2D and 3D high resolution gradient echo functional imaging of the brain: venous contributions to signal in motor cortex studies

Quantification of cerebral blood volume changes caused by visual stimulation at 3 T using DANTE-prepared dual-echo EPI

PURPOSE

We investigate the influence of moving blood-attenuation effects when using "delay alternating with nutation for tailored excitation" (DANTE) pulses in conjunction with blood oxygen level dependent (BOLD) of functional MRI (fMRI) at 3 T. Based on the effects of including DANTE pulses, we propose quantification of cerebral blood volume (CBV) changes following functional stimulation.

METHODS

Eighteen volunteers in total underwent fMRI scans at 3 T. Seven volunteers were scanned to investigate the effects of DANTE pulses on the fMRI signal. CBV changes in response to visual stimulation were quantified in 11 volunteers using a DANTE-prepared dual-echo EPI sequence.

RESULTS

The inflow effects from flowing blood in arteries and draining vein effects from flowing blood in large veins can be suppressed by use of a DANTE preparation module. Using DANTE-prepared dual-echo EPI, we quantitatively measured intravascular-weighted microvascular CBV changes of 25.4%, 29.8%, and 32.6% evoked by 1, 5, and 10 Hz visual stimulation, respectively. The extravascular fraction (∆S/S)_extra at TE = 30 ms in total BOLD signal was determined to be 64.8 ± 3.4%, which is in line with previous extravascular component estimation at 3 T. Results show that the microvascular CBV changes are linearly dependent on total BOLD changes at TE = 30 ms with a slope of 0.113, and this relation is independent of stimulation frequency and subject.

CONCLUSION

The DANTE preparation pulses can be incorporated into a standard EPI fMRI sequence for the purpose of minimizing inflow effects and reducing draining veins effects in large vessels. Additionally, the DANTE-prepared dual-echo EPI sequence is a promising fast imaging tool for quantification of intravascular-weighted CBV change in the microvascular space at 3 T.

Research on BOLD-fMRI Data Denoising Based on Bayesian Estimation and Adaptive Wavelet Threshold

The acquisition of functional magnetic resonance imaging (fMRI) images of blood oxygen level-dependent (BOLD) effect and the signals to be analyzed is based on weak changes in the magnetic field caused by small changes in blood oxygen physiological levels, which are weak signals and complex in noise. In order to model and analyze the pathological and hemodynamic parameters of BOLD-fMRI images effectively, it is urgent to use effective signal analysis techniques to reduce the interference of noise and artifacts. In this paper, the noise characteristics of functional magnetic resonance imaging and the traditional signal denoising methods are analyzed. The Bayesian decision criterion takes into account the probability of the total occurrence of all kinds of references and the loss caused by misjudgment and has strong discriminability. So, an improved adaptive wavelet threshold denoising method based on Bayesian estimation is proposed. By using the correlation characteristics of multiscale wavelet coefficients, the corresponding wavelet components of useful signals and noises are processed differently; while retaining useful frequency information, the noise is weakened to the greatest extent. The new adaptive threshold wavelet denoising method based on Bayesian estimation is applied to the actual experiment, and the results of OEF (oxygen extraction fraction) are optimized. A series of simulation experiments are carried out to verify the effectiveness of the proposed method.

A temporal decomposition method for identifying venous effects in task-based fMRI

The spatial resolution of functional magnetic resonance imaging (fMRI) is fundamentally limited by effects from large draining veins. Here we describe an analysis method that provides data-driven estimates of these effects in task-based fMRI. The method involves fitting a one-dimensional manifold that characterizes variation in response timecourses observed in a given dataset, and then using identified early and late timecourses as basis functions for decomposing responses into components related to the microvasculature (capillaries and small venules) and the macrovasculature (large veins), respectively. We show the removal of late components substantially reduces the superficial cortical depth bias of fMRI responses and helps eliminate artifacts in cortical activity maps. This method provides insight into the origins of the fMRI signal and can be used to improve the spatial accuracy of fMRI.

A critical assessment of data quality and venous effects in sub-millimeter fMRI

Advances in hardware, pulse sequences, and reconstruction techniques have made it possible to perform functional magnetic resonance imaging (fMRI) at sub-millimeter resolution while maintaining high spatial coverage and acceptable signal-to-noise ratio. Here, we examine whether sub-millimeter fMRI can be used as a routine method for obtaining accurate measurements of fine-scale local neural activity. We conducted fMRI in human visual cortex during a simple event-related visual experiment (7 T, gradient-echo EPI, 0.8-mm isotropic voxels, 2.2-s sampling rate, 84 slices), and developed analysis and visualization tools to assess the quality of the data. Our results fall along three lines of inquiry. First, we find that the acquired fMRI images, combined with appropriate surface-based processing, provide reliable and accurate measurements of fine-scale blood oxygenation level dependent (BOLD) activity patterns. Second, we show that the highly folded structure of cortex causes substantial biases on spatial resolution and data visualization. Third, we examine the well-recognized issue of venous contributions to fMRI signals. In a systematic assessment of large sections of cortex measured at a fine scale, we show that time-averaged T₂*-weighted EPI intensity is a simple, robust marker of venous effects. These venous effects are unevenly distributed across cortex, are more pronounced in gyri and outer cortical depths, and are, to a certain degree, in consistent locations across subjects relative to cortical folding. Furthermore, we show that these venous effects are strongly correlated with BOLD responses evoked by the experiment. We conclude that sub-millimeter fMRI can provide robust information about fine-scale BOLD activity patterns, but special care must be exercised in visualizing and interpreting these patterns, especially with regards to the confounding influence of the brain's vasculature. To help translate these methodological findings to neuroscience research, we provide practical suggestions for both high-resolution and standard-resolution fMRI studies.

Imaging at ultrahigh magnetic fields: History, challenges, and solutions

Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and spectroscopy studies of humans at 4 T and animal models at 9.4 T, leading to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has provided numerous technological solutions to challenges posed at these ultrahigh fields, and demonstrated the existence of significant advantages in signal-to-noise ratio and biological information content. Primary difference from lower fields is the deviation from the near field regime at the radiofrequencies (RF) corresponding to hydrogen resonance conditions. At such ultrahigh fields, the RF is characterized by attenuated traveling waves in the human body, which leads to image non-uniformities for a given sample-coil configuration because of destructive and constructive interferences. These non-uniformities were initially considered detrimental to progress of imaging at high field strengths. However, they are advantageous for parallel imaging in signal reception and transmission, two critical technologies that account, to a large extend, for the success of ultrahigh fields. With these technologies and improvements in instrumentation and imaging methods, today ultrahigh fields have provided unprecedented gains in imaging of brain function and anatomy, and started to make inroads into investigation of the human torso and extremities. As extensive as they are, these gains still constitute a prelude to what is to come given the increasingly larger effort committed to ultrahigh field research and development of ever better instrumentation and techniques.

