Deep Learning Segmentation of the Nucleus Basalis of Meynert on 3T MRI.

BACKGROUND AND PURPOSE: The nucleus basalis of Meynert is a key subcortical structure that is important in arousal and cognition and has been explored as a deep brain stimulation target but is difficult to study due to its small size, variability among patients, and lack of contrast on 3T MR imaging. Thus, our goal was to establish and evaluate a deep learning network for automatic, accurate, and patient-specific segmentations with 3T MR imaging. MATERIALS AND METHODS: Patient-specific segmentations can be produced manually; however, the nucleus basalis of Meynert is difficult to accurately segment on 3T MR imaging, with 7T being preferred. Thus, paired 3T and 7T MR imaging data sets of 21 healthy subjects were obtained. A test data set of 6 subjects was completely withheld. The nucleus was expertly segmented on 7T, providing accurate labels for the paired 3T MR imaging. An external data set of 14 patients with temporal lobe epilepsy was used to test the model on brains with neurologic disorders. A 3D-Unet convolutional neural network was constructed, and a 5-fold cross-validation was performed. RESULTS: The novel segmentation model demonstrated significantly improved Dice coefficients over the standard probabilistic atlas for both healthy subjects (mean, 0.68 [SD, 0.10] versus 0.45 [SD, 0.11], P = .002, t test) and patients (0.64 [SD, 0.10] versus 0.37 [SD, 0.22], P < .001). Additionally, the model demonstrated significantly decreased centroid distance in patients (1.18 [SD, 0.43] mm, 3.09 [SD, 2.56] mm, P = .007). CONCLUSIONS: We developed the first model, to our knowledge, for automatic and accurate patient-specific segmentation of the nucleus basalis of Meynert. This model may enable further study into the nucleus, impacting new treatments such as deep brain stimulation.

Adaptive Language Mapping Paradigms for Presurgical Language Mapping.

BACKGROUND AND PURPOSE: Functional MR imaging is widely used for preoperative language assessment in candidates for resective neurosurgery. Language mapping paradigms that are adaptive to participant performance have the potential to engage the language network more robustly and consistently, resulting in more accurate functional maps. The aim of the current study was to compare two adaptive paradigms with the recommended language mapping paradigms that constitute the current standard of care. MATERIALS AND METHODS: Seventy-three patients undergoing fMRI for language lateralization and/or localization completed an adaptive semantic matching paradigm, an adaptive phonological judgment paradigm, and two standard paradigms: sentence completion and word generation. The paradigms were compared in terms of the degree to which they yielded lateralized language maps and the extent of activation in frontal, temporal, and parietal language regions. RESULTS: The adaptive semantic paradigm resulted in the most strongly lateralized activation maps, the greatest extent of frontal and temporal activations, and the greatest proportion of overall satisfactory language maps. The adaptive phonological paradigm identified anterior inferior parietal phonological encoding regions in most patients, unlike any of the other paradigms. CONCLUSIONS: The adaptive language mapping paradigms investigated have several psychometric advantages compared with currently recommended paradigms. Adoption of these paradigms could increase the likelihood of obtaining satisfactory language maps in each individual patient.

The Contribution of Common Surgically Implanted Hardware to Functional MR Imaging Artifacts.

