CVRmap-a complete cerebrovascular reactivity mapping post-processing BIDS toolbox.
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ABSTRACT:
SUBMITTER: Rovai A
PROVIDER: S-EPMC10973431 | biostudies-literature | 2024 Mar
REPOSITORIES: biostudies-literature
Publications
CVRmap-a complete cerebrovascular reactivity mapping post-processing BIDS toolbox.
Rovai A A Lolli V V Trotta N N Goldman S S De Tiège X X
Scientific reports 20240327 1
Cerebrovascular Reactivity (CVR) refers to the ability of cerebral blood vessels to dilate or constrict under the effect of vasoactive substances and can be estimated using functional Magnetic Resonance Imaging (fMRI). Computation of CVR maps is relevant in various brain diseases and requires specialized data processing. We introduce CVRmap, an opensource software that automates the computation of CVR map. The toolbox complies with the Brain Imaging Data Structure (BIDS) standards. ...[more]
Similar Datasets
Project description:Cerebrovascular reactivity (CVR), the ability of cerebral vessels to dilate or constrict, has been shown to provide valuable information in the diagnosis and treatment evaluation of patients with various cerebrovascular conditions. CVR mapping is typically performed using hypercapnic gas inhalation as a vasoactive challenge while collecting BOLD images, but the inherent need of gas inhalation and the associated apparatus setup present a practical obstacle in applying it in routine clinical use. Therefore, we aimed to develop a new method to map CVR using resting-state BOLD data without the need of gas inhalation. This approach exploits the natural variation in respiration and measures its influence on BOLD MRI signal. In this work, we first identified a surrogate of the arterial CO2 fluctuation during spontaneous breathing from the global BOLD signal. Second, we tested the feasibility and reproducibility of the proposed approach to use the above-mentioned surrogate as a regressor to estimate voxel-wise CVR. Third, we validated the "resting-state CVR map" with a conventional CVR map obtained with hypercapnic gas inhalation in healthy volunteers. Finally, we tested the utility of this new approach in detecting abnormal CVR in a group of patients with Moyamoya disease, and again validated the results using the conventional gas inhalation method. Our results showed that global BOLD signal fluctuation in the frequency range of 0.02-0.04Hz contains the most prominent contribution from natural variation in arterial CO2. The CVR map calculated using this signal as a regressor is reproducible across runs (ICC=0.91±0.06), and manifests a strong spatial correlation with results measured with a conventional hypercapnia-based method in healthy subjects (r=0.88, p<0.001). We also found that resting-state CVR was able to identify vasodilatory deficit in patients with steno-occlusive disease, the spatial pattern of which matches that obtained using the conventional gas method (r=0.71±0.18). These results suggest that CVR obtained with resting-state BOLD may be a useful alternative in detecting vascular deficits in clinical applications when gas challenge is not feasible.
| S-EPMC5321860 | biostudies-literature
Project description:Cerebrovascular reactivity (CVR), an index of brain vessel's dilatory capacity, is typically measured using hypercapnic gas inhalation or breath-holding as a vasoactive challenge. However, these methods require considerable subject cooperation and could be challenging in clinical studies. More recently, there have been attempts to use resting-state BOLD data to map CVR by utilizing spontaneous changes in breathing pattern. However, in subjects who have small fluctuations in their spontaneous breathing pattern, the CVR results could be noisy and unreliable. In this study, we aim to develop a new method for CVR mapping that does not require gas-inhalation yet provides substantially higher sensitivity than resting-state CVR mapping. This new method is largely based on resting-state scan, but introduces intermittent modulation of breathing pattern in the subject to enhance fluctuations in their end-tidal CO2 (EtCO2) level. Here we examined the comfort level, sensitivity, and accuracy of this method in two studies. First, in 8 healthy young subjects, we developed the intermittent breath-modulation method using two different modulation frequencies, 6 s per breath and 12 s per breath, respectively, and compared the results to three existing CVR methods, specifically hypercapnic gas inhalation, breath-holding, and resting-state. Our results showed that the comfort level of the 6-s breath-modulation method was significantly higher than breath-holding (p = 0.007) and CO2-inhalation (p = 0.015) methods, while not different from the resting-state, i.e. free breathing method (p = 0.52). When comparing the sensitivity of CVR methods, the breath-modulation methods revealed higher Z-statistics compared to the resting-state scan (p < 0.008) and was comparable to breath-holding results. Next, we tested the feasibility of breath-modulation CVR mapping (6 s per breath) in 21 cognitively normal elderly participants and compared quantitative CVR values to that obtained with the CO2-inhalation method. Whole-brain CVR was found to be 0.150 ± 0.055 and 0.154 ± 0.032 %ΔBOLD/mmHg for the breath-modulation and CO2-inhalation method, respectively, with a significant correlation between them (y = 0.97x, p = 0.007). CVR mapping with intermittent breath modulation may be a useful method that combines the advantages of resting-state and CO2-inhalation based approaches.
