Hippocampal and cerebellar volumetry in serially acquired MRI volume scans

In this work, we describe methodologies for serial volumetric measurements of hippocampi and cerebella. Serial scans were co-registered and intensity matched prior to the volumetric measurements. Manual drawing was used to define the boundaries of the hippocampi. For the cerebellar volumetric measurements, the brain was automatically segmented from the co-registered scans; manual drawing was used to define the boundary between the cerebellum and the cerebrum and brainstem. The operator was blinded to the nature of the subject (patient or normal control) and the chronological order of the scans. The coefficient of reliability of hippocampal volume measurements in a group of 20 controls was 0.078 cm(3) (3.1% of the mean baseline volume); for the cerebellum, the value was 3.8 cm(3) (3.0% of the mean baseline volume). We conclude that the methods presented are valid and that the software provides a useful integrated tool for the quantitative analysis of structural changes in serially acquired volume MRI data in prospective, blinded studies.     

Feasibility of 3D harmonic contrast imaging

Improved endocardial border delineation with the application of contrast agents should allow for less complex and faster tracing algorithms for left ventricular volume analysis. We developed a fast rotating phased array transducer for 3D imaging of the heart with harmonic capabilities making it suitable for contrast imaging. In this study the feasibility of 3D harmonic contrast imaging is evaluated in vitro. A commercially available tissue mimicking flow phantom was used in combination with Sonovue. Backscatter power spectra from a tissue and contrast region of interest were calculated from recorded radio frequency data. The spectra and the extracted contrast to tissue ratio from these spectra were used to optimize the excitation frequency, the pulse length and the receive filter settings of the transducer. Frequencies ranging from 1.66 to 2.35 MHz and pulse lengths of 1.5, 2 and 2.5 cycles were explored. An increase of more than 15 dB in the contrast to tissue ratio was found around the second harmonic compared with the fundamental level at an optimal excitation frequency of 1.74 MHz and a pulse length of 2.5 cycles. Using the optimal settings for 3D harmonic contrast recordings volume measurements of a left ventricular shaped agar phantom were performed. Without contrast the extracted volume data resulted in a volume error of 1.5%, with contrast an accuracy of 3.8% was achieved. The results show the feasibility of accurate volume measurements from 3D harmonic contrast images. Further investigations will include the clinical evaluation of the presented technique for improved assessment of the heart.     

Using nine degrees-of-freedom registration to correct for changes in voxel size in serial MRI studies

Quantitative longitudinal brain magnetic resonance (MR) studies may be confounded by scanner-related drifts in voxel sizes. Total intracranial volume (TIV) normalisation is commonly used to correct serial cerebral volumetric measurements for these drifts. We hypothesised that automated rigid-body registration of whole brain incorporating automatic scaling correction might also correct for such fluctuations, and might be a more practical alternative. Twenty-three subjects (12 patients with Alzheimer's disease [AD] and 11 controls) had at least two serial T1-weighted volumetric brain MR scans. Ten scans from the control subjects were artificially scaled (stretched) by 1.5, 3.0, 4.6 and 6.1%. A 9-degrees-of-freedom (9dof) registration was used to register the scaled scans back onto the original scans and corresponding scaling factors compared to TIV measurements. A further nine 1-year repeat scans from the AD subjects were artificially scaled and registered (9dof) to baseline. The two correction methods were further assessed using multiple serial scans for each of the 23 subjects (resulting in 49 scan pairs). All serial scans were registered (9dof) to baseline. TIV was measured on all scans. It was found that the 9dof registration successfully recovered the artificially generated scaling changes. Scaling correction using 9dof registration did not alter the amount of brain atrophy measured over the 1-year period in the AD subjects. The 9dof volume scaling factors were very similar to the TIV ratios (repeat TIV over baseline TIV), but less variable (p < 0.001), in both artificial and 'real' scenarios. In the latter, the volume scaling factors allowed identification of two time-points in which a 3% change in voxel size had occurred. Both the 9dof brain registration and TIV correction were successfully able to correct for these fluctuations. Significant shifts in voxel size are a problem in longitudinal brain imaging studies. It is important that such changes are adjusted for: 9dof registration, which is automated and computationally inexpensive, may be superior to the more labour-intensive TIV correction for this purpose.     