Detection of fast oscillating magnetic fields using dynamic multiple TR imaging and Fourier analysis

Neuronal oscillations produce oscillating magnetic fields. There have been trials to detect neuronal oscillations using MRI, but the detectability in in vivo is still in debate. Major obstacles to detecting neuronal oscillations are (i) weak amplitudes, (ii) fast oscillations, which are faster than MRI temporal resolution, and (iii) random frequencies and on/off intervals. In this study, we proposed a new approach for direct detection of weak and fast oscillating magnetic fields. The approach consists of (i) dynamic acquisitions using multiple times to repeats (TRs) and (ii) an expanded frequency spectral analysis. Gradient echo echo-planar imaging was used to test the feasibility of the proposed approach with a phantom generating oscillating magnetic fields with various frequencies and amplitudes and random on/off intervals. The results showed that the proposed approach could precisely detect the weak and fast oscillating magnetic fields with random frequencies and on/off intervals. Complex and phase spectra showed reliable signals, while no meaningful signals were observed in magnitude spectra. A two-TR approach provided an absolute frequency spectrum above Nyquist sampling frequency pixel by pixel with no a priori target frequency information. The proposed dynamic multiple-TR imaging and Fourier analysis are promising for direct detection of neuronal oscillations and potentially applicable to any pulse sequences.

What is feasible with imaging human brain function and connectivity using functional magnetic resonance imaging

When we consider all of the methods we employ to detect brain function, from electrophysiology to optical techniques to functional magnetic resonance imaging (fMRI), we do not really have a 'golden technique' that meets all of the needs for studying the brain. We have methods, each of which has significant limitations but provide often complimentary information. Clearly, there are many questions that need to be answered about fMRI, which unlike other methods, allows us to study the human brain. However, there are also extraordinary accomplishments or demonstration of the feasibility of reaching new and previously unexpected scales of function in the human brain. This article reviews some of the work we have pursued, often with extensive collaborations with other co-workers, towards understanding the underlying mechanisms of the methodology, defining its limitations, and developing solutions to advance it. No doubt, our knowledge of human brain function has vastly expanded since the introduction of fMRI. However, methods and instrumentation in this dynamic field have evolved to a state that discoveries about the human brain based on fMRI principles, together with information garnered at a much finer spatial and temporal scale through other methods, are poised to significantly accelerate in the next decade.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'.

Using a novel source-localized phase regressor technique for evaluation of the vascular contribution to semantic category area localization in BOLD fMRI

Numerous studies have shown that gradient-echo blood oxygen level dependent (BOLD) fMRI is biased toward large draining veins. However, the impact of this large vein bias on the localization and characterization of semantic category areas has not been examined. Here we address this issue by comparing standard magnitude measures of BOLD activity in the Fusiform Face Area (FFA) and Parahippocampal Place Area (PPA) to those obtained using a novel method that suppresses the contribution of large draining veins: source-localized phase regressor (sPR). Unlike previous suppression methods that utilize the phase component of the BOLD signal, sPR yields robust and unbiased suppression of large draining veins even in voxels with no task-related phase changes. This is confirmed in ideal simulated data as well as in FFA/PPA localization data from four subjects. It was found that approximately 38% of right PPA, 14% of left PPA, 16% of right FFA, and 6% of left FFA voxels predominantly reflect signal from large draining veins. Surprisingly, with the contributions from large veins suppressed, semantic category representation in PPA actually tends to be lateralized to the left rather than the right hemisphere. Furthermore, semantic category areas larger in volume and higher in fSNR were found to have more contributions from large veins. These results suggest that previous studies using gradient-echo BOLD fMRI were biased toward semantic category areas that receive relatively greater contributions from large veins.

The Anatomical and Functional Organization of the Human Visual Pulvinar

The pulvinar is the largest nucleus in the primate thalamus and contains extensive, reciprocal connections with visual cortex. Although the anatomical and functional organization of the pulvinar has been extensively studied in old and new world monkeys, little is known about the organization of the human pulvinar. Using high-resolution functional magnetic resonance imaging at 3 T, we identified two visual field maps within the ventral pulvinar, referred to as vPul1 and vPul2. Both maps contain an inversion of contralateral visual space with the upper visual field represented ventrally and the lower visual field represented dorsally. vPul1 and vPul2 border each other at the vertical meridian and share a representation of foveal space with iso-eccentricity lines extending across areal borders. Additional, coarse representations of contralateral visual space were identified within ventral medial and dorsal lateral portions of the pulvinar. Connectivity analyses on functional and diffusion imaging data revealed a strong distinction in thalamocortical connectivity between the dorsal and ventral pulvinar. The two maps in the ventral pulvinar were most strongly connected with early and extrastriate visual areas. Given the shared eccentricity representation and similarity in cortical connectivity, we propose that these two maps form a distinct visual field map cluster and perform related functions. The dorsal pulvinar was most strongly connected with parietal and frontal areas. The functional and anatomical organization observed within the human pulvinar was similar to the organization of the pulvinar in other primate species.

SIGNIFICANCE STATEMENT

The anatomical organization and basic response properties of the visual pulvinar have been extensively studied in nonhuman primates. Yet, relatively little is known about the functional and anatomical organization of the human pulvinar. Using neuroimaging, we found multiple representations of visual space within the ventral human pulvinar and extensive topographically organized connectivity with visual cortex. This organization is similar to other nonhuman primates and provides additional support that the general organization of the pulvinar is consistent across the primate phylogenetic tree. These results suggest that the human pulvinar, like other primates, is well positioned to regulate corticocortical communication.

Scanning fast and slow: current limitations of 3 Tesla functional MRI and future potential

Functional MRI at 3T has become a workhorse for the neurosciences, e.g., neurology, psychology, and psychiatry, enabling non-invasive investigation of brain function and connectivity. However, BOLD-based fMRI is a rather indirect measure of brain function, confounded by physiology related signals, e.g., head or brain motion, brain pulsation, blood flow, intermixed with susceptibility differences close or distant to the region of neuronal activity. Even though a plethora of preprocessing strategies have been published to address these confounds, their efficiency is still under discussion. In particular, physiological signal fluctuations closely related to brain supply may mask BOLD signal changes related to "true" neuronal activation. Here we explore recent technical and methodological advancements aimed at disentangling the various components, employing fast multiband vs. standard EPI, in combination with fast temporal ICA. Our preliminary results indicate that fast (TR <0.5 s) scanning may help to identify and eliminate physiologic components, increasing tSNR and functional contrast. In addition, biological variability can be studied and task performance better correlated to other measures. This should increase specificity and reliability in fMRI studies. Furthermore, physiological signal changes during scanning may then be recognized as a source of information rather than a nuisance. As we are currently still undersampling the complexity of the brain, even at a rather coarse macroscopic level, we should be very cautious in the interpretation of neuroscientific findings, in particular when comparing different groups (e.g., age, sex, medication, pathology, etc.). From a technical point of view our goal should be to sample brain activity at layer specific resolution with low TR, covering as much of the brain as possible without violating SAR limits. We hope to stimulate discussion toward a better understanding and a more quantitative use of fMRI.

Whole-brain three-dimensional T2-weighted BOLD functional magnetic resonance imaging at 7 Tesla

PURPOSE

A new acquisition scheme for T2-weighted spin-echo BOLD fMRI is introduced.

METHODS

It uses a T2-preparation module to induce blood-oxygenation-level-dependent (BOLD) contrast, followed by a single-shot three-dimensional (3D) fast gradient-echo readout with short echo time (TE). It differs from most spin-echo BOLD sequences in that BOLD contrast is generated before the readout, which eliminates the "dead time" due to long TE required for T2 contrast, and substantially improves acquisition efficiency. This approach, termed "3D T2prep-GRE," was implemented at 7 Tesla (T) with a typical spatial (2.5 × 2.5 × 2.5 mm(3) ) and temporal (TR = 2.3 s) resolution for functional MRI (fMRI) and whole-brain coverage (55 slices), and compared with the widely used 2D spin-echo EPI sequence.

