Correcting for Superficial Bias in 7T Gradient Echo fMRI.
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ABSTRACT:
SUBMITTER: Huang P
PROVIDER: S-EPMC8494131 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:PurposeTo develop a distortion correction method for echo planar imaging (EPI) that is able to measure dynamic changes in B0 .Theory and methodsThe approach we propose is based on single-echo EPI with a jittering of the echo time between two values for alternate time points. Field maps are calculated between phase images from adjacent volumes and are used to remove distortion from corresponding magnitude images. The performance of our approach was optimized using an analytical model and by comparison with field maps from dual-echo EPI. The method was tested in functional MRI experiments at 7T with motor tasks and compared with the conventional static approach.ResultsUnwarping using our method was accurate even for head rotations up to 8.2°, where the static approach introduced errors up to 8.2 mm. Jittering the echo time between 19 and 25 ms had no measurable effect on blood oxygenation level-dependent (BOLD) sensitivity. Our approach reduced the distortions in activated regions to <1 mm and repositioned active voxels correctly.ConclusionThis method yields accurate distortion correction in the presence of motion. No reduction in BOLD sensitivity was observed. As such, it is suitable for application in a wide range of functional MRI experiments. Magn Reson Med 76:1388-1399, 2016. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
| S-EPMC5082535 | biostudies-literature
Project description:Compressed sensing (CS) may be useful for accelerating data acquisitions in high-resolution fMRI. However, due to the inherent slow temporal dynamics of the hemodynamic signals and concerns of potential statistical power loss, the CS approach for fMRI (CS-fMRI) has not been extensively investigated. To evaluate the utility of CS in fMRI application, we systematically investigated the properties of CS-fMRI using computer simulations and in vivo experiments of rat forepaw sensory and odor stimulations with gradient-recalled echo (GRE) and echo planar imaging (EPI) sequences. Various undersampling patterns along the phase-encoding direction were studied and k-t FOCUSS was used as the CS reconstruction algorithm, which exploits the temporal redundancy of images. Functional sensitivity, specificity, and time courses were compared between fully-sampled and CS-fMRI with reduction factors of 2 and 4. CS-fMRI with GRE, but not with EPI, improves the statistical sensitivity for activation detection over the fully sampled data when the ratio of the fMRI signal change to noise is low. CS improves the temporal resolution and reduces temporal noise correlations. While CS reduces the functional response amplitudes, the noise variance is also reduced to make the overall activation detection more sensitive. Consequently, CS is a valuable fMRI acceleration approach, especially for GRE fMRI studies.
| S-EPMC4021580 | biostudies-literature
Project description:PurposeTo develop a 7T simultaneous multi-slice (SMS) 2D gradient-echo sequence for susceptibility contrast imaging, and to compare its quality to 3D imaging.MethodsA frequency modulated and phase cycled RF pulse was designed to simultaneously excite multiple slices in multi-echo 2D gradient-echo imaging. The imaging parameters were chosen to generate images with susceptibility contrast, including T2*-weighted magnitude/phase images, susceptibility-weighted images and quantitative susceptibility/R2* maps. To compare their image quality with 3D gradient-echo imaging, both 2D and 3D imaging were performed on 11 healthy volunteers and 4 patients with multiple sclerosis (MS). The signal to noise ratio (SNR) in gray and white matter and their contrast to noise ratio (CNR) was simulated for the 2D and 3D magnitude images using parameters from the imaging. The experimental SNRs and CNRs were measured in gray/white matter and deep gray matter structures on magnitude, phase, R2* and QSM images from volunteers and the visibility of MS lesions on these images from patients was visually rated. All SNRs and CNRs were compared between the 2D and 3D imaging using a paired t-test.ResultsAlthough the 3D magnitude images still had significantly higher SNRs (by 13.0~17.6%), the 2D magnitude and QSM images generated significantly higher gray/white matter or globus pallidus/putamen contrast (by 13.3~87.5%) and significantly higher MS lesion contrast (by 5.9~17.3%).Conclusion2D SMS gradient-echo imaging can serve as an alternative to often used 3D imaging to obtain susceptibility-contrast-weighted images, with an advantage of providing better image contrast and MS lesion sensitivity.