BACKGROUND AND PURPOSE: Blood oxygenation level-dependent MR imaging is increasingly used clinically to noninvasively assess cerebrovascular reactivity and/or language and motor function. However, many patients have metallic implants, which will induce susceptibility artifacts, rendering the functional information uninformative. Here, we calculate and interpret blood oxygenation level-dependent MR imaging artifact impact arising from surgically implanted hardware. MATERIALS AND METHODS: A retrospective analysis of all blood oxygenation level-dependent MRIs (n = 343; B0 = 3T; TE = 35 ms; gradient echo EPI) acquired clinically (year range = 2006-2014) at our hospital was performed. Blood oxygenation level-dependent MRIs were most commonly prescribed for patients with cerebrovascular disease (n = 80) or patients undergoing language or motor localization (n = 263). Artifact volume (cubic centimeters) and its impact on clinical interpretation were determined by a board-certified neuroradiologist. RESULTS: Mean artifact volume associated with intracranial hardware was 4.3 ± 3.2 cm(3) (range = 1.1-9.4 cm(3)). The mean artifact volume from extracranial hardware in patients with cerebrovascular disease was 28.4 ± 14.0 cm(3) (range = 6.1-61.7 cm(3)), and in patients with noncerebrovascular disease undergoing visual or motor functional mapping, it was 39.9 (3)± 27.0 cm(3) (range = 6.9-77.1 cm(3)). The mean artifact volume for ventriculoperitoneal shunts was 95.7 ± 39.3 cm(3) (range = 64.0-139.6 cm(3)). Artifacts had no-to-mild effects on clinical interpretability in all patients with intracranial implants. Extracranial hardware artifacts had no-to-moderate impact on clinical interpretability, with the exception of 1 patient with 12 KLS-Martin maxDrive screws with severe artifacts precluding clinical interpretation. All examined ventriculoperitoneal shunts resulted in moderate-to-severe artifacts, limiting clinical interpretation. CONCLUSIONS: Blood oxygenation level-dependent MR imaging yields interpretable functional maps in most patients beyond a small (30-40 cm(3)) artifact surrounding the hardware. Exceptions were ventriculoperitoneal shunts, particularly those with programmable valves and siphon gauges, and large numbers of KLS-Martin maxDrive screws.

Comparison of functional MRI image realignment tools using a computer-generated phantom.

This study discusses the development of a computer-generated phantom to compare the effects of image realignment programs on functional MRI (fMRI) pixel activation. The phantom is a whole-head MRI volume with added random noise, activation, and motion. It allows simulation of realistic head motions with controlled areas of activation. Without motion, the phantom shows the effects of realignment on motion-free data sets. Prior to realignment, the phantom illustrates some activation corruption due to motion. Finally, three widely used realignment packages are examined. The results showed that the most accurate algorithms are able to increase specificity through accurate realignment while maintaining sensitivity through effective resampling techniques. In fact, accurate realignment alone is not a powerful indicator of the most effective algorithm in terms of true activation.

Cortical activation during Braille reading is influenced by early visual experience in subjects with severe visual disability: a correlational fMRI study.

Functional magnetic resonance imaging was performed on blind adults resting and reading Braille. The strongest activation was found in primary somatic sensory/motor cortex on both cortical hemispheres. Additional foci of activation were situated in the parietal, temporal, and occipital lobes where visual information is processed in sighted persons. The regions were differentiated most in the correlation of their time courses of activation with resting and reading. Differences in magnitude and expanse of activation were substantially less significant. Among the traditionally visual areas, the strength of correlation was greatest in posterior parietal cortex and moderate in occipitotemporal, lateral occipital, and primary visual cortex. It was low in secondary visual cortex as well as in dorsal and ventral inferior temporal cortex and posterior middle temporal cortex. Visual experience increased the strength of correlation in all regions except dorsal inferior temporal and posterior parietal cortex. The greatest statistically significant increase, i.e., approximately 30%, was in ventral inferior temporal and posterior middle temporal cortex. In these regions, words are analyzed semantically, which may be facilitated by visual experience. In contrast, visual experience resulted in a slight, insignificant diminution of the strength of correlation in dorsal inferior temporal cortex where language is analyzed phonetically. These findings affirm that posterior temporal regions are engaged in the processing of written language. Moreover, they suggest that this function is modified by early visual experience. Furthermore, visual experience significantly strengthened the correlation of activation and Braille reading in occipital regions traditionally involved in the processing of visual features and object recognition suggesting a role for visual imagery.

Normal human right and left ventricular mass, systolic function, and gender differences by cine magnetic resonance imaging.