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 the 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.     

Reproducibility of MRI-derived measurements of right ventricular volumes and myocardial mass

Magnetic resonance (MR) imaging has been shown to provide accurate measurements of right ventricular (RV) volumes and myocardial mass. The purpose of this study was to evaluate the reproducibility of MR imaging, which in clinical practice may be as important as its absolute accuracy. The reproducibility of MR imaging measurements of the right ventricle was assessed by analyzing 40 serial functional MR imaging examinations of the right ventricle with variance component analysis. Standard deviations and 95% ranges for change were: for RV myocardial mass, 5.9 and 16 g; and for RV ejection fraction, 6.0% and 16%, respectively. Reproducibility was similar for cine and spin-echo MR imaging. The intraobserver and interobserver errors were especially large, indicating that observer subjectivity is the limiting factor in the interpretation of the MR images. This study suggests that the reproducibility of RV measurements is adequate to detect RV hypertrophy and a low ejection fraction in the individual patient. For accurate follow-up examinations, whereby smaller changes are to be detected, the reproducibility of MR imaging measurements may not be sufficient. More effort is needed to improve the reproducibility of MR imaging measurements.     

Quantitative quality assurance in a multicenter HARDI clinical trial at 3 T

A phantom-based quality assurance (QA) protocol was developed for a multicenter clinical trial including high angular resolution diffusion imaging (HARDI). A total of 27 3 T MR scanners from 2 major manufacturers, GE (Discovery and Signa scanners) and Siemens (Trio and Skyra scanners), were included in this trial. With this protocol, agar phantoms doped to mimic relaxation properties of brain tissue are scanned on a monthly basis, and quantitative procedures are used to detect spiking and to evaluate eddy current and Nyquist ghosting artifacts. In this study, simulations were used to determine alarm thresholds for minimal acceptable signal-to-noise ratio (SNR). Our results showed that spiking artifact was the most frequently observed type of artifact. Overall, Trio scanners exhibited less eddy current distortion than GE scanners, which in turn showed less distortion than Skyra scanners. This difference was mainly caused by the different sequences used on these scanners. The SNR for phantom scans was closely correlated with the SNR from volunteers. Nearly all of the phantom measurements with artifact-free images were above the alarm threshold, suggesting that the scanners are stable longitudinally. Software upgrades and hardware replacement sometimes affected SNR substantially but sometimes did not. In light of these results, it is important to monitor longitudinal SNR with phantom QA to help interpret potential effects on in vivo measurements. Our phantom QA procedure for HARDI scans was successful in tracking scanner performance and detecting unwanted artifacts.     

Transfer characteristics of arterial pulsatile force in regional intracranial tissue using dynamic diffusion MRI: A phantom study

Introduction

To clarify the mechanism underlying apparent diffusion coefficient (ADC) changes in regional intracranial tissue during the cardiac cycle, we investigated relationships among ADC changes, volume loading, and intracranial pressure using a hemodialyzer phantom in magnetic resonance imaging (MRI).

Materials and Methods

The hemodialyzer phantom consisted of hollow fibers (HF), the external space of HFs (ES), and a gateway of dialysis solution, filled with syrup solution and air. The high-volume and low-volume loadings were periodically applied to HFs by a to-and-fro flow pump, and syrup solution was permitted to enter or leave HFs during the volume loading cycles. ADC maps at each volume loading phase were obtained using ECG-triggered single-shot diffusion echo-planar imaging. Dynamic phase contrast MRI was also used to measure volume loading to the phantom. We compared the ADC changes, volume loading, and intracranial pressure in the phantom during the cardiac cycle.