| S-EPMC6636815 | biostudies-literature
Project description:A spatial mismatch of up to 14 mm between optimal transcranial magnetic stimulation (TMS) site and functional magnetic resonance imaging (fMRI) signal has consistently been reported for the primary motor cortex. The underlying cause might be the effect of magnetic susceptibility around large draining veins in Gradient-Echo blood oxygenation level-dependent (GRE-BOLD) fMRI. We tested whether alternative fMRI sequences such as Spin-Echo (SE-BOLD) or Arterial Spin-Labeling (ASL) assessing cerebral blood flow (ASL-CBF) may localize neural activity closer to optimal TMS positions and primary motor cortex than GRE-BOLD. GRE-BOLD, SE-BOLD, and ASL-CBF signal changes during right thumb abductions were obtained from 15 healthy subjects at 3 Tesla. In 12 subjects, tissue at fMRI maxima was stimulated with neuronavigated TMS to compare motor-evoked potentials (MEPs). Euclidean distances between the fMRI center-of-gravity (CoG) and the TMS motor mapping CoG were calculated. Highest SE-BOLD and ASL-CBF signal changes were located in the anterior wall of the central sulcus [Brodmann Area 4 (BA4)], whereas highest GRE-BOLD signal changes were significantly closer to the gyral surface. TMS at GRE-BOLD maxima resulted in higher MEPs which might be attributed to significantly higher electric field strengths. TMS-CoGs were significantly anterior to fMRI-CoGs but distances were not statistically different across sequences. Our findings imply that spatial differences between fMRI and TMS are unlikely to be caused by spatial unspecificity of GRE-BOLD fMRI but might be attributed to other factors, e.g., interactions between TMS-induced electric field and neural tissue. Differences between techniques should be kept in mind when using fMRI coordinates as TMS (intervention) targets.
| S-EPMC6870385 | biostudies-literature
Project description:PurposeTo evaluate the potential for bias in functional magnetic resonance imaging (fMRI) aging studies resulting from age-related differences in magnetic field distributions that can impact echo time and functional contrast.Materials and methodsMagnetic field maps were taken on 31 younger adults (age: 22 ± 2.9 years) and 46 older adults (age: 66 ± 4.5 years) on a 3T scanner. Using the spatial gradients of the magnetic field map for each participant, an echo planar imaging (EPI) trajectory was simulated. The effective echo time, time at which the k-space trajectory is the closest to the center of k-space, was calculated. This was used to examine both within-subject and across-age-group differences in the effective echo time maps. The blood oxygenation level-dependent (BOLD) percent signal change resulting from those echo time shifts was also calculated to determine their impact on fMRI aging studies.ResultsFor a single subject, the effective echo time varied as much as ±5 msec across the brain. An unpaired t-test between the effective echo time across age groups resulted in significant differences in several regions of the brain (P < 0.01). The difference in echo time was only ∼1 msec, however, which is not expected to have an important impact on BOLD fMRI percent signal change (<4%).ConclusionSusceptibility-induced magnetic field gradients induce local echo-time shifts in gradient echo fMRI images, which can cause variable BOLD sensitivity across the brain. However, the age-related differences in BOLD signal are expected to be small for an fMRI study at 3T.Level of evidence1 J. Magn. Reson. Imaging 2017;45:207-214.
| S-EPMC5156585 | biostudies-literature
Project description:PurposeTo quantitatively assess the effects of high degree and order (1st -4th+ ) relative to 1st -2nd degree B0 shimming at 7 Tesla (T) on gradient-echo echo planar imaging (GE-EPI) and blood-oxygen-level dependent (BOLD) activation.MethodsSimulations and GE-EPI were performed at (2mm)3 and (3mm)3 resolution, evaluating the temporal signal-to-noise ratio (tSNR), transverse relaxivity ( R2*), BOLD % signal change and activated pixel counts in a breath-hold task.ResultsComparing the 1st -4th+ degree with 1st -2nd degree shimmed B0 maps generated spatially varying regions of ?|B0|=|B01-2|-|B01-4+|. As binned in 10-Hz intervals, the two center ?|B0 | (±10?Hz) bins maintained the B0 offset of 48.6% of gray-matter pixels. In the positive ?|B0 | bins greater than 10?Hz, the 1st -4th+ degree shimming improved the B0 offset in 41.1%; in negative ?|B0 | bins less than -10?Hz, the offset worsened in 10.2% of the pixels. In the positive ?|B0 | bins, we found variable but significant increases in BOLD sensitivity; the negative ?|B0 | bins showed significant decreases. In the breath-hold studies, positive bins showed significantly increased activated pixel numbers (+5-29%), whereas negative bins showed -18 to 0% decline.Conclusion1st -4th+ degree shimming maintained B0 homogeneity over central brain regions while improving most of the other regions, including the inferior frontal lobe. Magn Reson Med 78:1734-1745, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
| S-EPMC6084307 | biostudies-literature
Project description:ObjectivesTo apply the MB (multiband) excitation and blipped-CAIPI (blipped-controlled aliasing in parallel imaging) techniques in a spin and gradient-echo (SAGE) EPI sequence to improve the slice coverage for vessel architecture imaging (VAI).Materials and methodsBoth MB excitation and blipped-CAIPI with in-plane parallel imaging were incorporated into a gradient-echo (GE)/spin-echo (SE) EPI sequence for simultaneous tracking of the dynamic MR signal changes in both GE and SE contrasts after the injection of contrast agent. MB and singleband (SB) excitation were compared using a 20-channel head coil at 3 Tesla, and high-resolution MB VAI could be performed in 32 glioma patients.ResultsWhole-brain covered high resolution VAI can be achieved after applying multiband excitation with a factor of 2 and in-plane parallel imaging with a factor of 3. The quality of the images resulting from MB acceleration was comparable to those from the SB method: images were reconstructed without any loss of spatial resolution or severe distortions. In addition, MB and SB signal-to-noise ratios (SNR) were similar. A relative low g-factor induced from the MB acceleration method was achieved after using a blipped-CAIPI technique (1.35 for GE and 1.33 for SE imaging). Performing quantitative VAI, we found that, among all VAI parametric maps, microvessel type indicator (MTI), distance map (I) and vascular-induced bolus peak-time shift (VIPS) were highly correlated. Likewise, VAI parametric maps of slope, slope length and short axis were highly correlated.ConclusionsMultiband accelerated SAGE successfully doubles the number of readout slices in the same measurement time when compared to conventional readout sequences. The corresponding VAI parametric maps provide insights into the complexity and heterogeneity of vascular changes in glioma.