| S-EPMC7292765 | biostudies-literature
Project description:Background Comprehensive hemodynamic impairment mapping using blood oxygenation-level dependent (BOLD) cerebrovascular reactivity (CVR) can be used to identify hemodynamically relevant symptomatic unilateral carotid artery disease. Methods and Results This prospective cohort study was conducted between February 2015 and July 2020 at the Clinical Neuroscience Center of the University Hospital Zurich, Zurich, Switzerland. One hundred two patients with newly diagnosed symptomatic unilateral internal carotid artery (ICA) occlusion or with 70% to 99% ICA stenosis were included. An age-matched healthy cohort of 12 subjects underwent an identical BOLD functional magnetic resonance imaging examination. Using BOLD functional magnetic resonance imaging with a standardized CO2 stimulus, CVR impairment was evaluated. Moreover, embolic versus hemodynamic ischemic patterns were evaluated on diffusion-weighted imaging. Sixty-seven patients had unilateral ICA occlusion and 35 patients unilateral 70% to 99% ICA stenosis. Patients with ICA occlusion exhibited lower whole-brain and ipsilateral hemisphere mean BOLD-CVR values as compared with healthy subjects (0.12±0.08 versus 0.19±0.04, P=0.004 and 0.09±0.09 versus 0.18±0.04, P<0.001) and ICA stenosis cohort (0.12±0.08 versus 0.16±0.05, P=0.01 and 0.09±0.09 versus 0.15±0.05, P=0.01); however, only 40 (58%) patients of the cohort showed significant BOLD-CVR impairment. Conversely, there was no difference in mean BOLD-CVR values between healthy patients and patients with ICA stenosis, although 5 (14%) patients with ICA stenosis showed a significant BOLD-CVR impairment. No significant BOLD-CVR difference was discernible between patients with hemodynamic ischemic infarcts versus those with embolic infarct distribution (0.11±0.08 versus 0.13±0.06, P=0.12). Conclusions Comprehensive BOLD-CVR mapping allows for identification of hemodynamically relevant symptomatic unilateral carotid artery stenosis or occlusion.
| S-EPMC8477889 | biostudies-literature
Project description:Cerebrovascular reactivity (CVR) is typically assessed with a carbon dioxide (CO2) stimulus combined with BOLD fMRI. Recently, resting-state (RS) BOLD fMRI has been shown capable of generating CVR maps, providing a potential for broader CVR applications in neuroimaging studies. However, prior RS-CVR studies have primarily been performed at a spatial resolution of 3-4 mm voxel sizes. It remains unknown whether RS-CVR can also be obtained at high-resolution without major degradation in image quality. In this study, we investigated RS-CVR mapping based on resting-state BOLD MRI across a range of spatial resolutions in a group of healthy subjects, in an effort to examine the feasibility of RS-CVR measurement at high resolution. Comparing the results of RS-CVR with the maps obtained by the conventional CO2-inhalation method, our results suggested that good CVR map quality can be obtained at a voxel size as small as 2 mm isotropic. Our results also showed that, RS-CVR maps revealed resolution-dependent sensitivity. However, even at a high resolution of 2 mm isotropic voxel size, the voxel-wise sensitivity is still greater than that of typical task-evoked fMRI. Scan duration affected the sensitivity of RS-CVR mapping, but had no significant effect on its accuracy. These findings suggest that RS-CVR mapping can be applied at a similar resolution as state-of-the-art fMRI studies, which will broaden the use of CVR mapping in basic science and clinical applications including retrospective analysis of previously collected fMRI data.
