How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging

Continuity, divergence, and the evolution of brain language pathways

Recently, the assumption of evolutionary continuity between humans and non-human primates has been used to bolster the hypothesis that human language is mediated especially by the ventral extreme capsule pathway that mediates auditory object recognition in macaques. Here, we argue for the importance of evolutionary divergence in understanding brain language evolution. We present new comparative data reinforcing our previous conclusion that the dorsal arcuate fasciculus pathway was more significantly modified than the ventral extreme capsule pathway in human evolution. Twenty-six adult human and twenty-six adult chimpanzees were imaged with diffusion-weighted MRI and probabilistic tractography was used to track and compare the dorsal and ventral language pathways. Based on these and other data, we argue that the arcuate fasciculus is likely to be the pathway most essential for higher-order aspects of human language such as syntax and lexical–semantics.

Reconstruction of scattered data in fetal diffusion MRI

In this paper we present a method for reconstructing diffusion-weighted MRI data on regular grids from scattered data. The proposed method has the advantage that no specific diffusion model needs to be assumed. Previous work assume the tensor model, but this is not suitable under certain conditions like intravoxel orientational heterogeneity (IVOH). Data reconstruction is particularly important when studying the fetal brain in utero, since registration methods applied for movement and distortion correction produce scattered data in spatial and diffusion domains. We propose the use of a groupwise registration method, and a dual spatio-angular interpolation by using radial basis functions (RBF). Leave-one-out experiments performed on adult data showed a high accuracy of the method. The application to fetal data showed an improvement in the quality of the sequences according to objective criteria based on fractional anisotropy (FA) maps, and differences in the tractography results.

Correction of vibration artifacts in DTI using phase-encoding reversal (COVIPER)

Diffusion tensor imaging is widely used in research and clinical applications, but still suffers from substantial artifacts. Here, we focus on vibrations induced by strong diffusion gradients in diffusion tensor imaging, causing an echo shift in k-space and consequential signal-loss. We refined the model of vibration-induced echo shifts, showing that asymmetric k-space coverage in widely used Partial Fourier acquisitions results in locally differing signal loss in images acquired with reversed phase encoding direction (blip-up/blip-down). We implemented a correction of vibration artifacts in diffusion tensor imaging using phase-encoding reversal (COVIPER) by combining blip-up and blip-down images, each weighted by a function of its local tensor-fit error. COVIPER was validated against low vibration reference data, resulting in an error reduction of about 72% in fractional anisotropy maps. COVIPER can be combined with other corrections based on phase encoding reversal, providing a comprehensive correction for eddy currents, susceptibility-related distortions and vibration artifact reduction.

Aberrations in the arcuate fasciculus are associated with auditory verbal hallucinations in psychotic and in non-psychotic individuals

The pathophysiology of auditory verbal hallucinations (AVH) is still unclear. Cognitive as well as electrophysiological studies indicate that a defect in sensory feedback (corollary discharge) may contribute to the experience of AVH. This could result from disruption of the arcuate fasciculus, the major tract connecting frontal and temporo-parietal language areas. Previous diffusion tensor imaging studies indeed demonstrated abnormalities of this tract in schizophrenia patients with AVH. It is, however, difficult to disentangle specific associations with AVH in this patient group as many other factors, such as other positive and negative symptoms, medication or halted education could likewise have affected tract integrity. We therefore investigated AVH in relative isolation and studied a group of non-psychotic individuals with AVH as well as patients with AVH and non-hallucinating matched controls. We compared tract integrity of the arcuate fasiculus and of three other control tracts, between 35 non-psychotic individuals with AVH, 35 schizophrenia patients with AVH, and 36 controls using diffusion tensor imaging and magnetization transfer imaging. Both groups with AVH showed an increase in magnetization transfer ratio (MTR) in the arcuate fasciculus, but not in the other control tracts. In addition, a general decrease in fractional anisotropy (FA) for almost all bundles was observed in the patient group, but not in the non-psychotic individuals with AVH. As increased MTR in the arcuate fasciculus was present in both hallucinating groups, a specific association with AVH seems plausible. Decreases in FA, on the other hand, seem to be related to other disease processes of schizophrenia.

Rich-club organization of the human connectome

The human brain is a complex network of interlinked regions. Recent studies have demonstrated the existence of a number of highly connected and highly central neocortical hub regions, regions that play a key role in global information integration between different parts of the network. The potential functional importance of these "brain hubs" is underscored by recent studies showing that disturbances of their structural and functional connectivity profile are linked to neuropathology. This study aims to map out both the subcortical and neocortical hubs of the brain and examine their mutual relationship, particularly their structural linkages. Here, we demonstrate that brain hubs form a so-called "rich club," characterized by a tendency for high-degree nodes to be more densely connected among themselves than nodes of a lower degree, providing important information on the higher-level topology of the brain network. Whole-brain structural networks of 21 subjects were reconstructed using diffusion tensor imaging data. Examining the connectivity profile of these networks revealed a group of 12 strongly interconnected bihemispheric hub regions, comprising the precuneus, superior frontal and superior parietal cortex, as well as the subcortical hippocampus, putamen, and thalamus. Importantly, these hub regions were found to be more densely interconnected than would be expected based solely on their degree, together forming a rich club. We discuss the potential functional implications of the rich-club organization of the human connectome, particularly in light of its role in information integration and in conferring robustness to its structural core.

Correction of geometric distortion in fMRI data

The early functional MRI research programme at the National Institutes of Health, described by Robert Turner in an accompanying article in this volume, was the first to combine echo planar imaging (EPI) and high field in the pursuit of fMRI. As such, it soon became apparent that one of the obstacles to interpreting fMRI data using EPI was the presence of geometric distortions caused by static field inhomogeneities. This meant that EPI data did not properly align spatially with conventionally acquired MRI scans that showed structural information. This article describes some of the approaches that have been adopted to ensure that spatial warping caused by field inhomogeneities can be corrected so that functional and structural information can be co-aligned.

The effects of connection reconstruction method on the interregional connectivity of brain networks via diffusion tractography

Estimating the interregional structural connections of the brain via diffusion tractography is a complex procedure and the parameters chosen can affect the outcome of the connectivity matrix. Here, we investigated the influence of different connection reconstruction methods on brain connectivity networks. Specifically, we applied three connection reconstruction methods to the same set of diffusion MRI data, initiating tracking from deep white matter (method #1, M1), from the gray matter/white matter interface (M2), and from the gray/white matter interface with thresholded tract volume rather than the connection probability as the connectivity index (M3). Small-world properties, hub identification, and hemispheric asymmetry in connectivity patterns were then calculated and compared across methods. Despite moderate to high correlations in the graph-theoretic measures across different methods, significant differences were observed in small-world indices, identified hubs, and hemispheric asymmetries, highlighting the importance of reconstruction method on network parameters. Consistent with the prior reports, the left precuneus was identified as a hub region in all three methods, suggesting it has a prominent role in brain networks.