Results

ADC changes synchronized significantly with absolute volumetric flow rate change. The maximum ADC change was higher in high-volume loading cycles than in low-volume loading cycles. Results showed that the water molecules in ES fluctuated according to the force transferred from HF to ES. ADC changes were dependent upon the volumetric flow rate during the cardiac cycle.

Conclusions

Our original phantom allowed us to clarify the mechanism underlying water fluctuations in intracranial tissues. Measurement of maximum changes in ADC is an effective method to define the transfer characteristics of the arterial pulsatile force in regional intracranial tissue.     

Intracranial vascular feature changes in time of flight MR angiography in patients undergoing carotid revascularization surgery

PurposeTo characterize the intracranial vascular features extracted from time of flight (TOF) images and their changes from baseline to follow-up in patients undergoing carotid revascularization, using arterial spin labeling (ASL) cerebral blood flow (CBF) measurement as a reference.MethodsIn this retrospective study, brain TOF and ASL images of 99 subjects, acquired before, within 48 h, and/or 6 months after, carotid revascularization surgery were analyzed. TOF images were analyzed using a custom software (iCafe) to quantify intracranial vascular features, including total vessel length, total vessel volume, and number of branches. Mean whole-brain CBF was calculated from ASL images. ASL scans showing low ASL signal in the entire flow territory of an internal carotid artery (ICA), which may be caused by labeling failure, were excluded. Changes and correlations between time points were analyzed separately for TOF intracranial vascular features and ASL CBF.ResultsSimilar to ASL CBF, TOF vascular features (i.e. total vessel length, total vessel volume and number of branches) increased dramatically from baseline to post-surgery, then returned to a level slightly higher than the baseline in long-term follow-up (All P < 0.05). Correlation between time points was observed for all three TOF vascular features but not for ASL CBF.ConclusionIntracranial vascular features, including total vessel length, total vessel volume and number of branches, extracted from TOF images are useful in detecting brain blood flow changes induced by carotid revascularization surgery.     

A quantitative comparison of two methods to correct eddy current-induced distortions in DT-MRI

Eddy current-induced geometric distortions of single-shot, diffusion-weighted, echo-planar (DW-EP) images are a major confounding factor to the accurate determination of water diffusion parameters in diffusion tensor MRI (DT-MRI). Previously, it has been suggested that these geometric distortions can be removed from brain DW-EP images using affine transformations determined from phantom calibration experiments using iterative cross-correlation (ICC). Since this approach was first described, a number of image-based registration methods have become available that can also correct eddy current-induced distortions in DW-EP images. However, as yet no study has investigated whether separate eddy current calibration or image-based registration provides the most accurate way of removing these artefacts from DT-MRI data. Here we compare how ICC phantom calibration and affine FLIRT (http://www.fmrib.ox.ac.uk), a popular image-based multi-modal registration method that can correct both eddy current-induced distortions and bulk subject motion, perform when registering DW-EP images acquired with different slice thicknesses (2.8 and 5 mm) and b-values (1000 and 3000 s/mm(2)). With the use of consistency testing, it was found that ICC was a more robust algorithm for correcting eddy current-induced distortions than affine FLIRT, especially at high b-value and small slice thickness. In addition, principal component analysis demonstrated that the combination of ICC phantom calibration (to remove eddy current-induced distortions) with rigid body FLIRT (to remove bulk subject motion) provided a more accurate registration of DT-MRI data than that achieved by affine FLIRT.     