RESULTS

In fMRI experiments of simultaneous visual/motor activities, 3D T2prep-GRE showed minimal distortion and little signal dropout across the whole brain. Its lower power deposition allowed greater spatial coverage (55 versus 17 slices with identical TR, resolution and power level), temporal SNR (60% higher) and CNR (35% higher) efficiency than 2D spin-echo EPI. It also showed smaller T2* contamination.

CONCLUSION

This approach is expected to be useful for ultra-high field fMRI, especially for regions near air cavities. The concept of using T2-preparation to generate BOLD contrast can be combined with many other sequences at any field strength.

High-resolution structural and functional assessments of cerebral microvasculature using 3D Gas ΔR2*-mMRA

The ability to evaluate the cerebral microvascular structure and function is crucial for investigating pathological processes in brain disorders. Previous angiographic methods based on blood oxygen level-dependent (BOLD) contrast offer appropriate visualization of the cerebral vasculature, but these methods remain to be optimized in order to extract more comprehensive information. This study aimed to integrate the advantages of BOLD MRI in both structural and functional vascular assessments. The BOLD contrast was manipulated by a carbogen challenge, and signal changes in gradient-echo images were computed to generate ΔR2* maps. Simultaneously, a functional index representing the regional cerebral blood volume was derived by normalizing the ΔR2* values of a given region to those of vein-filled voxels of the sinus. This method is named 3D gas ΔR2*-mMRA (microscopic MRA). The advantages of using 3D gas ΔR2*-mMRA to observe the microvasculature include the ability to distinguish air-tissue interfaces, a high vessel-to-tissue contrast, and not being affected by damage to the blood-brain barrier. A stroke model was used to demonstrate the ability of 3D gas ΔR2*-mMRA to provide information about poststroke revascularization at 3 days after reperfusion. However, this technique has some limitations that cannot be overcome and hence should be considered when it is applied, such as magnifying vessel sizes and predominantly revealing venous vessels.

Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

The Human Connectome Project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce 'functional connectivity'; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3T, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 s for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total dMRI data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 T magnetic field are also presented, targeting higher spatial resolution, enhanced specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields, and reduced power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure.

GESFIDE-PROPELLER approach for simultaneous R2 and R2* measurements in the abdomen

PURPOSE

To investigate the feasibility of combining GESFIDE with PROPELLER sampling approaches for simultaneous abdominal R2 and R2* mapping.

MATERIALS AND METHODS

R2 and R2* measurements were performed in 9 healthy volunteers and phantoms using the GESFIDE-PROPELLER and the conventional Cartesian-sampling GESFIDE approaches.

RESULTS

Images acquired with the GESFIDE-PROPELLER sequence effectively mitigated the respiratory motion artifacts, which were clearly evident in the images acquired using the conventional GESFIDE approach. There was no significant difference between GESFIDE-PROPELLER and reference MGRE R2* measurements (p=0.162) whereas the Cartesian-sampling based GESFIDE methods significantly overestimated R2* values compared to MGRE measurements (p<0.001).

CONCLUSION

The GESFIDE-PROPELLER sequence provided high quality images and accurate abdominal R2 and R2* maps while avoiding the motion artifacts common to the conventional Cartesian-sampling GESFIDE approaches.

Comparing the Microvascular Specificity of the 3- and 7-T BOLD Response Using ICA and Susceptibility-Weighted Imaging

In functional MRI it is desirable for the blood-oxygenation level dependent (BOLD) signal to be localized to the tissue containing activated neurons rather than the veins draining that tissue. This study addresses the dependence of the specificity of the BOLD signal – the relative contribution of the BOLD signal arising from tissue compared to venous vessels – on magnetic field strength. To date, studies of specificity have been based on models or indirect measures of BOLD sensitivity such as signal to noise ratio and relaxation rates, and assessment has been made in isolated vein and tissue voxels. The consensus has been that ultra-high field systems not only significantly increase BOLD sensitivity but also specificity, that is, there is a proportionately reduced signal contribution from draining veins. Specificity was not quantified in prior studies, however, due to the difficulty of establishing a reliable network of veins in the activated volume. In this study we use a map of venous vessel networks extracted from 7 T high resolution Susceptibility-Weighted Images to quantify the relative contributions of micro- and macro-vasculature to functional MRI results obtained at 3 and 7 T. High resolution measurements made here minimize the contribution of physiological noise and Independent Component Analysis (ICA) is used to separate activation from technical, physiological, and motion artifacts. ICA also avoids the possibility of timing-dependent bias from different micro- and macro-vasculature responses. We find a significant increase in the number of activated voxels at 7 T in both the veins and the microvasculature – a BOLD sensitivity increase – with the increase in the microvasculature being higher. However, the small increase in sensitivity at 7 T was not significant. For the experimental conditions of this study, our findings do not support the hypothesis of an increased specificity of the BOLD response at ultra-high field.

Feasibility of noninvasive quantitative measurements of intrarenal R(2) ' in humans using an asymmetric spin echo echo planar imaging sequence

The purpose of this study was to demonstrate the feasibility of an asymmetric spin echo (ASE) single-shot echo planar imaging (EPI) sequence for the noninvasive quantitative measurement of intrarenal R(2) ' in humans within 20 s. The reproducibility of R(2) ' measurements with the ASE-EPI sequence was assessed in nine healthy young subjects in repeated studies conducted over three consecutive days. Moreover, we also evaluated whether the ASE-EPI sequence-measured R(2) ' reflected the intrarenal oxygenation changes induced by furosemide in another group of normal human subjects (n = 10). Different flow attenuation gradients (b = 0, 40 and 80 s/mm(2) ) were utilized to examine the impact of the intravascular signal contribution on the estimation of intrarenal R(2) '. In the absence of flow dephasing gradients (b = 0 s/mm(2) ), the computed coefficient of variation (CV) of R(2) ' was 21.31 ± 4.52%, and the estimated R(2) ' value decreased slightly, but not statistically significantly (p > 0.05), after the administration of furosemide in the medullary region. However, CV of R(2) ' was much smaller in the presence of flow dephasing gradients (9.68 ± 3.58% with b = 40 s/mm(2) and 10.50 ± 3.62% with b = 80 s/mm(2) ). Moreover, a significant reduction in R(2) ' in the renal medulla was obtained (p < 0.05 for both b = 40 s/mm(2) and b = 80 s/mm(2) ) after the administration of furosemide, reflecting an increase in oxygen tension in the medullary region. In addition, R(2) ' measurements did not differ between the b = 40 s/mm(2) and b = 80 s/mm(2) scans, suggesting that small diffusion gradients were sufficient to minimize the intravascular signal contribution. In summary, we have demonstrated that renal R(2) ' can be obtained rapidly using an ASE-EPI sequence. The measurement was highly reproducible and reflected the expected intrarenal oxygenation changes induced by furosemide.