Impaired structural motor connectome in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease selectively affecting upper and lower motor neurons. Patients with ALS suffer from progressive paralysis and eventually die on average after three years. The underlying neurobiology of upper motor neuron degeneration and its effects on the complex network of the brain are, however, largely unknown. Here, we examined the effects of ALS on the structural brain network topology in 35 patients with ALS and 19 healthy controls. Using diffusion tensor imaging (DTI), the brain network was reconstructed for each individual participant. The connectivity of this reconstructed brain network was compared between patients and controls using complexity theory without - a priori selected - regions of interest. Patients with ALS showed an impaired sub-network of regions with reduced white matter connectivity (p = 0.0108, permutation testing). This impaired sub-network was strongly centered around primary motor regions (bilateral precentral gyrus and right paracentral lobule), including secondary motor regions (bilateral caudal middle frontal gyrus and pallidum) as well as high-order hub regions (right posterior cingulate and precuneus). In addition, we found a significant reduction in overall efficiency (p = 0.0095) and clustering (p = 0.0415). From our findings, we conclude that upper motor neuron degeneration in ALS affects both primary motor connections as well as secondary motor connections, together composing an impaired sub-network. The degenerative process in ALS was found to be widespread, but interlinked and targeted to the motor connectome.

Distortion correction for diffusion-weighted MRI tractography and fMRI in the temporal lobes

Single shot echo-planar imaging (EPI) sequences are currently the most commonly used sequences for diffusion-weighted imaging (DWI) and functional magnetic resonance imaging (fMRI) as they allow relatively high signal to noise with rapid acquisition time. A major drawback of EPI is the substantial geometric distortion and signal loss that can occur due to magnetic field inhomogeneities close to air-tissue boundaries. If DWI-based tractography and fMRI are to be applied to these regions, then the distortions must be accurately corrected to achieve meaningful results. We describe robust acquisition and processing methods for correcting such distortions in spin echo (SE) EPI using a variant of the reversed direction k space traversal method with a number of novel additions. We demonstrate that dual direction k space traversal with maintained diffusion-encoding gradient strength and direction results in correction of the great majority of eddy current-associated distortions in DWI, in addition to those created by variations in magnetic susceptibility. We also provide examples to demonstrate that the presence of severe distortions cannot be ignored if meaningful tractography results are desired. The distortion correction routine was applied to SE-EPI fMRI acquisitions and allowed detection of activation in the temporal lobe that had been previously found using PET but not conventional fMRI.

Microstructural alterations of the arcuate fasciculus in schizophrenia patients with frequent auditory verbal hallucinations

Auditory verbal hallucinations (AVH) is a common and stressful symptom of schizophrenia. Disrupted connectivity between frontal and temporo-parietal language areas, giving rise to the misattribution of inner speech, is speculated to underlie this phenomenon. Disrupted connectivity should be reflected in the microstructure of the arcuate fasciculi (AF); the main connection between frontal and temporo-parietal language areas. In this study we compared microstructural properties of the AF and three other fiber tracts (cortical spinal tract, cingulum and uncinate fasciculus), between 44 schizophrenia patients with chronic severe hallucinations and 42 control subjects using diffusion tensor imaging (DTI) and magnetic transfer imaging (MTI). The DTI scans were used to compute fractional anisotropy (FA) and to reconstruct the fiber bundles of interest, while the MTI scans were used to compute magnetic transfer ratio (MTR) values. The patient group showed a general decrease in FA for all bundles. In the arcuate fasciculus this decreased FA was coupled to a significant increase in MTR values. A correlation was found between mean MTR values in both arcuate fasciculi and the severity of positive symptoms. The combination of decreased FA and increased MTR values observed in the arcuate fasciculi in patients suggests increased free water concentrations, probably caused by degraded integrity of the axons or the supportive glia cells. This suggests that disintegrated fiber integrity in the connection between frontal and temporo-parietal language areas in the schizophrenia patients is associated with their liability for auditory verbal hallucinations.

Orientation entropy analysis of diffusion tensor in healthy and myelopathic spinal cord

The majority of nerve fibers in the spinal cord run longitudinally, playing an important role in connecting the brain to the peripheral nerves. There is a growing interest in applying diffusion tensor imaging (DTI) to the evaluation of spinal cord microarchitecture. The current study sought to compare the organization of longitudinal nerve fibers between healthy and myelopathic spinal cords using entropy-based analysis of principal eigenvector mapping. A total of 22 subjects were recruited, including 14 healthy subjects, seven cervical myelopathy (CM) patients with single-level compression, and one patient suffering from multi-level compression. Diffusion tensor magnetic resonance (MR) images of the cervical spinal cord were obtained using a pulsed gradient, spin-echo echo-planar imaging (SE-EPI) sequence with a 3T MR system. Regions of interest (ROIs) were drawn manually to cover the spinal cord, and Shannon entropy was calculated in principal eigenvector maps. The results revealed no significant differences in orientation entropy values along the whole length of cervical spinal cord in healthy subjects (C2-3: 0.73±0.05; C3-4: 0.71±0.07; C4-5: 0.72±0.048; C5-6: 0.71±0.07; C6-7: 0.72±0.07). In contrast, orientation entropy values in myelopathic cord were significantly higher at the compression site (0.91±0.03), and the adjacent levels (above: 0.85±0.03; below: 0.83±0.05). This study provides a novel approach to analyze the orientation information in diffusion MR images of healthy and diseased spinal cord. These results indicate that orientation entropy can be applied to determine the contribution of each compression level to the overall disorganization of principal nerve tracts of myelopathic spinal cord in cases with multi-level compression.

A stable sparse fear memory trace in human amygdala

Pavlovian fear conditioning is highly conserved across species, providing a powerful model of aversive learning. In rodents, fear memory is stored and reactivated under the influence of the amygdala. There is no evidence for an equivalent mechanism in primates, and an opposite mechanism is proposed whereby primate amygdala contributes only to an initial phase of aversive learning, subsequently ceding fear memory to extra-amygdalar regions. Here, we reexamine this question by exploiting human high-resolution functional magnetic resonance imaging in conjunction with multivariate methods. By assuming a sparse neural coding, we show it is possible, at an individual subject level, to discriminate responses to conditioned (CS+ and CS-) stimuli in both basolateral and centro-cortical amygdala nuclei. The strength of this discrimination increased over time and was tightly coupled to the behavioral expression of fear, consistent with an expression of a stable fear memory trace. These data highlight that the human basolateral and centro-cortical amygdala support initial learning as well more enduring fear memory storage. A sparse neuronal representation for fear, here revealed by multivariate pattern classification, resolves why an enduring memory trace has proven elusive in previous human studies.