Partial volume effects in MRI studies of multiple sclerosis

We have estimated the accuracy of volume measurements of multiple sclerosis (MS) lesions made using magnetic resonance imaging (MRI) for lesions of comparable diameter to the image slice thickness. We used a phantom containing objects of known volume and obtained images using a range of slice thicknesses. Measurements on the phantom were used to assess a theoretical model, which was then employed to investigate the effects of image dimensions and geometry upon volume measurement accuracy. We observed measured volume to be dependent upon slice thickness. Thin slices gave the most accurate estimate of volume. As slice thickness increased relative to object diameter, the error in the volume measurement increased (to as much as 100%), the volume measured being dependent on the position of the object relative to the slice center. Using a signal intensity threshold value of 50% to outline objects gave results closest to the actual volume. As expected, a lower threshold value tended to give higher volume estimates (up to 100% larger), as did a semi-automated local edge detection technique. For accurate volume measurement, the slice thickness should be no more than a fifth of anticipated object diameter. For typical MS lesions (7 mm in diameter), this implies using a 1.5-mm slice thickness. For serial studies, a repositioning error of 1 mm could lead to differences in the volume measurement of individual lesions of up to 12% between studies for lesions of typical MS size and 5-mm slice thickness. These results emphasize the need for accurate patient repositioning, relatively thin slices, for regular quality assurance checks to ensure that pixel size and slice position are correct and stable over time, and that lesion outlining is performed in a consistent fashion. We would recommend the use of a 3D sequence with 1 mm cubic voxels for accurate measurements of MS lesions.     

Automatic quantification of muscle volumes in magnetic resonance imaging scans of the lower extremities

Muscle volume measurements are essential for an array of diseases ranging from peripheral arterial disease, muscular dystrophies, neurological conditions to sport injuries and aging. In the clinical setting, muscle volume is not routinely measured due to the lack of standardized ways for its repeatable quantification. In this paper, we present magnetic resonance muscle quantification (MRMQ), a method for the automatic quantification of thigh muscle volume in magnetic resonance imaging (MRI) scans. MRMQ integrates a thigh segmentation and nonuniform image gradient correction step, followed by feature extraction and classification. The classification step leverages prior probabilities, introducing prior knowledge to a maximum a posteriori classifier. MRMQ was validated on 344 slices taken from 60 MRI scans. Experiments for the fully automatic detection of muscle volume in MRI scans demonstrated an averaged accuracy, sensitivity and specificity for leave-one-out cross-validation of 88.3%, 93.6% and 87.2%, respectively.     

Correction of intensity nonuniformity in spin-echo T(1)-weighted images

This paper presents a method to correct intensity nonuniformity in spin-echo T(1)-weighted images and particularly the inhomogeneities due to RF transmission imperfections which have tissue-dependent effects through the T(1) relaxation times. This method is based on the use of a uniform phantom, first for classic normalization by division by the phantom images, and second for T(1)-correction using the RF transmitted cartography. We present experimental results from a bi-phasic (oil/water) phantom and from a salmon with a 0.2 T imager. The results demonstrate the efficiency of the method in the two cases and its ability to cope with partial volume effect.     

A two-compartment gel phantom for optimization and quality assurance in clinical BOLD fMRI

Clinical applications of blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) depend heavily on robust paradigms, imaging methods and analysis procedures. In this work, as a means to optimize and perform quality assurance of the entire imaging and analysis chain, a phantom that provides a well known and reproducible signal change similar to a block type fMRI experiment is presented. It consists of two gel compartments with slightly different T2 that dynamically enter and leave the imaged volume. The homogeneous gel in combination with a cylindrical geometry results in a well-defined T*2 difference causing a signal difference between the two compartments in T*2-weighted MR images. From time series data obtained with the phantom, maps of percent signal change (PSC) and t-values are calculated. As an example of image parameter optimisation, the phantom is demonstrated to be useful for accurate determination of the influence of echo time (TE) on BOLD fMRI results, taking the t-value as a measure of sensitivity. In addition, the phantom is proposed as a tool for quality assurance (QA) since reproducible time series and t-maps are obtained in a series of independent repeat experiments. The phantom is relatively simple to build and can therefore be used by any clinical fMRI center.     

