up to 250ms) resolutions, as compared to optimized EPI schemes. Additionally, we apply motion correction directly to the k-space raw data, enabling flexible motion-corrected reconstructions; the desired temporal resolution to observe hemodynamic responses can be chosen after scanning. By showing activation in the calcarine sulcus of 20 participants completing an ON-OFF visual paradigm, we demonstrate the reliability of our method for applications in cognitive neuroscience research.

neuroscience↗

bioRxiv2021

Multi T1-weighted contrast imaging and T1 mapping with Compressed sensing FLAWS at 3T

The Fluid And White matter Suppression (FLAWS) MRI sequence allows for the acquisition of multiple T1-weighted contrasts in a single sequence acquisition. However, its acquisition time is prohibitive for use in clinical practice when the k-space is linearly downsampled and reconstructed using the Generalized Autocalibrating Partially Parallel Acquisition (GRAPPA) technique. This study proposes a FLAWS sequence optimization tailored to allow for the acquisition of FLAWS images with a Cartesian phyllotaxis k-space undersampling and compressed sensing (CS) reconstruction at 3T. The CS FLAWS sequence parameters were determined using a method previously employed to optimize FLAWS imaging at 1.5T and 7T. In-vivo experiments show that the proposed CS FLAWS optimization allows to reduce the FLAWS sequence acquisition time from 8 mins to 6 mins without decreasing the FLAWS image quality. In addition, this study demonstrates for the first time that T1-weighted imaging with low B1 sensitivity and T1 mapping can be performed with the FLAWS sequence at 3T for both GRAPPA and CS reconstructions. The FLAWS T1 mapping was validated using in-silico, in-vitro and in-vivo experiments with comparison against the inversion recovery turbo spin echo and MP2RAGE T1 mappings. These new results suggest that the recent advances in FLAWS imaging allow to combine the MP2RAGE imaging benefits (T1-weigthed imaging with low B1 sensitivity and T1 mapping) and with the previous version of FLAWS imaging benefits (multi T1-weighted contrast imaging) in a single 6 mins sequence acquisition. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

neuroscience↗

bioRxiv2018

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

We proposed a method for segmentation of brain tissues--gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF)--using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FreeSurfer, FSL, and SPM12. The processing time of the proposed method (28 {+/-} 0 s) was significantly shorter than those of FSL and SPM12 (444 {+/-} 4 s and 159 {+/-} 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained by FSL than with those obtained by SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and WM in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.

neuroscience↗