Tract-based magnetic resonance spectroscopy of the cingulum bundles at 7 T

The cingulum bundle is a white matter fiber bundle in the human brain that is believed to be implicated in various neurological and psychiatric diseases. Subtle disease-related differences in metabolite concentrations in the cingulum tracts that may underlie these diseases may be detected using MR spectroscopic information. However, to date, limited signal to noise and lack of spatial resolution have prevented a reliable and reproducible measurement of metabolites in the cingulum bundle in vivo. Here we propose a new method that combines MR spectroscopic imaging at 7 T with fiber tracking to select only those MR spectroscopy voxels that are actually part of the cingulum bundles. The spectra of the selected spectroscopy voxels are processed per voxel and then combined yielding one spectrum at high spectral resolution for each cingulum bundle. In this way sensitivity is increased, as large parts of the cingulum are included while partial volume effects with both gray matter and white matter from other tracts is kept to a minimum. Three healthy volunteers were scanned to assess the feasibility of the method. For all three healthy volunteers spectra for the left and right cingulum tracts were computed, partial volume fractions calculated and metabolite fractions were quantified yielding similar results suggesting that tract-based MR spectroscopy allows us to study metabolic concentrations of individual white matter fiber bundles with high sensitivity and high specificity.

Anomalous diffusion measured by a twice-refocused spin echo pulse sequence: analysis using fractional order calculus

PURPOSE

To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence.

MATERIALS AND METHODS

The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2600 s/mm(2). For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β, and μ values and the goodness-of-fit in three specific regions of interest (ROIs) in white matter, gray matter, and cerebrospinal fluid, respectively, were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively.

RESULTS

The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents.

CONCLUSION

The diffusion-induced signal attenuation in a TRSE pulse sequence can be described by an FC diffusion model at high b-values. This model performs equally well for data acquired from the human brain tissues with a TRSE pulse sequence or a conventional Stejskal-Tanner sequence.

Multi-parametric neuroimaging reproducibility: a 3-T resource study

Modern MRI image processing methods have yielded quantitative, morphometric, functional, and structural assessments of the human brain. These analyses typically exploit carefully optimized protocols for specific imaging targets. Algorithm investigators have several excellent public data resources to use to test, develop, and optimize their methods. Recently, there has been an increasing focus on combining MRI protocols in multi-parametric studies. Notably, these have included innovative approaches for fusing connectivity inferences with functional and/or anatomical characterizations. Yet, validation of the reproducibility of these interesting and novel methods has been severely hampered by the limited availability of appropriate multi-parametric data. We present an imaging protocol optimized to include state-of-the-art assessment of brain function, structure, micro-architecture, and quantitative parameters within a clinically feasible 60-min protocol on a 3-T MRI scanner. We present scan-rescan reproducibility of these imaging contrasts based on 21 healthy volunteers (11 M/10 F, 22-61 years old). The cortical gray matter, cortical white matter, ventricular cerebrospinal fluid, thalamus, putamen, caudate, cerebellar gray matter, cerebellar white matter, and brainstem were identified with mean volume-wise reproducibility of 3.5%. We tabulate the mean intensity, variability, and reproducibility of each contrast in a region of interest approach, which is essential for prospective study planning and retrospective power analysis considerations. Anatomy was highly consistent on structural acquisition (~1-5% variability), while variation on diffusion and several other quantitative scans was higher (~<10%). Some sequences are particularly variable in specific structures (ASL exhibited variation of 28% in the cerebral white matter) or in thin structures (quantitative T2 varied by up to 73% in the caudate) due, in large part, to variability in automated ROI placement. The richness of the joint distribution of intensities across imaging methods can be best assessed within the context of a particular analysis approach as opposed to a summary table. As such, all imaging data and analysis routines have been made publicly and freely available. This effort provides the neuroimaging community with a resource for optimization of algorithms that exploit the diversity of modern MRI modalities. Additionally, it establishes a baseline for continuing development and optimization of multi-parametric imaging protocols.

Magnetic resonance imaging near metal implants

The desire to apply magnetic resonance imaging (MRI) techniques in the vicinity of embedded metallic hardware is increasing. The soft-tissue contrast available with MR techniques is advantageous in diagnosing complications near an increasing variety of MR-safe metallic hardware. Near such hardware, the spatial encoding mechanisms utilized in conventional MRI methods are often severely compromised. Mitigating these encoding difficulties has been the focus of numerous research investigations over the past two decades. Such approaches include view-angle tilting, short echo-time projection reconstruction acquisitions, single-point imaging, prepolarized MRI, and postprocessing image correction. Various technical advances have also enabled the recent development of two alternative approaches that have shown promising clinical potential. Here, the physical principals and proposed solutions to the problem of MRI near embedded metal are discussed.

Regional specificity of MRI contrast parameter changes in normal ageing revealed by voxel-based quantification (VBQ)

Normal ageing is associated with characteristic changes in brain microstructure. Although in vivo neuroimaging captures spatial and temporal patterns of age-related changes of anatomy at the macroscopic scale, our knowledge of the underlying (patho)physiological processes at cellular and molecular levels is still limited. The aim of this study is to explore brain tissue properties in normal ageing using quantitative magnetic resonance imaging (MRI) alongside conventional morphological assessment. Using a whole-brain approach in a cohort of 26 adults, aged 18–85 years, we performed voxel-based morphometric (VBM) analysis and voxel-based quantification (VBQ) of diffusion tensor, magnetization transfer (MT), R1, and R2* relaxation parameters. We found age-related reductions in cortical and subcortical grey matter volume paralleled by changes in fractional anisotropy (FA), mean diffusivity (MD), MT and R2*. The latter were regionally specific depending on their differential sensitivity to microscopic tissue properties. VBQ of white matter revealed distinct anatomical patterns of age-related change in microstructure. Widespread and profound reduction in MT contrasted with local FA decreases paralleled by MD increases. R1 reductions and R2* increases were observed to a smaller extent in overlapping occipito-parietal white matter regions. We interpret our findings, based on current biophysical models, as a fingerprint of age-dependent brain atrophy and underlying microstructural changes in myelin, iron deposits and water. The VBQ approach we present allows for systematic unbiased exploration of the interaction between imaging parameters and extends current methods for detection of neurodegenerative processes in the brain. The demonstrated parameter-specific distribution patterns offer insights into age-related brain structure changes in vivo and provide essential baseline data for studying disease against a background of healthy ageing.