Contrast-enhanced magnetic resonance microangiography reveals remodeling of the cerebral microvasculature in transgenic ArcAβ mice

Amyloid-β (Aβ) deposition in the cerebral vasculature is accompanied by remodeling which has a profound influence on vascular integrity and function. In the current study we have quantitatively assessed the age-dependent changes of the cortical vasculature in the arcAβ model of cerebral amyloidosis. To estimate the density of the cortical microvasculature in vivo, we used contrast-enhanced magnetic resonance microangiography (CE-μMRA). Three-dimensional gradient echo datasets with 60 μm isotropic resolution were acquired in 4- and 24-month-old arcAβ mice and compared with wild-type (wt) control mice of the same age before and after administration of superparamagnetic iron oxide nanoparticles. After segmentation of the cortical vasculature from difference images, an automated algorithm was applied for assessing the number and size distribution of intracortical vessels. With CE-μMRA, cerebral arteries and veins with a diameter of less than the nominal pixel resolution (60 μm) can be visualized. A significant age-dependent reduction in the number of functional intracortical microvessels (radii of 20-80 μm) has been observed in 24-month-old arcAβ mice compared with age-matched wt mice, whereas there was no difference between transgenic and wt mice of 4 months of age. Immunohistochemistry demonstrated strong fibrinogen and Aβ deposition in small- and medium-sized vessels, but not in large cerebral arteries, of 24-month-old arcAβ mice. The reduced density of transcortical vessels may thus be attributed to impaired perfusion and vascular occlusion caused by deposition of Aβ and fibrin. The study demonstrated that remodeling of the cerebrovasculature can be monitored noninvasively with CE-μMRA in mice.

The story of the initial dip in fMRI

Over the past 20 years much attention has been given to characterizing the spatial accuracy of fMRI based signals and to techniques that improve on its co-localization with neuronal activity. While the vast majority of fMRI studies have always used the conventional positive BOLD signal, alternative contrast options have demonstrated superior spatial specificity. One of these options surfaced shortly after the initial BOLD fMRI demonstrations and was motivated by optical imaging studies which revealed an early signal change that was much smaller but spatially more specific than the delayed positive response. This early signal change was attributed to oxygenation changes prior to any subsequent blood flow increases. After observation of this biphasic hemodynamic response in fMRI, because this early response resulted in a small MR signal decrease prior to the onset of the large signal increase, it became known as the "initial dip". While the initial dip in fMRI was subsequently reported by many studies, including those in humans, monkeys, and cats, there were conflicting views about the associated mechanisms and whether it could be generalized across brain regions or species, in addition to whether or not it would prove fruitful for neuroscience. These discrepancies, along with the implications that the initial dip might increase the spatial specificity of BOLD fMRI from 2 to 3mm to something more closely associated with neural activity, resulted in lot of buzz and controversy in the community for many years. In this review, the authors provide an account of the story of the initial dip in MR based functional imaging from the Minnesota perspective, where the first demonstrations, characterizations, and applications of the initial dip commenced.

The role of susceptibility weighted imaging in functional MRI

The development of functional brain magnetic resonance imaging (fMRI) has been a boon for neuroscientists and radiologists alike. It provides for fundamental information on brain function and better diagnostic tools to study disease. In this paper, we will review some of the early concepts in high resolution gradient echo imaging with a particular emphasis on susceptibility weighted imaging (SWI) and MR angiography (MRA). We begin with the history of our own experience in this area, followed by a discussion of the role of high resolution in studying the vasculature of the brain and how this relates to the BOLD (blood oxygenation level dependent) signal. We introduce the role of SWI and susceptibility mapping (SWIM) in fMRI and close with recommendations for future high resolution experiments.

Respiratory self-gated multiple gradient recalled echo sequence for free-breathing abdominal R2* mapping

Abdominal effective transverse relaxation rate (R(2)*) mapping is critical for a wide range of applications. However, respiratory motion can lead to significant image quality deterioration and R(2)* overestimation. For this work, we explored the feasibility of combining respiratory self-gating techniques with a multiple gradient-recalled echo sequence for free-breathing abdominal R(2)* measurements. In a series of eight normal volunteers, respiratory self-gated-multiple gradient-recalled echo methods effectively avoided motion artifacts to produce quantitative R(2)* measurements in liver, spleen, and kidneys that were comparable to R(2)* measurements produced while breath-holding. Respiratory self-gated-multiple gradient-recalled echo methods demonstrated the potential to avoid the need for breath-holding during abdominal R(2)* mapping. For clinical application, respiratory self-gated-multiple gradient-recalled echo approaches could be particularly useful for R(2)* measurements in those patients unable or unwilling to sustain sufficiently long breath-holds to avoid motion artifacts.

Characterisation of the BOLD response time course at different levels of the auditory pathway in non-human primates

Non-human-primate fMRI is becoming increasingly recognised as the missing link between the widely applied methods of human imaging and intracortical animal electrophysiology. A crucial requirement for the optimal application of this method is the precise knowledge of the time course of the Blood Oxygenation Level Dependent (BOLD) signal. We mapped the BOLD signal time course in the inferior colliculus (IC), medial geniculate body (MGB) and in tonotopically defined fields in the auditory cortex of two macaques. The results show little differences in the BOLD-signal time courses within the auditory pathway. However, we observed systematic differences in the magnitude of the change in the BOLD signal with significantly stronger signal changes in field A1 of the auditory cortex compared to field R. The measured time course of the signal was in good agreement with similar studies in human auditory cortex but showed considerable differences to data reported from macaque visual cortex. Consistent with the studies in humans we measured a peak in the BOLD response around 4 s after the onset of 2-s broadband noise stimuli while previous studies recorded from the primary visual cortex of the same species reported the earliest peaks to short visual stimuli several seconds later. The comparison of our results with previous studies does not support differences in haemodynamic responses within the auditory system between human and non-human primates. Furthermore, the data will aid optimal design of future auditory fMRI studies in non-human primates.

Is cortical vasculature functionally organized?

The cortical vasculature is a well-structured and organized system, but the extent to which it is organized with respect to the neuronal functional architecture is unknown. In particular, does vasculature follow the same functional organization as cortical columns? In principle, cortical columns that share tuning for stimulus features like orientation may often be active together and thus require oxygen and metabolic nutrients together. If the cortical vasculature is built to serve these needs, it may also tend to aggregate and amplify orientation specific signals and explain why they are available in fMRI data at very low resolution.

Quantification of venous blood signal contribution to BOLD functional activation in the auditory cortex at 3 T

Most modern techniques for functional magnetic resonance imaging (fMRI) rely on blood-oxygen-level-dependent (BOLD) contrast as the basic principle for detecting neuronal activation. However, the measured BOLD effect depends on a transfer function related to neurophysiological changes accompanying electrical neural activation. The spatial accuracy and extension of the region of interest are determined by vascular effect, which introduces incertitude on real neuronal activation maps. Our efforts have been directed towards the development of a new methodology that is capable of combining morphological, vascular and functional information; obtaining new insight regarding foci of activation; and distinguishing the nature of activation on a pixel-by-pixel basis. Six healthy volunteers were studied in a parametric auditory functional experiment at 3 T; activation maps were overlaid on a high-resolution brain venography obtained through a novel technique. The BOLD signal intensities of vascular and nonvascular activated voxels were analyzed and compared: it was shown that nonvascular active voxels have lower values for signal peak (P<10(-7)) and area (P<10(-8)) with respect to vascular voxels. The analysis showed how venous blood influenced the measured BOLD signals, supplying a technique to filter possible venous artifacts that potentially can lead to misinterpretation of fMRI results. This methodology, although validated in the auditory cortex activation, maintains a general applicability to any cortical fMRI study, as the basic concepts on which it relies on are not limited to this cortical region. The results obtained in this study can represent the basis for new methodologies and tools that are capable of adding further characterization to the BOLD signal properties.