| S-EPMC10406303 | biostudies-literature
Project description:The cerebral vascular network regulates blood flow distribution by adjusting vessel diameters, and consequently resistance to flow, in response to metabolic demands (neurovascular coupling) and changes in perfusion pressure (autoregulation). Deliberate changes in carbon dioxide (CO2) partial pressure may be used to challenge this regulation and assess its performance since CO2 also acts to change vessel diameter. Cerebrovascular reactivity (CVR), the ratio of cerebral blood flow (CBF) response to CO2 stimulus is currently used as a performance metric. However, the ability of CVR to reflect the responsiveness of a particular vascular region is confounded by that region's inclusion in the cerebral vascular network, where all regions respond to the global CO2 stimulus. Consequently, local CBF responses reflect not only changes in the local vascular resistance but also the effect of changes in local perfusion pressure resulting from redistribution of flow within the network. As a result, the CBF responses to CO2 take on various non-linear patterns that are not well-described by straight lines. We propose a method using a simple model to convert these CBF response patterns to the pattern of resistance responses that underlie them. The model, which has been used previously to explain the steal phenomenon, consists of two vascular branches in parallel fed by a major artery with a fixed resistance unchanging with CO2. One branch has a reference resistance with a sigmoidal response to CO2, representative of a voxel with a robust response. The other branch has a CBF equal to the measured CBF response to CO2 of any voxel under examination. Using the model to calculate resistance response patterns of the examined branch showed sigmoidal patterns of resistance response, regardless of the measured CBF response patterns. The sigmoid parameters of the resistance response pattern of examined voxels may be mapped to their anatomical location. We show an example for a healthy subject and for a patient with steno-occlusive disease to illustrate. We suggest that these maps provide physiological insight into the regulation of CBF distribution.
| S-EPMC6020782 | biostudies-literature
Project description:In conventional neuroimaging, cerebrovascular reactivity (CVR) is quantified primarily using the blood-oxygenation level-dependent (BOLD) functional MRI (fMRI) signal, specifically, as the BOLD response to intravascular carbon dioxide (CO2) modulations, in units of [%ΔBOLD/mmHg]. While this method has achieved wide appeal and clinical translation, the tolerability of CO2-related tasks amongst patients and the elderly remains a challenge in more routine and large-scale applications. In this work, we propose an improved method to quantify CVR by exploiting intrinsic fluctuations in CO2 and corresponding changes in the resting-state BOLD signal (rs-qCVR). Our rs-qCVR approach requires simultaneous monitoring of PETCO2, cardiac pulsation and respiratory volume. In 16 healthy adults, we compare our quantitative CVR estimation technique to the prospective CO2-targeting based CVR quantification approach (qCVR, the "standard"). We also compare our rs-CVR to non-quantitative alternatives including the resting-state fluctuation amplitude (RSFA), amplitude of low-frequency fluctuation (ALFF) and global-signal regression. When all subjects were pooled, only RSFA and ALFF were significantly associated with qCVR. However, for characterizing regional CVR variations within each subject, only the PETCO2-based rs-qCVR measure is strongly associated with standard qCVR in 100% of the subjects (p≤0.1). In contrast, for the more qualitative CVR measures, significant within-subject association with qCVR was only achieved in 50-70% of the subjects. Our work establishes the feasibility of extracting quantitative CVR maps using rs-fMRI, opening the possibility of mapping functional connectivity and qCVR simultaneously.
| S-EPMC5148619 | biostudies-literature
Project description:Cerebrovascular reactivity (CVR) is a prognostic indicator of cerebrovascular health. Estimating CVR from endogenous end-tidal carbon dioxide (CO2) fluctuation and MRI signal recorded under resting state can be difficult due to the poor signal-to-noise ratio (SNR) of signals. Thus, we aimed to improve the method of estimating CVR from end-tidal CO2 and MRI signals. We proposed a coherence weighted general linear model (CW-GLM) to estimate CVR from the Fourier coefficients weighted by the signal coherence in frequency domain, which confers two advantages. First, it requires no signal alignment in time domain, which simplifies experimental methods. Second, it limits the GLM analysis within the frequency band where CO2 and MRI signals are highly correlated, which automatically suppresses noise and nuisance signals. We compared the performance of our method with time-domain GLM (TD-GLM) and frequency-domain GLM (FD-GLM) in both synthetic and in-vivo data; wherein we calculated CVR from signals recorded under both resting state and sinusoidal stimulus. In synthetic data, CW-GLM has a remarkable performance on CVR estimation from narrow band signals with a mean-absolute error of 0.7 % (gray matter) and 1.2 % (white matter), which was lower than all the other methods. Meanwhile, CW-GLM maintains a comparable performance on CVR estimation from resting signals, with a mean-absolute error of 4.1 % (gray matter) and 8 % (white matter). The superior performance was maintained across the 36 in-vivo measurements, with CW-GLM exhibiting limits of agreement of -16.7 % - 9.5 % between CVR calculated from the resting and sinusoidal CO2 paradigms which was 12 % - 209 % better than current time-domain methods. Evaluating of the cross-coherence spectrum revealed highest signal coherence within the frequency band from 0.01 Hz to 0.05 Hz, which overlaps with previously recommended frequency band (0.02 Hz to 0.04 Hz) for CVR analysis. Our data demonstrates that CW-GLM can work as a self-adaptive band-pass filter to improve CVR robustness, while also avoiding the need for signal temporal alignment.