Deep and superficial amygdala nuclei projections revealed in vivo by probabilistic tractography

Despite a homogenous macroscopic appearance on magnetic resonance images, subregions of the amygdala express distinct functional profiles as well as corresponding differences in connectivity. In particular, histological analysis shows stronger connections for superficial (i.e., centromedial and cortical), compared with deep (i.e., basolateral and other), amygdala nuclei to lateral orbitofrontal cortex and stronger connections of deep compared with superficial, nuclei to polymodal areas in the temporal pole. Here, we use diffusion weighted imaging with probabilistic tractography to investigate these connections in humans. We use a data-driven approach to segment the amygdala into two subregions using k-means clustering. The identified subregions are spatially contiguous and their location corresponds to deep and superficial nuclear groups. Quantification of the connection strength between these amygdala clusters and individual target regions corresponds to qualitative histological findings in non-human primates, indicating such findings can be extrapolated to humans. We propose that connectivity profiles provide a potentially powerful approach for in vivo amygdala parcellation and can serve as a guide in studies that exploit functional and anatomical neuroimaging.

Entropy-based analysis for diffusion anisotropy mapping of healthy and myelopathic spinal cord

The present study utilized diffusion MR imaging and fractional anisotropy (FA) mapping to delineate the microstructure of spinal cord. The concept of Shannon entropy was introduced to analyze the complex microstructure of healthy and injured spinal cords based on FA map. A total of 30 volunteers were recruited in this study with informed consent, including 13 healthy adult subjects (group A, 25±3 years), 12 healthy elderly subjects (group B, 53±7 years) and 5 cervical spondylotic myelopathy (CSM) patients (group C, 53±15 years). Diffusion MRI images of cervical spinal cord were taken using pulsed gradient spin-echo-echo-planar imaging (SE-EPI) sequence with a 3T MR system. The region of interest was defined to cover the spinal cord in FA maps. The Shannon entropy of FA values of voxels in the cord was calculated as well as the average FA values. The significant differences were determined among three groups using one-way ANOVA and post-hoc test. As compared with adult and elderly healthy subjects, the entropy of whole spinal cord was significantly lower in CSM patients (group A: 6.07±0.18; B: 6.01±0.23; C: 5.32±0.44; p<0.05). Whereas there were no significant difference in FA values among groups (group A: 0.62±0.08; B: 0.64±0.09; C: 0.64±0.12). In CSM patients, there was a loss of architectural structural complexity in the cervical spinal cord tissue as noted by the lower Shannon entropy value. It indicated the potential application of entropy-based analysis for the diagnosis of the severity of chronic compressive spinal cord injuries, i.e. CSM.

Intercenter differences in diffusion tensor MRI acquisition

PURPOSE

To assess the effect on diffusion tensor (DT) magnetic resonance imaging (MRI) of acquiring data with different scanners.

MATERIALS AND METHODS

Forty-four healthy controls and 36 multiple sclerosis patients with low disability were studied using eight MR scanners with acquisition protocols that were as close to a standard protocol as possible. Between 7 and 13 subjects were studied in each center. Region-of-interest (ROI) and histogram-based analyses of fractional anisotropy (FA), axial (D(ax)), radial (D(rad)), and mean diffusivity (MD) were performed. The influence of variables such as the acquisition center and the control/patient group was determined with an analysis of variance (ANOVA) test.

RESULTS

The patient/control group explained approximately 25% of data variability of FA and D(rad) from midsagittal corpus callosum (CC) ROIs. Global FA, MD, and D(rad) in the white matter differentiated patients from controls, but with lower discriminatory power than for the CC. In the gray matter, MD discriminated patients from controls (30% of variability explained by group vs. 17% by center).

CONCLUSION

Significant variability of DT-MRI data can be attributed to the acquisition center, even when a standardized protocol is used. The use of appropriate segmentation methods and statistical models allows DT-derived metrics to differentiate patients from healthy controls.

Chimpanzee (Pan troglodytes) precentral corticospinal system asymmetry and handedness: a diffusion magnetic resonance imaging study

Background

Most humans are right handed, and most humans exhibit left-right asymmetries of the precentral corticospinal system. Recent studies indicate that chimpanzees also show a population-level right-handed bias, although it is less strong than in humans.

Methodology/Principal Findings

We used in vivo diffusion-weighted and T1-weighted magnetic resonance imaging (MRI) to study the relationship between the corticospinal tract (CST) and handedness in 36 adult female chimpanzees. Chimpanzees exhibited a hemispheric bias in fractional anisotropy (FA, left>right) and mean diffusivity (MD, right>left) of the CST, and the left CST was centered more posteriorly than the right. Handedness correlated with central sulcus depth, but not with FA or MD.

Conclusions/Significance

These anatomical results are qualitatively similar to those reported in humans, despite the differences in handedness. The existence of a left>right FA, right>left MD bias in the corticospinal tract that does not correlate with handedness, a result also reported in some human studies, suggests that at least some of the structural asymmetries of the corticospinal system are not exclusively related to laterality of hand preference.

Reducing distortions in diffusion-weighted echo planar imaging with a dual-echo blip-reversed sequence

The inherent distortions in echo-planar imaging that arise due to inhomogeneities in the static magnetic field can lead to difficulties when attempting to obtain structurally accurate diffusion-tensor imaging data. Parallel acceleration techniques can reduce the magnitude of these distortions but do not remove them entirely. Images can be corrected using a measured field map, but this is prone to error. One approach to correcting for these distortions, referred to here as "blip-reversed" echo-planar imaging, involves collecting a second set of images with the phase encoding reversed. Here, a novel approach to collecting blip-reversed echo-planar imaging data for diffusion-tensor imaging is presented: a dual-echo sequence is used in which the phase-encoding direction of the second echo is swapped compared to the first echo. This allows benefits of the blip-reversed approach to be exploited, with only a modest increase in scan time and, due to the extra data acquired, no significant loss of signal-to-noise efficiency. A novel approach to recombining blip-reversed data is also presented, which involves refining the measured field map, using an algorithm to minimize the difference between the corrected images. The field map refinement is also applicable to conventionally acquired blip-reversed sequences.

A diffusion tensor imaging study on the auditory system and tinnitus

Tinnitus is an auditory percept in the absence of an external sound source. Mechanisms in the central nervous system are believed to be key in the pathophysiology of tinnitus. Diffusion tensor imaging (DTI) is an MR imaging technique that allows in vivo exploration of white matter tissue in the human brain. Using a probabilistic DTI approach, we determined the characteristics of fiber tracts from the inferior colliculus to the medial geniculate body up to the primary auditory cortex. We also investigated the connections between the auditory system and the amygdala, which may be involved in some forms of tinnitus. White matter tracts were characterized by three quantities: the mean fractional anisotropy, the weighted mean fractional anisotropy and the path strength. All these quantities are measures of the patency of white matter tracts. The most important finding is an increased patency of the white matter tracts between the auditory cortex and the amygdala in tinnitus patients as compared to healthy controls.