The effect of labeling parameters on perfusion-based fMRI in nonhuman primates

The blood oxygenation level-dependent (BOLD) signal is the most commonly used modality of functional magnetic resonance imaging (fMRI) today. Although easy to implement, it is an ambiguous signal since it results from a combination of several hemodynamic factors. Functional cerebral blood flow changes, as measured by using arterial spin labeling (ASL), typically occur in the parenchyma and have been demonstrated to be more closely coupled to neural activation compared with BOLD. However, the intrinsically low signals from ASL techniques have hindered its widespread application to fMRI for basic research and even more so for clinical applications. Here, we report the first implementation of continuous ASL in the anaesthetized macaque at high magnetic field of 7 T. The technique was optimized to permit maximum signal-to-noise ratio of functional perfusion-based images at high spatial resolution. The effect of labeling parameters, such as label time and post-label delay (PLD), on functional cerebral blood flow (fCBF) in the visual cortex was evaluated. Functional cerebral blood flow maps did not change with increasing label time after 2,000 ms, indicating that a label time of 2,000 ms is sufficient for reliable mapping of fCBF. The percent changes obtained using fCBF were better localized to gray matter, than those obtained with BOLD. A short PLD of 200 ms revealed significantly higher fCBF changes at the cortical surface, indicating large-vessel contamination, than a long PLD of 800 ms. However, the effect of the PLD on fCBF was smaller than on baseline CBF. These results are of importance for high-resolution applications, and when accurate quantification is required for studies in monkeys as well as in humans.

Ultra-high field parallel imaging of the superior parietal lobule during mental maze solving

We used ultra-high field (7 T) fMRI and parallel imaging to scan the superior parietal lobule (SPL) of human subjects as they mentally traversed a maze path in one of four directions (up, down, left, right). A counterbalanced design for maze presentation and a quasi-isotropic voxel (1.46 x 1.46 x 2 mm thick) collection were implemented. Fifty-one percent of single voxels in the SPL were tuned to the direction of the maze path. Tuned voxels were distributed throughout the SPL, bilaterally. A nearest neighbor analysis revealed a "honeycomb" arrangement such that voxels tuned to a particular direction tended to occur in clusters. Three-dimensional (3D) directional clusters were identified in SPL as oriented centroids traversing the cortical depth. There were 13 same-direction clusters per hemisphere containing 22 voxels per cluster, on the average; the mean nearest-neighbor, same-direction intercluster distance was 9.4 mm. These results provide a much finer detail of the directional tuning in SPL, as compared to those obtained previously at 4 T (Gourtzelidis et al. Exp Brain Res 165:273-282, 2005). The more accurate estimates of quantitative clustering parameters in 3D brain space in this study were made possible by the higher signal-to-noise and contrast-to-noise ratios afforded by the higher magnetic field of 7 T as well as the quasi-isotropic design of voxel data collection.

Quantification of fMRI BOLD signal and volume applied to the somatosensory cortex

Functional magnetic resonance imaging based on blood-oxygenation-level-dependent (BOLD) signal variations is clinically used to investigate the impact of neurological disorders on brain function. Such disorders effect not only the localization but also the amplitude and extent of the BOLD signal. Statistical methods are useful to localize the BOLD signal but fail to quantify functional activity because they rely on arbitrary thresholds. This article presents a method that uses a priori defined VOI (volume of interest) and independently quantifies the mean BOLD signal and extent of the activated volume. The technique is based on the separation of the VOI signal difference distribution into a noise and an activation contribution. The technique does not require any threshold and is nearly independent of the preselected VOI size. The technique was verified in a test group of 17 subjects performing bilateral finger tapping. The results were compared with those of conventional analysis based on statistical tools. A standard imaging technique using FID-EPI (free induction decay echo-planar imaging, TR = 4000 ms, TE = 66 ms, 60 images activation, 60 images rest) was employed. The activated volume, V, and signal difference, deltaS, of the motor cortex were determined with an accuracy of sigma(V) = 17.1% and sigma(deltaS) = 3.6%, respectively. The activated volume of the left hemispheric motor area was significantly greater (P = 0.025) then in the right hemispheric, VL = 7.35 +/- 2.29 cm3 versus VR = 6.39 +/- 2.34 cm3. The result is consistent with the findings obtained by other techniques. On the other hand, the statistical methods did not yield any significant difference in activation between both hemispheres. The VOI-based method presented here is an additional tool to study the extent and amplitude of the BOLD signal.

Spatio-temporal point-spread function of fMRI signal in human gray matter at 7 Tesla

This study investigated the spatio-temporal properties of blood-oxygenation level-dependent (BOLD) functional MRI (fMRI) signals in gray matter, excluding the confounding, inaccurate contributions of large blood vessels. We quantified the spatial specificity of the BOLD response, and we investigated whether this specificity varies as a function of time from stimulus onset. fMRI was performed at 7 Tesla (T), where mapping signals of parenchymal origin are easily detected. Two abutting visual stimuli were adjusted to elicit responses centered on a flat gray matter region in V1. fMRI signals were sampled at high-resolution orthogonal to the retinotopic boundary between the representations of the stimuli. Signals from macro-vessels were masked out. Principal component analysis revealed that the first component in space accounted for 96.2+/-1.6% of the variance over time. The spatial profile of this time-invariant response was fitted with a model consisting of the convolution of a step function and a Gaussian point-spread-function (PSF). The mean full-width at half-maximal-height of the fitted PSF was 2.34+/-0.20 mm. Based on simulations of confounding effects, we estimate that BOLD PSF in human gray matter is smaller than 2 mm. A time-point to time-point analysis revealed that the PSF obtained during the 3rd (1.52 mm) and 4th (1.99 mm) seconds of stimulation were narrower than the mean PSF obtained from the 5th second on (2.42+/-0.15 mm). The position of the edge of the responding region was offset (1.72+/-0.07 mm) from the boundary of the stimulated region, indicating a spatial non-linearity. Simulations showed that the effective contrast between active and non-active columns is reduced 25-fold when imaged using a PSF whose width is equal to the cycle of the imaged columnar organization. Thus, the PSF of the hyper-oxygenated BOLD response in human gray matter is narrower than that reported at 1.5 T, where macro-vessels dominate the mapping signals. The initial phase of this response is more spatially specific than later phases. Data acquisition methods that suppress macro-vascular signals should increase the spatial specificity of BOLD fMRI. The choice of optimal stimulus duration represents a trade-off between the spatial specificity and the overhead associated with short stimulus duration.

Presurgical planning for tumor resectioning

Since the birth of functional magnetic resonance imaging (fMRI)-a noninvasive tool able to visualize brain function-now 15 years ago, several clinical applications have emerged. fMRI follows from the neurovascular coupling between neuronal electrical activity and cerebrovascular physiology that leads to three effects that can contribute to the fMRI signal: an increase in the blood flow velocity, in the blood volume and in the blood oxygenation level. The latter effect, gave the technique the name blood oxygenation level dependent (BOLD) fMRI. One of the major clinical uses is presurgical fMRI in patients with brain abnormalities. The goals of presurgical fMRI are threefold: 1) assessing the risk of neurological deficit that follows a surgical procedure, 2) selecting patients for invasive intraoperative mapping, and 3) guiding of the surgical procedure itself. These are reviewed here. Unfortunately, randomized trials or outcome studies that definitively show benefits to the final outcome of the patient when applying fMRI presurgically have not been performed. Therefore, fMRI has not yet reached the status of clinical acceptance. The final purpose of this article is to define a roadmap of future research and developments in order to tilt pre-surgical fMRI to the status of clinical validity and acceptance.

