Automated 3-D extraction of inner and outer surfaces of cerebral cortex from MRI

Automatic computer processing of large multidimensional images such as those produced by magnetic resonance imaging (MRI) is greatly aided by deformable models, which are used to extract, identify, and quantify specific neuroanatomic structures. A general method of deforming polyhedra is presented here, with two novel features. First, explicit prevention of self-intersecting surface geometries is provided, unlike conventional deformable models, which use regularization constraints to discourage but not necessarily prevent such behavior. Second, deformation of multiple surfaces with intersurface proximity constraints allows each surface to help guide other surfaces into place using model-based constraints such as expected thickness of an anatomic surface. These two features are used advantageously to identify automatically the total surface of the outer and inner boundaries of cerebral cortical gray matter from normal human MR images, accurately locating the depths of the sulci, even where noise and partial volume artifacts in the image obscure the visibility of sulci. The extracted surfaces are enforced to be simple two-dimensional manifolds (having the topology of a sphere), even though the data may have topological holes. This automatic 3-D cortex segmentation technique has been applied to 150 normal subjects, simultaneously extracting both the gray/white and gray/cerebrospinal fluid interface from each individual. The collection of surfaces has been used to create a spatial map of the mean and standard deviation for the location and the thickness of cortical gray matter. Three alternative criteria for defining cortical thickness at each cortical location were developed and compared. These results are shown to corroborate published postmortem and in vivo measurements of cortical thickness.     

Automated voxel-based 3D cortical thickness measurement in a combined Lagrangian–Eulerian PDE approach using partial volume maps

Accurate cortical thickness estimation is important for the study of many neurodegenerative diseases. Many approaches have been previously proposed, which can be broadly categorised as mesh-based and voxel-based. While the mesh-based approaches can potentially achieve subvoxel resolution, they usually lack the computational efficiency needed for clinical applications and large database studies. In contrast, voxel-based approaches, are computationally efficient, but lack accuracy. The aim of this paper is to propose a novel voxel-based method based upon the Laplacian definition of thickness that is both accurate and computationally efficient. A framework was developed to estimate and integrate the partial volume information within the thickness estimation process. Firstly, in a Lagrangian step, the boundaries are initialized using the partial volume information. Subsequently, in an Eulerian step, a pair of partial differential equations are solved on the remaining voxels to finally compute the thickness. Using partial volume information significantly improved the accuracy of the thickness estimation on synthetic phantoms, and improved reproducibility on real data. Significant differences in the hippocampus and temporal lobe between healthy controls (NC), mild cognitive impaired (MCI) and Alzheimer’s disease (AD) patients were found on clinical data from the ADNI database. We compared our method in terms of precision, computational speed and statistical power against the Eulerian approach. With a slight increase in computation time, accuracy and precision were greatly improved. Power analysis demonstrated the ability of our method to yield statistically significant results when comparing AD and NC. Overall, with our method the number of samples is reduced by 25% to find significant differences between the two groups.     

Fusion of autoradiographs with an MR volume using 2-D and 3-D linear transformations

In the past years, the development of 3-D medical imaging has enabled the 3-D imaging of in vivo tissues, from an anatomical (MR, CT) or even functional (fMRI, PET, SPECT) point of view. However, despite immense technological progress, the resolution of these images is still short of the level of anatomical or functional details that in vitro imaging (e.g., histology, autoradiography) permits. The motivation of this work is to compare fMRI activations to activations observed in autoradiographic images from the same animals. We aim to fuse post-mortem autoradiographic data with a pre-mortem anatomical MR image. We first reconstruct a 3-D volume from the 2-D autoradiographic sections, coherent both in geometry and intensity. Then, this volume is fused with the MR image. This way, we ensure that the reconstructed 3-D volume can be superimposed onto the MR image that represents the reference anatomy. We demonstrate that this fusion can be achieved by using only simple global transformations (rigid and/or affine, 2-D and 3-D), while yielding very satisfactory results.     

Measurement of cortical thickness using an automated 3-D algorithm: a validation study

A validation study was conducted to assess the accuracy of the algorithm developed by MacDonald et al. (1999) for measuring cortical thickness. This algorithm automatically determines the cortical thickness by 3-D extraction of the inner and outer surfaces of the cerebral cortex from an MRI scan. A manual method of tagging the grey-csf and grey-white interface was used on 20 regions (10 cortical areas found in each hemisphere) in 40 MRIs of the brain to validate the algorithm. The regions were chosen throughout the cortex to get broad assessment of the algorithm's performance. Accuracy was determined by an anatomist tagging the csf-grey and grey-white borders of selected gyri and by allowing the algorithm to determine the csf-grey and grey-white borders and the corresponding cortical thickness of the same region. Results from the manual and automatic methods were statistically compared using overall ANOVA and paired t tests for each region. The manual and automatic methods were in agreement for all but 4 of the 20 regions tested. The four regions where there were significant differences between the two methods were the insula left and right, the right cuneus, and the right parahippocampus. We conclude that the automatic algorithm is valid for most of the cortex and provides a viable alternative to manual methods of determining cortical thickness in vivo. However, caution should be taken when measuring the regions mentioned previously where the results of the algorithm can be biased by surrounding grey structures.     