Human fronto-tectal and fronto-striatal-tectal pathways activate differently during anti-saccades

Almost all cortical areas in the vertebrate brain take part in recurrent connections through the subcortical basal ganglia (BG) nuclei, through parallel inhibitory and excitatory loops. It has been suggested that these circuits can modulate our reactions to external events such that appropriate reactions are chosen from many available options, thereby imposing volitional control over behavior. The saccade system is an excellent model system to study cortico-BG interactions. In this study two possible pathways were investigated that might regulate automaticity of eye movements in the human brain; the cortico-tectal pathway, running directly between the frontal eye fields (FEF) and superior colliculus (SC) and the cortico-striatal pathway from the FEF to the SC involving the caudate nucleus (CN) in the BG. In an event-related functional magnetic resonance imaging (fMRI) paradigm participants made pro- and anti-saccades. A diffusion tensor imaging (DTI) scan was made for reconstruction of white matter tracts between the FEF, CN and SC. DTI fiber tracts were used to divide both the left and right FEF into two sub-areas, projecting to either ipsilateral SC or CN. For each of these FEF zones an event-related fMRI timecourse was extracted. In general activity in the FEF was larger for anti-saccades. This increase in activity was lateralized with respect to anti-saccade direction in FEF zones connected to the SC but not for zones only connected to the CN. These findings suggest that activity along the contralateral FEF-SC projection is responsible for directly generating anti-saccades, whereas the pathway through the BG might merely have a gating function withholding or allowing a pro-saccade.

Functionally linked resting-state networks reflect the underlying structural connectivity architecture of the human brain

During rest, multiple cortical brain regions are functionally linked forming resting-state networks. This high level of functional connectivity within resting-state networks suggests the existence of direct neuroanatomical connections between these functionally linked brain regions to facilitate the ongoing interregional neuronal communication. White matter tracts are the structural highways of our brain, enabling information to travel quickly from one brain region to another region. In this study, we examined both the functional and structural connections of the human brain in a group of 26 healthy subjects, combining 3 Tesla resting-state functional magnetic resonance imaging time-series with diffusion tensor imaging scans. Nine consistently found functionally linked resting-state networks were retrieved from the resting-state data. The diffusion tensor imaging scans were used to reconstruct the white matter pathways between the functionally linked brain areas of these resting-state networks. Our results show that well-known anatomical white matter tracts interconnect at least eight of the nine commonly found resting-state networks, including the default mode network, the core network, primary motor and visual network, and two lateralized parietal-frontal networks. Our results suggest that the functionally linked resting-state networks reflect the underlying structural connectivity architecture of the human brain.

Efficient correction of inhomogeneous static magnetic field-induced distortion in Echo Planar Imaging

Single-shot Echo Planar Imaging (EPI) is one of the most efficient magnetic resonance imaging (MRI) acquisition schemes, producing relatively high-definition images in 100 ms or less. These qualities make it desirable for Diffusion Tensor Imaging (DTI), functional MRI (fMRI), and Dynamic Susceptibility Contrast MRI (DSC-MRI). However, EPI suffers from severe spatial and intensity distortion due to B(0) field inhomogeneity induced by magnetic susceptibility variations. Anatomically accurate, undistorted images are essential for relating DTI and fMRI images with anatomical MRI scans, and for spatial registration with other modalities. We present here a fast, robust, and accurate procedure for correcting EPI images from such spatial and intensity distortions. The method involves acquisition of scans with opposite phase encoding polarities, resulting in opposite spatial distortion patterns, and alignment of the resulting images using a fast nonlinear registration procedure. We show that this method, requiring minimal additional scan time, provides superior accuracy relative to the more commonly used, and more time consuming, field mapping approach. This method is also highly computationally efficient, allowing for direct "real-time" implementation on the MRI scanner. We further demonstrate that the proposed method can be used to recover dropouts in gradient echo (BOLD and DSC-MRI) EPI images.

Structural correlates of preterm birth in the adolescent brain

OBJECTIVE

The Stockholm Neonatal Project involves a prospective, cross-sectional, population-based, cohort monitored for 12 to 17 years after birth; it was started with the aim of investigating the long-term structural correlates of preterm birth and comparing findings with reports on similar cohorts.

METHODS

High-resolution anatomic and diffusion tensor imaging data measuring diffusion in 30 directions were collected by using a 1.5-T MRI scanner. A total of 143 adolescents (12.18-17.7 years of age) participated in the study, including 74 formerly preterm infants with birth weights of <or=1500 g (range: 645-1486 g) and 69 term control subjects. The 2 groups were well matched with respect to demographic and socioeconomic data. The anatomic MRI data were used for calculation of total brain volumes and voxelwise comparison of gray matter (GM) volumes. The diffusion tensor imaging data were used for voxelwise comparison of white matter (WM) microstructural integrity.

RESULTS

The formerly preterm individuals possessed 8.8% smaller GM volume and 9.4% smaller WM volume. The GM and WM volumes of individuals depended on gestational age and birth weight. The reduction in GM could be attributed bilaterally to the temporal lobes, central, prefrontal, orbitofrontal, and parietal cortices, caudate nuclei, hippocampi, and thalami. Lower fractional anisotropy was observed in the posterior corpus callosum, fornix, and external capsules.

CONCLUSIONS

Although preterm birth was found to be a risk factor regarding long-term structural brain development, the outcome was milder than in previous reports. This may be attributable to differences in social structure and neonatal care practices.

New surgical technique reduces the susceptibility artefact at air-tissue interfaces on in vivo cerebral MRI in the Göttingen minipig

Advanced and exclusive software solutions are offered to reduce susceptibility artefacts on MRI echo-planar sequences. We present a straightforward surgical technique to reduce the cortical distortion and signal loss that normally occur using diffusion tensor imaging (DTI) of the Göttingen minipig brain. Pronounced pneumatisation of the minipig cranium causes considerable susceptibility artefacts at the air/tissue interface around the frontal sinuses. Five Göttingen minipigs had burr holes drilled through the outer lamina of the skull bilaterally at the level of bregma. The underlying frontal sinuses were filled with a suspension of an MRI-compatible alginate. DTI was obtained before and after placing the medium in the sinus, quantifying the change using mutual information and Wilcoxon's rank-sum test. Fibertracking algorithms were applied to visualize the effect of treatment. We showed that the susceptibility artefacts were reduced at the air, bone and brain interfaces and that major cortical fiberbundles could be reliably visualized. This study demonstrated that DTI fibertracking of cortical bundles in experimental animals with extensive skull pneumatisation is feasible even when advanced software is unavailable.

New methods in diffusion-weighted and diffusion tensor imaging

Considerable strides have been made by countless individual researchers in diffusion-weighted imaging (DWI) to push DWI from an experimental tool, limited to a few institutions with specialized instrumentation, to a powerful tool used routinely for diagnostic imaging. The field of DWI constantly evolves, and progress has been made on several fronts. These developments are primarily composed of improved robustness against patient and physiologic motion, increased spatial resolution, new biophysical and tissue models, and new clinical applications for DWI. This article aims to provide a succinct overview of some of these new developments and a description of some of the major challenges associated with DWI.