Generalised cerebral atrophy following temporal lobectomy for intractable epilepsy associated with mesial temporal sclerosis

Studies of post-operative imaging data have mainly concentrated on brain atrophy following radiotherapy and/or chemotherapy. We have investigated the effect of conventional surgery on the unresected brain tissue based on the comparison of magnetic resonance images acquired pre- and post-operatively in 13 subjects with a history of mesio-temporal epilepsy. The pre- and post-operative scans were co-registered prior to volumetric analysis. The total brain volume (TBV) was calculated by semi-automated segmentation, and the total volume loss was the difference between the post-operative and pre-operative TBV. The total volume of resection was determined by manual delineation in the post-operative scan. The atrophy volume in the post-operative scan was calculated as the difference between the total volume loss and the resection volume. In 6 cases, there was generalised cerebral atrophy of the order 4-5% of the total brain volume. In addition to the automated volumetric technique, the images were assessed by two expert neuroradiologists. There was complete correspondence between their assessment and the automated technique. The causes and significance of this phenomenon are unknown but it requires further investigation as it may be related to seizure control and neuropsychological changes following epilepsy surgery.     

How does brain MRI lesion volume change on serial scans in patients with multiple sclerosis?

Although lesion load changes on conventional T₂-weighted brain magnetic resonance imaging (MRI) scans from patients with multiple sclerosis (MS) are used to monitor the effect of treatment, there is no clear definition of how lesion load changes over years according to the lesion load present at a baseline evaluation. In the present study, we evaluated the relationship between lesion load changes over time and lesion load at a baseline evaluation in a group of untreated patients with MS. We scanned nineteen patients on two separate occasions with a mean interval 16.4 months between the two examinations. In each scanning session, a scan with forty contiguous 3-mm-thick axial slices was acquired. We assessed MRI lesion loads using a semi-automated local thresholding technique. Both a linear (p < 0.0001) and a quadratic component (p = 0.0008) of the baseline volume were significant in describing the follow-up volume. The equation to model this finding was as follows: V_f = β₀ V_b + β₁ (V_b)², where V_f is the lesion volume at follow-up, V_b is the lesion volume at baseline, β₀ = 0.834 (SE = 0.098), and β₁ = 0.014 (SE = 0.003) (mL)⁻¹. Our data indicate that lesion volume changes detectable on serial brain MRI studies from patients with MS are dependent on the extent of lesion burden present on the baseline MRI scans. This finding has to be considered when planning phase III trials.     

Computer-assisted enhanced volumetric segmentation magnetic resonance imaging data using a mixture of artificial neural networks

An accurate computer-assisted method able to perform regional segmentation on 3D single modality images and measure its volume is designed using a mixture of unsupervised and supervised artificial neural networks. Firstly, an unsupervised artificial neural network is used to estimate representative textures that appear in the images. The region of interest of the resultant images is selected by means of a multi-layer perceptron after a training using a single sample slice, which contains a central portion of the 3D region of interest.The method was applied to magnetic resonance imaging data collected from an experimental acute inflammatory model (T(2) weighted) and from a clinical study of human Alzheimer's disease (T(1) weighted) to evaluate the proposed method. In the first case, a high correlation and parallelism was registered between the volumetric measurements, of the injured and healthy tissue, by the proposed method with respect to the manual measurements (r = 0.82 and p < 0.05) and to the histopathological studies (r = 0.87 and p < 0.05). The method was also applied to the clinical studies, and similar results were derived of the manual and semi-automatic volumetric measurement of both hippocampus and the corpus callosum (0.95 and 0.88).     

A parametric imaging approach for the segmentation of ultrasound data

When an ultrasonic examination is performed, a segmentation tool would often be very useful, either for the detection of pathologies, the early diagnosis of cancer or the follow-up of the lesions. Such a tool must be both reliable and accurate. However, because of the relatively reduced quality of ultrasound images due to the speckled texture, the segmentation of ultrasound data is a difficult task. We have previously proposed to tackle the problem using a multiresolution Bayesian region-based algorithm. For computation time purposes, a multiresolution version has been implemented. In order to improve the quality of the segmentation, we propose to perform the segmentation not only from the envelope image but to combine more information about the properties of the tissues in the segmentation process. Several acoustical parameters have thus been computed, either directly from the images or from the radio-frequency (RF) signal.