Our objective was to establish normal ranges of left and right ventricular mass and function with cine magnetic resonance imaging (MRI) and to determine gender differences. Seventy-five healthy subjects (age range 8-55, mean 28 yr) were studied with cine MRI. Ten dogs were imaged for autopsy validation with a mean difference between actual and MRI-determined mass of 0.2 A +/- 8.4 g. Intraobserver and interobserver variability and interstudy variability were 5-6%. All parameters were significantly different between males and females except ejection fraction and the left ventricular mass to end-diastolic volume ratio. Agreement with published autopsy series, including gender differences, was excellent. This study presents normative MRI data that can be used for comparing individual patients and for further study of right and left ventricular interaction.

Alterations in pulmonary artery flow patterns and shear stress determined with three-dimensional phase-contrast magnetic resonance imaging in Fontan patients.

OBJECTIVE: This study compares in vivo pulmonary blood flow patterns and shear stresses in patients with either the direct atrium-pulmonary artery connection or the bicaval tunnel connection of the Fontan procedure to those in normal volunteers. Comparisons were made with the use of three-dimensional phase contrast magnetic resonance imaging. METHODS: Three-dimensional velocities, flows, and pulmonary artery cross-sectional areas were measured in both pulmonary arteries of each subject. Axial, circumferential, and radial shear stresses were calculated with the use of velocities and estimates of viscosity. RESULTS: The axial velocities were not significantly different between subject groups. However, the flows and cross-sectional areas were higher in the normal group than in the two patient groups in both pulmonary arteries. The group with the bicaval connection had circular swirling in the cross section of both pulmonary arteries, causing higher shear stresses than in the controls. The disorder caused by the connection of the atrium to the pulmonary artery caused an increase in some shear stresses over the controls, but not higher than those found in the group having a bicaval tunnel. CONCLUSIONS: We found that pulmonary flow was equally reduced compared with normal flow in both patient groups. This reduction in flow can be attributed in part to the reduced size of the pulmonary arteries in both patient groups without change in axial velocity. We also found higher shear stress acting on the wall of the vessels in the patients having a bicaval tunnel, which may alter endothelial function and affect the longevity of the repair.

Normal three-dimensional pulmonary artery flow determined by phase contrast magnetic resonance imaging.

In this study, an application was developed to measure three-dimensional blood flow in the main, right, and left pulmonary arteries of seven healthy volunteers using phase contrast magnetic resonance imaging (MRI). Presently, no other noninvasive technique is capable of providing this information. Flow, mean velocity, kinetic energy, and cross-sectional area were measured at multiple phases of the cardiac cycle and were consistent with previously reported values measured with one-dimensional velocity encoded MRI and Doppler echocardiography. Additionally, axial, circumferential, and radial shear stresses near the wall of the vessel at multiple phases of the cardiac cycle were estimated using the in-plane velocities. All three shear stresses were relatively constant along the vessel wall and throughout the cardiac cycle (approximately 7 dyn/cm2). This three-dimensional characterization of normal pulmonary blood flow provides a base line to which effects of altered pulmonary artery flow patterns in disease can be compared. [Morgan, V. L., T. P. Graham, Jr., and C. H. Lorenz. Circulation Suppl. 94:I-417 (abstract), 1996].

Application of linear optimization techniques to MRI phase contrast blood flow measurements.

The goal of this study was to use linear optimization techniques as a systematic method of cine phase contrast pulse sequence design and to apply this technique to the measurement of blood flow in vivo. The optimized waveforms were validated in a constant flow phantom with average velocities ranging from 5 to 50 cm/s. The same optimized sequence was also run in a segmented k-space variation with five phase encoding lines per segment. The magnetic resonance (MR) derived velocity measurements were accurate over the entire range of velocities tested (p < .05) in both cases. The same optimized pulse sequence was applied to the measurement of flow in main pulmonary artery of five normal volunteers and compared with stroke volumes and cardiac outputs calculated from right ventricular volume measurements. These measurements showed a mean difference between the MR phase contrast calculated stroke volume and the volumetric stroke volume measurement of 9.8 +/- 11.6%. The mean difference between the calculated phase contrast cardiac output and the volumetric cardiac output was 4.4 +/- 10%. These results imply that optimization techniques are an efficient method for designing cine phase contrast pulse sequences.