Microstructural organization of the cingulum tract and the level of default mode functional connectivity

The default mode network is a functionally connected network of brain regions that show highly synchronized intrinsic neuronal activation during rest. However, less is known about the structural connections of this network, which could play an important role in the observed functional connectivity patterns. In this study, we examined the microstructural organization of the cingulum tract in relation to the level of resting-state default mode functional synchronization. Resting-state functional magnetic resonance imaging and diffusion tensor imaging data of 45 healthy subjects were acquired on a 3 tesla scanner. Both structural and functional connectivity of the default mode network were examined. In all subjects, the cingulum tract was identified from the total collection of reconstructed tracts to interconnect the precuneus/posterior cingulate cortex and medial frontal cortex, key regions of the default mode network. A significant positive correlation was found between the average fractional anisotropy value of the cingulum tract and the level of functional connectivity between the precuneus/posterior cingulate cortex and medial frontal cortex. Our results suggest a direct relationship between the structural and functional connectivity measures of the default mode network and contribute to the understanding of default mode network connectivity.

Correction of B0 susceptibility induced distortion in diffusion-weighted images using large-deformation diffeomorphic metric mapping

Geometric distortion caused by B0 inhomogeneity is one of the most important problems for diffusion-weighted images (DWI) using single-shot, echo planar imaging (SS-EPI). In this study, large-deformation, diffeomorphic metric mapping (LDDMM) algorithm has been tested for the correction of geometric distortion in diffusion tensor images (DTI). Based on data from nine normal subjects, the amount of distortion caused by B0 susceptibility in the 3-T magnet was characterized. The distortion quality was validated by manually placing landmarks in the target and DTI images before and after distortion correction. The distortion was found to be up to 15 mm in the population-averaged map and could be more than 20 mm in individual images. Both qualitative demonstration and quantitative statistical results suggest that the highly elastic geometric distortion caused by spatial inhomogeneity of the B0 field in DTI using SS-EPI can be effectively corrected by LDDMM. This postprocessing method is especially useful for correcting existent DTI data without phase maps.

A tractography comparison between turboprop and spin-echo echo-planar diffusion tensor imaging

The development of accurate, non-invasive methods for mapping white matter fiber-tracts is of critical importance. However, fiber-tracking is typically performed on diffusion tensor imaging (DTI) data obtained with echo-planar-based imaging techniques (EPI), which suffer from susceptibility-related image artifacts, and image warping due to eddy-currents. Thus, a number of white matter fiber-bundles mapped using EPI-based DTI data are distorted and/or terminated early. This severely limits the clinical potential of fiber-tracking. In contrast, Turboprop-MRI provides images with significantly fewer susceptibility and eddy-current-related artifacts than EPI. The purpose of this work was to compare fiber-tracking results obtained from DTI data acquired with Turboprop-DTI and EPI-based DTI. It was shown that, in brain regions near magnetic field inhomogeneities, white matter fiber-bundles obtained with EPI-based DTI were distorted and/or partially detected, when magnetic susceptibility-induced distortions were not corrected. After correction, residual distortions were still present and several fiber-tracts remained partially detected. In contrast, when using Turboprop-DTI data, all traced fiber-tracts were in agreement with known anatomy. The inter-session reproducibility of tractography results was higher for Turboprop than EPI-based DTI data in regions near field inhomogeneities. Thus, Turboprop may be a more appropriate DTI data acquisition technique for tracing white matter fibers near regions with significant magnetic susceptibility differences, as well as in longitudinal studies of such fibers. However, the intra-session reproducibility of tractography results was higher for EPI-based than Turboprop DTI data. Thus, EPI-based DTI may be more advantageous for tracing fibers minimally affected by field inhomogeneities.

The effect of physiological noise in phase functional magnetic resonance imaging: from blood oxygen level-dependent effects to direct detection of neuronal currents

Recently, the possibility to use both magnitude and phase image sets for the statistical evaluation of fMRI has been proposed, with the prospective of increasing both statistical power and the spatial specificity. In the present work, several issues that affect the spatial and temporal stability in fMRI phase time series in the presence of physiologic noise processes are reviewed, discussed and illustrated by experiments performed at 3 T. The observed phase value is a fingerprint of the underlying voxel averaged magnetic field variations. Those related to physiological processes can be considered static or dynamic in relation to the temporal scale of a 2D acquisition and will play out on different spatial scales as well: globally across the entire images slice, and locally depending on the constituents and their relative fractions inside the MRI voxel. The 'static' respiration-induced effects lead to magneto-mechanic scan-to-scan variations in the global magnetic field but may also contribute to local BOLD fluctuations due to respiration-related variations in arterial carbon dioxide. Likewise, the 'dynamic' cardiac-related effects will lead to global susceptibility effects caused by pulsatile motion of the brain as well as local blood pressure-related changes in BOLD and changes in blood flow velocity. Finally, subject motion may lead to variations in both local and global tissue susceptibility that will be especially pronounced close to air cavities. Since dissimilar manifestations of physiological processes can be expected in phase and in magnitude images, a direct relationship between phase and magnitude scan-to-scan fluctuations cannot be assumed a priori. Therefore three different models were defined for the phase stability, each dependent on the relation between phase and magnitude variations and the best will depend on the underlying noise processes. By experiments on healthy volunteers at rest, we showed that phase stability depends on the type of post-processing and can be improved by reducing the low-frequency respiration-induced mechano-magnetic effects. Although the manifestations of physiological noise were in general more pronounced in phase than in magnitude images, due to phase wraps and global Bo effects, we suggest that a phase stability similar to that found in magnitude could theoretically be achieved by adequate correction methods. Moreover, as suggested by our experimental data regarding BOLD-related phase effects, phase stability could even supersede magnitude stability in voxels covering dense microvascular networks with BOLD-related fluctuations as the dominant noise contributor. In the interest of the quality of both BOLD-based and nc-MRI methods, future studies are required to find alternative methods that can improve phase stability, designed to match the temporal and spatial scale of the underlying neuronal activity.

Integrated SENSE DTI with correction of susceptibility- and eddy current-induced geometric distortions

Diffusion tensor imaging (DTI) is vulnerable to geometric distortions caused by subject-dependent susceptibility effects and diffusion-weighting direction-dependent eddy currents. Although the introduction of sensitivity encoding (SENSE) has reduced the overall distortions for the same imaging matrix size, this benefit is offset by the increasing demand for higher spatial resolution. Thus, significant distortions remain or are exacerbated in high-resolution SENSE DTI acquisitions. While the susceptibility-induced distortions cause global spatial misregistration, the direction-dependent eddy current-induced distortions cause misregistration among different diffusion-weighted images, leading to errors in the derivation of the diffusion tensor in virtually all voxels, and consequently in resulting diffusion parameters as well as in fiber tracking. Here, we apply a comprehensive approach that corrects for both susceptibility- and eddy current-induced distortions to high-resolution SENSE DTI acquisitions, and demonstrate its effectiveness, efficiency, and reliability in vivo as well as its advantages over a twice-refocused spin-echo sequence. This method should find increased use in modern DTI experiments where SENSE acquisitions are commonly used.