| S-EPMC10822713 | biostudies-literature
Project description:With recent technological advances in microscopy and image acquisition of tissue sections, further developments of tools are required for viewing, transforming, and analyzing the ever-increasing amounts of high-resolution data produced. In the field of neuroscience, histological images of whole rodent brain sections are commonly used for investigating brain connections as well as cellular and molecular organization in the normal and diseased brain, but present a problem for the typical neuroscientist with no or limited programming experience in terms of the pre- and post-processing steps needed for analysis. To meet this need we have designed Nutil, an open access and stand-alone executable software that enables automated transformations, post-processing, and analyses of 2D section images using multi-core processing (OpenMP). The software is written in C++ for efficiency, and provides the user with a clean and easy graphical user interface for specifying the input and output parameters. Nutil currently contains four separate tools: (1) A transformation toolchain named "Transform" that allows for rotation, mirroring and scaling, resizing, and renaming of very large tiled tiff images. (2) "TiffCreator" enables the generation of tiled TIFF images from other image formats such as PNG and JPEG. (3) A "Resize" tool completes the preprocessing toolset and allows downscaling of PNG and JPEG images with output in PNG format. (4) The fourth tool is a post-processing method called "Quantifier" that enables the quantification of segmented objects in the context of regions defined by brain atlas maps generated with the QuickNII software based on a 3D reference atlas (mouse or rat). The output consists of a set of report files, point cloud coordinate files for visualization in reference atlas space, and reference atlas images superimposed with color-coded objects. The Nutil software is made available by the Human Brain Project (https://www.humanbrainproject.eu) at https://www.nitrc.org/projects/nutil/.
| S-EPMC7472695 | biostudies-literature
Project description:Microglia and the border-associated macrophages contribute to the modulation of cerebral blood flow, but the mechanisms have remained uncertain. Here, we show that microglia regulate the cerebral blood flow baseline and the responses to whisker stimulation or intra-cisternal magna injection of adenosine triphosphate, but not intra-cisternal magna injection of adenosine in mice model. Notably, microglia repopulation corrects these cerebral blood flow anomalies. The microglial-dependent regulation of cerebral blood flow requires the adenosine triphosphate-sensing P2RY12 receptor and ectonucleotidase CD39 that initiates the dephosphorylation of extracellular adenosine triphosphate into adenosine in both male and female mice. Pharmacological inhibition or CX3CR1-CreER-mediated deletion of CD39 mimics the cerebral blood flow anomalies in microglia-deficient mice and reduces the upsurges of extracellular adenosine following whisker stimulation. Together, these results suggest that the microglial CD39-initiated breakdown of extracellular adenosine triphosphate co-transmitter is an important step in neurovascular coupling and the regulation of cerebrovascular reactivity.
2024-06-01 | GSE245107 | GEO
Project description:Blood oxygenation level-dependent fMRI contrast depends on the volume and oxygenation of blood flowing through the circulatory system. The effects on image intensity depend temporally on the arrival of blood within a voxel, and signal can be monitored during the time course of such blood flow. It has been previously shown that the passage of global endogenous variations in blood volume and oxygenation can be tracked as blood passes through the brain by determining the strength and peak time lag of their cross-correlation with blood oxygenation level-dependent data. By manipulating blood composition using transient hypercarbia and hyperoxia, we can induce much larger oxygenation and volume changes in the blood oxygenation level-dependent signal than result from natural endogenous fluctuations. This technique was used to examine cerebrovascular parameters in healthy subjects (n = 8) and subjects with intracranial stenosis (n = 22), with a subgroup of intracranial stenosis subjects scanned before and after surgical revascularization (n = 6). The halfwidth of cross-correlation lag times in the brain was larger in IC stenosis subjects (21.21 ± 14.22 s) than in healthy control subjects (8.03 ± 3.67), p < 0.001, and was subsequently reduced in regions that co-localized with surgical revascularization. These data show that blood circulatory timing can be measured robustly and longitudinally throughout the brain using simple respiratory challenges.
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