In a previous study, two parametric images were involved in the segmentation process. The parameter represented the integrated backscatter (IBS) and the mean central frequency (MCF), which is a measurement related to the attenuation of ultrasound waves in the media. In this study, parameters representative of the scattering conditions in the tissue are evaluated in the multiparametric segmentation process. They are extracted from the K-distribution (,b) and the Nakagami distribution (m,Ω) and are related to the local density of scatterers (,m), the size of the scatterers (b) and the backscattering properties of the medium (Ω).

The acoustical features are calculated locally on a sliding window. This procedure allows to built parametric mapping representing the particular characteristics of the medium. To test the influence of the acoustical parameters in the segmentation process, a set of numerical phantoms has been computed using the Field software developed by J.A. Jensen. Each phantom consists in two regions with two different acoustical properties: the density of scatterers and the scattering amplitude. From both the simulated RF signals and envelope images, the parameters have been computed; their relevance to represent a particular characteristic of the medium is evaluated. The segmentation has been processed for each phantom. The ability of each parameter to improve the segmentation results is validated. A agar–gel phantom has also been created, in order to test the accuracy of the parameters in conditions closer to the in vivo ultrasound imaging. This phantom contains four inclusions with different concentrations of silica. A B&K ultrasound device provides the RF data. The quantification of the segmentation quality is based on the rate of correctly classified pixels and it has been computed for all the parameters either from the field images or the phantom images. The large improvement in the segmentation results obtained reveals that the multiparametric segmentation scheme proposed in this study can be a reliable tool for the processing of noisy ultrasound data.     

On the use of water phantom images to calibrate and correct eddy current induced artefacts in MR diffusion tensor imaging

The accurate determination of absolute measures of diffusion anisotropy in vivo using single-shot, echo-planar imaging techniques requires the acquisition of a set of high signal-to-noise ratio, diffusion-weighted images that are free from eddy current induced image distortions. Such geometric distortions can be characterized and corrected in brain imaging data using magnification (M), translation (T), and shear (S) distortion parameters derived from separate water phantom calibration experiments. Here we examine the practicalities of using separate phantom calibration data to correct high b-value diffusion tensor imaging data by investigating the stability of these distortion parameters, and hence the eddy currents, with time. It is found that M, T, and S vary only slowly with time (i.e., on the order of weeks), so that calibration scans need not be performed after every patient examination. This not only minimises the scan time required to collect the calibration data, but also the computational time needed to characterize these eddy current induced distortions. Examples of how measurements of diffusion anisotropy are improved using this post-processing scheme are also presented.     

Reproducibility of the quantitative assessment of cartilage morphology and trabecular bone structure with magnetic resonance imaging at 7 T

To assess the reproducibility of quantitative measurements of cartilage morphology and trabecular bone structure of the knee at 7 T, high-resolution sagittal spoiled gradient-echo images and high-resolution axial fully refocused steady-state free-precession (SSFP) images from six healthy volunteers were acquired with a 7-T scanner. The subjects were repositioned between repeated scans to test the reproducibility of the measurements. The reproducibility of each measurement was evaluated using the coefficient(s) of variation (CV). The computed CV were 1.13% and 1.55% for cartilage thickness and cartilage volume, respectively, and were 2.86%, 1.07%, 2.27% and 3.30% for apparent bone volume over total volume fraction (app.BV/TV), apparent trabecular number (app.Tb.N), apparent trabecular separation (app.Tb.Sp) and apparent trabecular thickness (app.Tb.Th), respectively. The results demonstrate that quantitative assessment of cartilage morphology and trabecular bone structure is reproducible at 7 T and motivates future musculoskeletal applications seeking the high-field strength's superior signal-to-noise ratio.