Concurrent correction of geometric distortion and motion using the map-slice-to-volume method in echo-planar imaging

The accuracy of measuring voxel intensity changes between stimulus and rest images in fMRI echo-planar imaging (EPI) data is severely degraded in the presence of head motion. In addition, EPI is sensitive to susceptibility-induced geometric distortions. Head motion causes image shifts and associated field map changes that induce different geometric distortion at different time points. Conventionally, geometric distortion is "corrected" with a static field map independently of image registration. That approach ignores all field map changes induced by head motion. This work evaluates the improved motion correction capability of mapping slice to volume with concurrent iterative field corrected reconstruction using updated field maps derived from an initial static field map that has been spatially transformed and resampled. It accounts for motion-induced field map changes for translational and in-plane rotation motion. The results from simulated EPI time series data, in which motion, image intensity and activation ground truths are available, show improved accuracy in image registration, field corrected image reconstruction and activation detection.

Diffusion tensor imaging and tractwise fractional anisotropy statistics: quantitative analysis in white matter pathology

Background

Information on anatomical connectivity in the brain by measurements of the diffusion of water in white matter tracts lead to quantification of local tract directionality and integrity.

Methods

The combination of connectivity mapping (fibre tracking, FT) with quantitative diffusion fractional anisotropy (FA) mapping resulted in the approach of results based on group-averaged data, named tractwise FA statistics (TFAS). The task of this study was to apply these methods to group-averaged data from different subjects to quantify differences between normal subjects and subjects with defined alterations of the corpus callosum (CC).

Results

TFAS exhibited a significant FA reduction especially in the CC, in agreement with region of interest (ROI)-based analyses.

Conclusion

In summary, the applicability of the TFAS approach to diffusion tensor imaging studies of normal and pathologically altered brains was demonstrated.

Preservation of diffusion tensor properties during spatial normalization by use of tensor imaging and fibre tracking on a normal brain database

White matter connectivity in the human brain can be mapped by diffusion tensor magnetic resonance imaging (DTI). After reconstruction, the diffusion tensors, the diffusion amplitude and the diffusion direction can be displayed on a morphological background. Consequently, diffusion tensor fibre tracking can be applied as a non-invasive in vivo technique for the delineation and quantification of specific white matter pathways. The aim of this study was to show that normalization to the Montreal Neurological Institute (MNI) stereotaxic standard space preserves specific diffusion features. Therefore, techniques for tensor imaging and fibre tracking were applied to the normalized brains as well as to the group averaged brain data. A normalization step of individual data was included by registration to a scanner- and sequence-specific DTI template data set which was created from a normal database transformed to MNI space. The algorithms were tested and validated for a group of 13 healthy controls.

Acquisition and voxelwise analysis of multi-subject diffusion data with tract-based spatial statistics

There is much interest in using magnetic resonance diffusion imaging to provide information on anatomical connectivity in the brain by measuring the diffusion of water in white matter tracts. Among the measures, the most commonly derived from diffusion data is fractional anisotropy (FA), which quantifies local tract directionality and integrity. Many multi-subject imaging studies are using FA images to localize brain changes related to development, degeneration and disease. In a recent paper, we presented a new approach, tract-based spatial statistics (TBSS), which aims to solve crucial issues of cross-subject data alignment, allowing localized cross-subject statistical analysis. This works by transforming the data from the centers of the tracts that are consistent across a study's subjects into a common space. In this protocol, we describe the MRI data acquisition and analysis protocols required for TBSS studies of localized change in brain connectivity across multiple subjects.

Connectivity-based parcellation of human cortex using diffusion MRI: Establishing reproducibility, validity and observer independence in BA 44/45 and SMA/pre-SMA

The identification of specialized, functional regions of the human cortex is a vital precondition for neuroscience and clinical neurosurgery. Functional imaging modalities are used for their delineation in living subjects, but these methods rely on subject cooperation, and many regions of the human brain cannot be activated specifically. Diffusion tractography is a novel tool to identify such areas in the human brain, utilizing underlying white matter pathways to separate regions of differing specialization. We explore the reproducibility, generalizability and validity of diffusion tractography-based localization in four functional areas across subjects, timepoints and scanners, and validate findings against fMRI and post-mortem cytoarchitectonic data. With reproducibility across modalities, clustering methods, scanners, timepoints, and subjects in the order of 80-90%, we conclude that diffusion tractography represents a useful and objective tool for parcellation of the human cortex into functional regions, enabling studies into individual functional anatomy even when there are no specific activation paradigms available.

Retrospective distortion correction for 3D MR diffusion tensor microscopy using mutual information and Fourier deformations

Magnetic resonance diffusion tensor imaging (DTI) can be complicated by distortions that contribute to errors in tissue characterization and loss of fine structures. This work presents a correction scheme based on retrospective registration via mutual information (MI), using Fourier transform (FT)-based deformations to enhance the reliability of the entropy-based image registration. The registration methodology is applied to correct distortions in 3D high-resolution DTI datasets, incorporating a complete set of affine deformations. The results demonstrate that the proposed methodology can consistently and significantly reduce the number of misregistered pixels, leading to marked improvement in the visualization of internal brain white matter (WM) structure via DTI. Post-registration analysis revealed that eddy-current effects cannot fully account for the observed image distortions. Combined, these findings support the non-model-based, postprocessing approach for correcting distortions, and demonstrate the advantages of combining FT-based deformations and MI registration to enhance the practical utility of DTI.

Comparison of diffusion tensor imaging measurements at 3.0 T versus 1.5 T with and without parallel imaging

The diffusion properties of biological tissues are independent of magnetic field strength. Field strength, however, does affect the signal-to-noise ratio (SNR) and artifacts of diffusion-weighted (DW) images, which ultimately will influence the quantitative and spatial accuracy of diffusion tensor imaging (DTI). In this article, the effects of field strength on DTI are reviewed. The effects of parallel imaging also are discussed. A small study comparing DTI measurements both as a function of field strength (1.5 T and 3.0 T) and parallel imaging was performed. Overall, the SNR of the DW images roughly doubled going from 1.5 T to 3.0 T, and there was a relatively small decrease in SNR (15% to 30%) when parallel imaging was used. The increased SNR at 3.0 T resulted in smaller variances in the estimated mean diffusivities and fractional anisotropies. As expected, the amount of echo-planar image distortion roughly doubled going from 1.5 T to 3.0 T, but was reduced by 50% when using parallel imaging. In summary, DTI studies at 3.0 T using parallel imaging will provide significantly improved DTI measurements relative to studies at 1.5 T.