Partial-k-space acquisition method for improved SNR efficiency and temporal resolution in 3D fMRI

Previous studies have shown the relative importance of physiological noise and thermal noise in 2D MR images. Since physiological noise is proportional to the signal, it can be the dominant component at the center of k-space. In this study we demonstrate that the signal-to-noise ratio (SNR) efficiency and temporal resolution for 3D functional MRI (fMRI) are increased by the use of a partial-k-space acquisition method. In partial-k-space methods, the high-spatial-frequency components are doubled in amplitude during reconstruction, resulting in twice as much noise from those components. However, in sum these contributions are relatively small compared to those at the low spatial frequencies, where physiological noise is dominant. Therefore, the effect on the final MR images is almost negligible due to the square summation rule. Thus, the partial-k-space 3D method sacrifices much less SNR than is expected from the thermal noise model, and the SNR efficiency is increased compared to a full-k-space acquisition since more time frames can be collected for the same scan time. Accordingly, the temporal resolution can be increased in 3D acquisitions because only partial coverage of k-space is necessary. Experimental results confirm that more activation with a higher average t-score is detected by this method.

Effects of mild hypoxic hypoxia on poststimulus undershoot of blood-oxygenation-level-dependent fMRI signal in the human visual cortex

Characteristics of the blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signal poststimulus undershoot in the visual cortex were studied at varying levels of arterial blood oxygen saturation (Ysat). Undershoot with an amplitude of -0.6+/-0.2% appeared after positive BOLD response (+1.7+/-0.5%) under control conditions. Cerebral blood volume (CBV), as determined with vascular-space-occupancy-dependent fMRI, increased by 26-43% during the positive BOLD peak, but the CBV proceeded at baseline level during the BOLD poststimulus undershoot. Mild hypoxic hypoxia (Ysat ranging from 0.82 to 0.89) had no effect on the amplitude or duration of poststimulus undershoot in activated BOLD pixels. Hypoxia did not influence CBV during the BOLD poststimulus undershoot. In contrast, the positive BOLD signal at the level of all activated pixels was smaller in hypoxia than in normoxia. The present results show that the BOLD poststimulus undershoot is not influenced by curtailed oxygen availability and that, during the undershoot, CBV is not different from resting state.

Measurements of tissue T1 spin-lattice relaxation time and discrimination of large draining veins using transient EPI data sets in BOLD-weighted fMRI acquisitions

The signal intensity during the dynamic approach to the equilibrium state of longitudinal magnetization is a function of sequence parameters, such as repetition time and flip angle, and depends on tissue characteristics, including longitudinal relaxation time of stationary tissue and the rate of blood inflow. A method is presented to extract information from data acquired during the transient state prior to T1 equilibrium using echo-planar acquisitions in T2*-weighted functional magnetic resonance imaging (fMRI) experiments. A voxel in a single slice acquisition is assumed to contain either stationary tissue or large vessels with flowing blood. Models are presented to characterize longitudinal magnetization relaxation of heterogeneous stationary tissue and blood inflow. The data were fitted to theoretical models for longitudinal relaxation of stationary tissue and inflowing blood assuming no residual signal prior to each RF excitation. Parameters were estimated at 3 T for each model using least squares estimation. A goodness-of-fit criterion was applied to exclude voxels that have transient data that does not fit the selected (best fit) model. Voxels that best fit the inflow model, measured at various TR and flip angles, were assumed to contain large draining veins and were excluded from functional maps. Histogram analysis of T1 distributions for activated voxels in a visual paradigm demonstrated the distributions are centered at T1 values of gray matter with tails at both sides of the center due to partial voluming of gray matter with white matter and CSF respectively. The mean gray matter volume fraction in activated voxels was about 0.9. The results indicate that transient data sets can provide additional information that is useful for both localization and characterization of the functionally relevant BOLD response.

High-resolution FMRI at 1.5T using balanced SSFP

The resolution in conventional BOLD FMRI is considerably lower than can be achieved with other MRI methods, and is insufficient for many important applications. One major difficulty in robustly improving spatial resolution is the poor image quality in BOLD FMRI, which suffers from distortions, blurring, and signal dropout. This work considers the potential for increased resolution with a new FMRI method based on balanced SSFP. This method establishes a blood oxygenation sensitive steady-state (BOSS) signal, in which the frequency sensitivity of balanced SSFP is used to detect the frequency shift of deoxyhemoglobin. BOSS FMRI is highly SNR efficient and does not suffer from image distortions or signal dropout, making this method an excellent candidate for high-resolution FMRI. This study presents the first demonstration of high-resolution BOSS FMRI, using an efficient 3D stack-of-segmented EPI readout and combined acquisition at multiple center frequencies. BOSS FMRI is shown to enable high-resolution FMRI data (1 x 1 x 2 mm(3)) in both visual and motor systems using standard hardware at 1.5 T. Currently, the major limitation of BOSS FMRI is its sensitivity to temporal and spatial field drift.

Effects of oxygen saturation on BOLD and arterial spin labelling perfusion fMRI signals studied in a motor activation task

Effects of oxygen availability on blood oxygenation level dependent (BOLD) and arterial spin labelling (ASL) perfusion functional magnetic resonance imaging (fMRI) signal changes upon motor activation were studied. Mild hypoxic hypoxia was induced by reducing the inspired oxygen content (FIO(2)) to 12%, decreasing blood oxygen saturation (Y) from 0.99 +/- 0.01 to 0.85 +/- 0.03. The fMRI signal characteristics were determined during finger tapping. BOLD activation volume decreased as a function of declining Y in the brain structures involved in execution of the motor task, however, the BOLD signal increase in activated parenchyma was not influenced by Y. ASL fMRI showed that the baseline CBF of 61.8 +/- 3.6 ml/100 g/min was not affected by hypoxic hypoxia. Similar to the BOLD fMRI, the volume of motor cortex areas displaying increase in perfusion by ASL fMRI decreased, but the signal change due to perfusion increase was not influenced in hypoxia. The present fMRI results show distinct patterns of haemodynamic and metabolic responses in the brain to motor task between normoxia and hypoxia. On one hand, neither BOLD nor ASL fMRI signal changes are influenced by hypoxia during motor activation. On the other hand, hypoxia attenuates increase in both BOLD and perfusion fMRI signals upon finger tapping from the levels determined in normoxia. These observations indicate that haemodynamic and metabolic responses may be heterogeneous in brain during execution of motor functions in mild hypoxia.

Heterogeneous oxygen extraction in the visual cortex during activation in mild hypoxic hypoxia revealed by quantitative functional magnetic resonance imaging

Functional magnetic resonance imaging (fMRI) techniques were used to study haemodynamic and metabolic responses in human visual cortex during varying arterial blood oxygen saturation levels (Y(sat), determined by pulse-oximeter) and stimulation with contrast-reversing checkerboards. The visual-evoked potential amplitude remained constant at lowered Y(sat) of 0.82+/-0.03. Similarly, fMRI cerebral blood flow (CBF) responses were unchanged during reduced Y(sat). In contrast, visual cortex volume displaying blood oxygen level-dependent (BOLD) fMRI response decreased as a function of Y(sat), but the BOLD signal change of 3.6%+/-1.4% was constant. Oxygen extraction ratio (OER) during visual activation showed values of 0.26+/-0.03 for normal Y(sat). At lowered Y(sat), two OER patterns were observed. Firstly, a reduced OER of 0.14+/-0.03 in the visual cortex structures showing BOLD in hypoxia was observed. Secondly, signs of much higher OER in other parts of visual cortex were obtained. T2*-weighted magnetic resonance imaging revealed signal increases by 0.8%+/-0.4% with visual activation during lowered Y(sat) in the visual cortex structures, which showed BOLD of 3.6% in magnitude under normoxia. Because the CBF response in the visual cortex was quantitatively similar during stimulation in normoxia and hypoxia, attenuated T2*-weighted signal increase in parts of visual cortex indicated high OER during visual activation in hypoxia, which was close to that encountered in the resting brain. These spatially localised regions of tissue oxygen extraction and metabolism argue for dissociation between CBF and BOLD fMRI signals in mild hypoxia. The findings point to heterogeneity with regard to oxygen requirement and its coupling to the haemodynamic response in the brain.