| S-EPMC6688807 | biostudies-literature
Project description:ObjectiveNeurons cluster into sub-millimeter spatial structures and neural activity occurs at millisecond resolutions; hence, ultimately, high spatial and high temporal resolutions are required for functional MRI. In this work, we implemented a spin-echo line-scanning (SELINE) sequence to use in high spatial and temporal resolution fMRI.Materials and methodsA line is formed by simply rotating the spin-echo refocusing gradient to a plane perpendicular to the excited slice and by removing the phase-encoding gradient. This technique promises a combination of high spatial and temporal resolution (250 μm, 500 ms) and microvascular specificity of functional responses. We compared SELINE data to a corresponding gradient-echo version (GELINE).ResultsWe demonstrate that SELINE showed much-improved line selection (i.e. a sharper line profile) compared to GELINE, albeit at the cost of a significant drop in functional sensitivity.DiscussionThis low functional sensitivity needs to be addressed before SELINE can be applied for neuroscientific purposes.
| S-EPMC10140128 | biostudies-literature
Project description:PurposeTo develop a method to reconstruct quantitative susceptibility mapping (QSM) from multi-echo, multi-flip angle data collected using strategically acquired gradient echo (STAGE) imaging.MethodsThe proposed QSM reconstruction algorithm, referred to as "structurally constrained Susceptibility Weighted Imaging and Mapping" scSWIM, performs an ℓ 1 and ℓ 2 regularization-based reconstruction in a single step. The unique contrast of the T1 weighted enhanced (T1WE) image derived from STAGE imaging was used to extract reliable geometry constraints to protect the basal ganglia from over-smoothing. The multi-echo multi-flip angle data were used for improving the contrast-to-noise ratio in QSM through a weighted averaging scheme. The measured susceptibility values from scSWIM for both simulated and in vivo data were compared to the: original susceptibility model (for simulated data only), the multi orientation COSMOS (for in vivo data only), truncated k-space division (TKD), iterative susceptibility weighted imaging and mapping (iSWIM), and morphology enabled dipole inversion (MEDI) algorithms. Goodness of fit was quantified by measuring the root mean squared error (RMSE) and structural similarity index (SSIM). Additionally, scSWIM was assessed in ten healthy subjects.ResultsThe unique contrast and tissue boundaries from T1WE and iSWIM enable the accurate definition of edges of high susceptibility regions. For the simulated brain model without the addition of microbleeds and calcium, the RMSE was best at 5.21ppb for scSWIM and 8.74ppb for MEDI thanks to the reduced streaking artifacts. However, by adding the microbleeds and calcium, MEDI's performance dropped to 47.53ppb while scSWIM performance remained the same. The SSIM was highest for scSWIM (0.90) and then MEDI (0.80). The deviation from the expected susceptibility in deep gray matter structures for simulated data relative to the model (and for the in vivo data relative to COSMOS) as measured by the slope was lowest for scSWIM + 1%(-1%); MEDI + 2%(-11%) and then iSWIM -5%(-10%). Finally, scSWIM measurements in the basal ganglia of healthy subjects were in agreement with literature.ConclusionThis study shows that using a data fidelity term and structural constraints results in reduced noise and streaking artifacts while preserving structural details. Furthermore, the use of STAGE imaging with multi-echo and multi-flip data helps to improve the signal-to-noise ratio in QSM data and yields less artifacts.
| S-EPMC7645168 | biostudies-literature
Project description:MOTIVATION:Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity. RESULTS:Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs. AVAILABILITY AND IMPLEMENTATION:Mango is open source and distributed through github at https://github.com/dphansti/mango. CONTACT:mpsnyder@standford.edu SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
| S-EPMC4592333 | biostudies-literature