Functional MR imaging at 3.0 T versus 1.5 T: a practical review

This article reviews and discusses recent findings in functional MRI at 1.5 and 3.0 T magnetic field strengths, in research and clinical applications. Particular attention is paid to comparative studies and to an explanation of the physical and biological dependencies leading to potential gains and tradeoffs of functional scanning at magnets with a high field strength.

Preoperative and intraoperative diffusion tensor imaging-based fiber tracking in glioma surgery

OBJECTIVE

To investigate the intraoperative displacement of major white matter tracts during glioma resection by comparing preoperative and intraoperative diffusion tensor imaging-based fiber tracking.

METHODS

In 37 patients undergoing glioma surgery, preoperative and intraoperative diffusion tensor imaging was performed with a 1.5-T magnetic resonance scanner applying an echo-planar imaging sequence with six diffusion directions. For three-dimensional tractography, we implemented a knowledge-based multiple-region-of-interest approach applying user-defined seed regions in the color-coded maps of fractional anisotropy. Tracking was initiated in both the retrograde and orthograde directions according to the direction of the principal eigenvector in each voxel of the region of interest. The tractography results were also assigned color, applying the convention used in color-coded fractional anisotropy maps.

RESULTS

Preoperative and intraoperative fiber tracking was technically feasible in all patients. Fiber tract visualization gave a quick and intuitive overview of the displaced course of white matter tracts in three-dimensional space. Comparison of preoperative and intraoperative tractography depicted a marked shifting of major white matter tracts during glioma removal. Maximum white matter tract shifting ranged from -8 to +15 mm (+2.7 +/- 6.0 mm; mean +/- standard deviation); in 29.7%, an inward and in 62.2%, an outward shifting was detected.

CONCLUSION

Comparing preoperative and intraoperative fiber tracking visualizes a marked shifting and deformation of major white matter tracts because of tumor removal. This shifting emphasizes the need for an intraoperative update of navigation systems during resection of deep-seated tumor portions near eloquent brain areas. Fiber tracking is a method not only for preoperative neurosurgical visualization but also for further intraoperative planning.

Correction for direction-dependent distortions in diffusion tensor imaging using matched magnetic field maps

Diffusion tensor imaging (DTI) has seen increased usage in clinical and basic science research in the past decade. By assessing the water diffusion anisotropy within biological tissues, e.g. brain, researchers can infer different fiber structures important for neural pathways. A typical DTI data set contains at least one base image and six diffusion-weighted images along non-collinear encoding directions. The resultant images can then be combined to derive the three principal axes of the diffusion tensor and their respective cross terms, which can in turn be used to compute fractional anisotropy (FA) maps, apparent diffusion coefficient (ADC) maps, and to construct axonal fibers. The above operations all assume that DTI images along different diffusion-weighting directions for the same brain register to each other without spatial distortions. This assumption is generally false, as the large diffusion-weighting gradients would usually induce eddy currents to generate diffusion-weighting direction-dependent field gradients, leading to mis-registration within the DTI data set. Traditional methods for correcting magnetic field-induced distortions do not usually take into account these direction-dependent eddy currents unique for DTI, and they are usually time-consuming because multiple phase images need to be acquired. In this report, we describe our theory and implementation of an efficient and effective method to correct for the main field and eddy current-induced direction-dependent distortions for DTI images under a unified framework to facilitate the daily practice of DTI acquisitions.

Fiber tracking in the cervical spine and inferior brain regions with reversed gradient diffusion tensor imaging

Diffusion tensor echo planar magnetic resonance imaging of the inferior brain regions and the spinal cord suffers from tissue-air and tissue-bone interfaces, which cause severe susceptibility-induced artifacts. These artifacts consist of image distortions in the phase encode direction and also affect signal intensity. To correct for these distortions, we used the reversed gradient method. We find that most in-plane voxel displacements in the inferior brain regions and the cervical spine can be corrected, yielding a good match of white matter fiber tracts with anatomical reference images. Furthermore, uninterrupted white matter fiber tracts going from the cervical spine up to cortical areas, derived from data acquired in a single acquisition, are presented.

Propeller EPI in the other direction

A new propeller EPI pulse sequence with reduced sensitivity to field inhomogeneities is proposed. Image artifacts such as blurring due to Nyquist ghosting and susceptibility gradients are investigated and compared with those obtained in previous propeller EPI studies. The proposed propeller EPI sequence uses a readout that is played out along the short axis of the propeller blade, orthogonal to the readout used in previous propeller methods. In contrast to long-axis readout propeller EPI, this causes the echo spacing between two consecutive phase-encoding (PE) lines to decrease, which in turn increases the k-space velocity in this direction and hence the pseudo-bandwidth. Long- and short-axis propeller EPI, and standard single-shot EPI sequences were compared on phantoms and a healthy volunteer. Diffusion-weighted imaging (DWI) was also performed on the volunteer. Short-axis propeller EPI produced considerably fewer image artifacts compared to the other two sequences. Further, the oblique blades for the long-axis propeller EPI were also prone to one order of magnitude higher residual ghosting than the proposed short-axis propeller EPI.

Foundations of advanced magnetic resonance imaging

During the past decade, major breakthroughs in magnetic resonance imaging (MRI) quality were made by means of quantum leaps in scanner hardware and pulse sequences. Some advanced MRI techniques have truly revolutionized the detection of disease states and MRI can now-within a few minutes-acquire important quantitative information noninvasively from an individual in any plane or volume at comparatively high resolution. This article provides an overview of the most common advanced MRI methods including diffusion MRI, perfusion MRI, functional MRI, and the strengths and weaknesses of MRI at high magnetic field strengths.

Correction of MR image distortions induced by metallic objects using a 3D cubic B-spline basis set: application to stereotactic surgical planning

Metallic implants in MRI cause spin-echo (SE) images to be distorted in the slice and frequency-encoding directions. Chang and Fitzpatrick (IEEE Trans Med Imaging 1992;11:319-329) proposed a distortion correction method (termed the CF method) based on the magnitude images from two SE acquisitions that differ only in the polarity of the frequency-encoding and slice-selection gradients. In the present study we solved some problems with the CF method, primarily by modeling the field inhomogeneities as a single 3D displacement field built by 3D cubic B-splines. The 3D displacement field was applied in the actual distortion direction in the slice/frequency-encoding plane. To account for patient head motion, a 3D rigid body motion correction was also incorporated in the model. Experiments on a phantom containing an aneurysm clip showed that the knot spacing between the B-splines is a very important factor in both the final image quality and the processing speed. Depending on the knot spacing and the image volume size, the number of unknowns range from a few thousands to over 100,000, leading to processing times ranging from minutes to days. Optimal knot spacing, a means of increasing the processing speed, and other parameters are investigated and discussed.