Visual responses of the human superior colliculus: a high-resolution functional magnetic resonance imaging study

The superior colliculus (SC) is a multimodal laminar structure located on the roof of the brain stem. The SC is a key structure in a distributed network of areas that mediate saccadic eye movements and shifts of attention across the visual field and has been extensively studied in nonhuman primates. In humans, it has proven difficult to study the SC with functional MRI (fMRI) because of its small size, deep location, and proximity to pulsating vascular structures. Here, we performed a series of high-resolution fMRI studies at 3 T to investigate basic visual response properties of the SC. The retinotopic organization of the SC was determined using the traveling wave method with flickering checkerboard stimuli presented at different polar angles and eccentricities. SC activations were confined to stimulation of the contralateral hemifield. Although a detailed retinotopic map was not observed, across subjects, the upper and lower visual fields were represented medially and laterally, respectively. Responses were dominantly evoked by stimuli presented along the horizontal meridian of the visual field. We also measured the sensitivity of the SC to luminance contrast, which has not been previously reported in primates. SC responses were nearly saturated by low contrast stimuli and showed only small response modulation with higher contrast stimuli, indicating high sensitivity to stimulus contrast. Responsiveness to stimulus motion in the SC was shown by robust activations evoked by moving versus static dot stimuli that could not be attributed to eye movements. The responses to contrast and motion stimuli were compared with those in the human lateral geniculate nucleus. Our results provide first insights into basic visual responses of the human SC and show the feasibility of studying subcortical structures using high-resolution fMRI.

Anatomical and functional brain imaging using high-resolution echo-planar spectroscopic imaging at 1.5 Tesla

High-resolution echo-planar spectroscopic imaging (EPSI) of water resonance (i.e. without water suppression) is proposed for anatomic and functional imaging of the human brain at 1.5 T. Water spectra with a resolution of 2.6 Hz and a bandwidth of 333 Hz were obtained in small voxels (1.7 x 1.7 x 3 mm3) across a single slice. Although water spectra appeared Lorentzian in most of the voxels in the brain, non-Lorentzian broadening of the water resonance was observed in voxels containing blood vessels. In functional experiments with a motor task, robust activation in motor cortices was observed in high-resolution T2* maps generated from the EPSI data. Shift of the water resonance frequency occurred during neuronal activation in motor cortices. The activation areas appeared to be more localized after excluding the voxels in which the lineshape of the water resonance had elevated T2* and became more non-Lorentzian during the motor task. These preliminary results suggest that high-resolution EPSI is a promising tool to study susceptibility-related effects, such as BOLD contrast, for improved anatomical and functional imaging of the brain.

Signal and noise characteristics of Hahn SE and GE BOLD fMRI at 7 T in humans

At very high magnetic fields, GE BOLD fMRI is expected to contain nonspecific contributions and behave differently than HSE fMRI data. Similarly, the two approaches can conceivably suffer from different contributions to temporal instabilities in a times series that ultimately determine the contrast-to-noise ratio (CNR). We investigate the signal and signal fluctuation characteristics in GE and HSE fMRI data with the imaging parameters separately optimized for each contrast at 7 T. In HSE fMRI, activation-induced fractional signal change (DeltaS/S) decreased rapidly, and the ratio of standard deviations of image-to-image fluctuations due to physiological processes (sigmaPhys) to thermal noise (sigmaTherm) remained constant with increasing voxel volume. In contrast, DeltaS/S as well as volume of activated voxels was virtually independent of voxel size for GE BOLD, and sigma(Phys)/sigmaTherm increased with increasing voxel size. The ratio of BOLD signal changes (GE/HSE) was much closer to 1 in tissue areas compared to vessel areas. These observations led to the conclusions that the spatial extent of the activation-induced DeltaS/S was much broader in the GE data, and that the physiological processes that give rise to the temporal fluctuations lost coherence over millimeter distances in HSE compared to GE fMRI data. While further studies are needed to characterize it fully, sigmaPhys in HSE data was clearly different than in GE data. It was concluded that HSE imaging yields a significantly reduced amount of nonspecific signals compared to GE imaging, and, would be the method of choice (over GE) for high-resolution applications in humans.

Retinotopic organization and functional subdivisions of the human lateral geniculate nucleus: a high-resolution functional magnetic resonance imaging study

Functional magnetic resonance imaging (fMRI) has provided intriguing insights into the topography and functional organization of visual cortical areas in the human brain. However, little is known about the functional anatomy of subcortical nuclei. Here, we used high-resolution fMRI (1.5 x 1.5 x 2 mm3) at 3 tesla to investigate the retinotopic organization of the human lateral geniculate nucleus (LGN). The central 15 degrees of the visual field were mapped using periodic flickering checkerboard stimuli that evoked a traveling wave of activity. The contralateral visual hemifield was represented with the lower field in the medial-superior portion and the upper field in the lateral-inferior portion of each LGN. The horizontal meridian was significantly overrepresented relative to the vertical meridian. The fovea was represented in posterior and superior portions, with increasing eccentricities represented more anteriorly. The magnification of the fovea relative to the periphery was similar to that described for human primary visual cortex. The magnocellular regions of the LGN were distinguished based on their sensitivity to low stimulus contrast and tended to be located in its inferior and medial portions. Our results demonstrate striking similarities in the topographic organization of the macaque and human LGN and support accounts of a constant magnification from the retina through the cortex in both species.

Acute cerebral ischemia in rats studied by Carr-Purcell spin-echo magnetic resonance imaging: assessment of blood oxygenation level-dependent and tissue effects on the transverse relaxation

Acute cerebral ischemia has been shown to be associated with an enhanced transverse relaxation rate in rat brain parenchyma, chiefly due to the blood oxygenation level-dependent (BOLD) effect. In this study, Carr-Purcell R(2) (CP R(2)), acquired both with short and long time intervals between centers of adiabatic pi-pulses (tau(CP)), was used to assess the contributions of BOLD and tissue effects to the transverse relaxation in two brain ischemia models of rat at 4.7 T. R(1rho) and diffusion MR images were also acquired in the same animals. During the first minutes of global ischemia, the long tau(CP) R(2) in brain parenchyma increased, whereas the short tau(CP) R(2) was unchanged. Based on the simulations, and using constraints of intravascular BOLD effect on parenchymal R(2), the former observation was ascribed to be due to susceptibility changes arising in the extravascular compartment. R(1rho) declined almost immediately after the onset of focal cerebral ischemia, and further declined during the evolution of ischemic damage. Interestingly, short tau(CP) CP R(2) started to decline after some 20 min of focal ischemia and declined over a time course similar to that of R(1rho), indicating that it may be an MRI marker for irreversible tissue changes in cerebral ischemia. The present results show that CP R(2) MRI can reveal both tissue- and blood-derived contrast changes in acute cerebral ischemia.

Circulatory basis of fMRI signals: relationship between changes in the hemodynamic parameters and BOLD signal intensity

Blood oxygenation level-dependent functional magnetic resonance imaging (BOLD-fMRI) is widely used as a tool for functional brain mapping. During brain activation, increases in the regional blood flow lead to an increase in blood oxygenation and a decrease in paramagnetic deoxygenated hemoglobin (deoxy-Hb), causing an increase in the MR signal intensity at the site of brain activation. However, not a few studies using fMRI have failed to detect activation of areas that ought to have been activated. We assigned BOLD-positive (an increase in the signal intensity), BOLD-negative (a decrease in the signal intensity), and BOLD-silent (no change) brain activation to respective circulatory conditions through a description of fMRI signals as a function of the concentration of oxygenated Hb (oxy-Hb) and deoxy-Hb obtained with near-infrared optical imaging (NIOI). Using this model, we explain the sensory motor paradox in terms of BOLD-positive, BOLD-negative, and BOLD-silent brain activation.

High field human imaging

This review article examines the state of knowledge regarding human imaging using MRI at high main magnetic field strengths. The article starts with a summary of the technical issues associated with magnetic field strengths in the range of 3-8 T, including magnet characteristics and the properties of radiofrequency magnetic fields, with special reference to sensitivity, power deposition, and homogeneity. The published data on tissue-water relaxation times in the brain is tabulated and the implications for contrast and pulse sequence implementation is elucidated. The behavior of the major fast imaging sequences, fast low angle shot (FLASH), rapid acquisition with relaxation enhancement (RARE), and echo planar imaging (EPI), is examined in this context. A number of anatomical images from 3 T systems are presented as examples. Particular attention is given to various forms of vascular imaging, namely, time of flight angiography, venography, and arterial spin labeling. The most complex changes in contrast with main magnetic field strength are in activation studies utilizing the blood oxygen level dependent mechanism, which are examined in detail. Improvements in spatial specificity are emphasized, particularly in conjunction with spin-echo imaging. The article concludes with a discussion of the current status and the potential impact of technical developments such as parallel imaging.

A PRESTO-SENSE sequence with alternating partial-Fourier encoding for rapid susceptibility-weighted 3D MRI time series

A 3D sequence for dynamic susceptibility imaging is proposed which combines echo-shifting principles (such as PRESTO), sensitivity encoding (SENSE), and partial-Fourier acquisition. The method uses a moderate SENSE factor of 2 and takes advantage of an alternating partial k-space acquisition in the "slow" phase encode direction allowing an iterative reconstruction using high-resolution phase estimates. Offering an isotropic spatial resolution of 4 x 4 x 4 mm(3), the novel sequence covers the whole brain including parts of the cerebellum in 0.5 sec. Its temporal signal stability is comparable to that of a full-Fourier, full-FOV EPI sequence having the same dynamic scan time but much less brain coverage. Initial functional MRI experiments showed consistent activation in the motor cortex with an average signal change slightly less than that of EPI.

Influence of baseline hematocrit on between-subject BOLD signal change using gradient echo and asymmetric spin echo EPI

The dependence of BOLD signal change (BSC) on baseline hematocrit is in the process of being characterized, primarily using conventional Gradient Echo (GE) echo planar imaging (EPI). We describe the first empiric exploration of this relationship using, in addition to GE, Spin Echo (SE) and two Asymmetric Spin Echo EPI sequences (ASE10 and ASE20), which are less susceptible to large vessel noise. Motor cortex BSC was measured (N = 17) and regressed against hematocrit and hemoglobin concentration using linear and non-linear functions. GE measurements of BSC yielded a positive linear relationship (r(2) = 0.240, p = 0.0459) whereas a positive non-linear relationship was observed using ASE10 (r(2) = 0.571, p = 0.0146). Results suggest that between-subjects BSC is significantly dependent on baseline hematocrit. The nature of dependence, and implications for quantitative studies vary with the vessel size selectivity of the imaging sequence, and with the effect of hematocrit on blood viscosity in the imaged vessels.

Three-dimensional BOLD fMRI with spin-echo characteristics using T2 magnetization preparation and echo-planar readouts

A new approach to mixed T(2)- and T(2) (*)-weighted BOLD fMRI is presented, which combines T(2) magnetization preparation (T2prep) with a series of EPI readouts. This technique allows full 3D, time-efficient imaging to be performed with low RF power deposition. Steady-state calculations are performed in order to study signal formation in 3D T2prep-EPI sequences. Results obtained under the hypothesis of ideal spoiling are compared to full Bloch equation solutions. The theoretical findings are validated by means of in vitro and in vivo signal measurements. Several variants of the 3D T2prep-EPI approach are shown to be usable for visual cortex fMRI and compared to conventional 3D coherent gradient-echo EPI. The relative sensitivity of these sequences is shown to be predictable by means of a simple DeltaT(2)/DeltaT(2) (*) model.

Comparison of the dependence of blood R2 and R2* on oxygen saturation at 1.5 and 4.7 Tesla

Gradient-echo (GRE) blood oxygen level-dependent (BOLD) effects have both intra- and extravascular contributions. To better understand the intravascular contribution in quantitative terms, the spin-echo (SE) and GRE transverse relaxation rates, R(2) and R(2)(*), of isolated blood were measured as a function of oxygenation in a perfusion system. Over the normal oxygenation saturation range of blood between veins, capillaries, and arteries, the difference between these rates, R'(2) = R(2)(*) - R(2), ranged from 1.5 to 2.1 Hz at 1.5 T and from 26 to 36 Hz at 4.7 T. The blood data were used to calculate the expected intravascular BOLD effects for physiological oxygenation changes that are typical during visual activation. This modeling showed that intravascular DeltaR(2)(*) is caused mainly by R(2) relaxation changes, namely 85% and 78% at 1.5T and 4.7T, respectively. The simulations also show that at longer TEs (>70 ms), the intravascular contribution to the percentual BOLD change is smaller at high field than at low field, especially for GRE experiments. At shorter TE values, the opposite is the case. For pure parenchyma, the intravascular BOLD signal changes originate predominantly from venules for all TEs at low field and for short TEs at high field. At longer TEs at high field, the capillary contribution dominates. The possible influence of partial volume contributions with large vessels was also simulated, showing large (two- to threefold) increases in the total intravascular BOLD effect for both GRE and SE.

A method for determining venous contribution to BOLD contrast sensory activation

While BOLD contrast reflects hemodynamic changes within capillaries serving neural tissue, it also has a venous component. Studies that have determined the relation of large blood vessels to the activation map indicate that veins are the source of the largest response, and the most delayed in time. It would be informative if the location of these large veins could be extracted from the properties of the functional responses, since vessels are not visible in BOLD contrast images. The present study describes a method for investigating whether measures taken from the functional response can reliably predict vein location, or at least be useful in down-weighting the venous contribution to the activation response, and illustrates this method using data from one subject. We combined fMRI at 3 Tesla with high-resolution anatomic imaging and MR venography to test whether the intrinsic properties of activation time courses corresponded to tissue type. Measures were taken from a gamma fit to the functional response. Mean magnitude showed a significant effect of tissue type (p < 0.001) where CSF > veins approximately gray matter > white matter. Mean delays displayed the same ranking across tissue types (p < 0.001), except that veins > gray matter. However, measures for all tissue types were distributed across an overlapping range. A logistic regression model correctly discriminated 72% of the veins from gray matter in the absence of independent information of macroscopic vessels (ROC = 0.72). While tissue classification was not perfect for this subject, weighting the T contrast by the predicted probabilities materially reduced the venous component to the activation map.