Automated detection of impervious surfaces using night-time light and Landsat images based on an iterative classification framework

ABSTRACT

A novel workflow for automated detecting of impervious surface by using night-time light and Landsat images at the individual city scale is proposed. This approach is composed by of three steps. In the beginning, urban, peri-urban and rural regions are detected from the night-time light image by a contour line algorithm. Then, using Landsat TM image, region-specific spectral index analysis is employed to generate initial training samples of urban land covers. Finally, an iterative classification framework is applied to select new training samples by integrating spectral and spatial information and to obtain the final mapping result. Experimental results of two cities show that the proposed method produces higher classification accuracy than the ones using the manual-sampling methods. Moreover, further validations suggested that the spatial information is able to effectively increase the producer’s accuracy of impervious surface. This automated approach is potentially important for large-scale regional impervious surface mapping and application.     

Automated 3-D registration of MR and CT images of the head

This paper discusses the application of voxel similarity measures in the automated registration of clinically acquired MR and CT data of the head. We describe a novel single-start multi-resolution approach to the optimization of these measures, and the issues involved in applying this to data having a range of different fields of view and sampling resolution. We compare four proposed measures of voxel similarity using the same optimization scheme when presented with 10 pairs of images with a range of initial misregistrations. The registration estimates are compared with those provided by manual point-based registration and evaluated by visual inspection to give an assessment of the robustness and accuracy of the different measures. One full-volume CT image set is used to investigate the performance of each measure when used to align truncated images from different regions in the head. The soft tissue correlation and mutual information measures were found to provide the most robust measures of misregistration, providing results comparable to or better than those from manual point-based registration for all but the most truncated image volumes.     

Segmentation of the skull in MRI volumes using deformable model and taking the partial volume effect into account

Segmentation of the skull in medical imagery is an important stage in applications that require the construction of realistic models of the head. Such models are used, for example, to simulate the behavior of electro-magnetic fields in the head and to model the electrical activity of the cortex in EEG and MEG data. In this paper, we present a new approach for segmenting regions of bone in MRI volumes using deformable models. Our method takes into account the partial volume effects that occur with MRI data, thus permitting a precise segmentation of these bone regions. At each iteration of the propagation of the model, partial volume is estimated in a narrow band around the deformable model. Our segmentation method begins with a pre-segmentation stage, in which a preliminary segmentation of the skull is constructed using a region-growing method. The surface that bounds the pre-segmented skull region offers an automatic 3D initialization of the deformable model. This surface is then propagated (in 3D) in the direction of its normal. This propagation is achieved using level set method, thus permitting changes to occur in the topology of the surface as it evolves, an essential capability for our problem. The speed at which the surface evolves is a function of the estimated partial volume. This provides a sub-voxel accuracy in the resulting segmentation.     

Flow index evaluation of 3-D volume flow images: an in vivo and in vitro study

Three-dimensional (3-D) ultrasound imaging has improved evaluation of organ circulation and might contribute new information on maternal and fetal blood supply. Flow index (FI) of 3-D color images has been proposed as a measure of perfusion. The aim of this study was to evaluate whether the 3-D FI is a parameter of volume flow and flow velocity in a human vessel and in a flow phantom. A 1-cm-long strip of the uterine artery was recorded in 3-D power Doppler (3D-PD) mode in a cross-sectional study of 170 normal singleton pregnancies between 26 and 42 weeks' gestation. A fixed ultrasound system installation was used during the examination. The VOCAL software integrated in the ultrasound unit calculated vessel volume and FI. Reproducibility of the measurements was tested. The method was also tested on a commercially available flow phantom. Reproducibility measurements gave satisfactory results, both in terms of inter- and intraobserver variation. Unexpectedly, in normal pregnancy, the uterine artery FI decreased slightly with gestation. Uterine artery vessel volume increased, however, with gestational age. A poor correlation was found between the FI and both flow velocity and volume flow in the flow phantom. In conclusion, 3D-PD imaging can give impressive anatomical pictures of organ vascular tree. However, the new FI is poorly related to flow velocity or volume of flow.     

Robust unsupervised segmentation of infarct lesion from diffusion tensor MR images using multiscale statistical classification and partial volume voxel reclassification

Manual region tracing method for segmentation of infarction lesions in images from diffusion tensor magnetic resonance imaging (DT-MRI) is usually used in clinical works, but it is time consuming. A new unsupervised method has been developed, which is a multistage procedure, involving image preprocessing, calculation of tensor field and measurement of diffusion anisotropy, segmentation of infarction volume based on adaptive multiscale statistical classification (MSSC), and partial volume voxel reclassification (PVVR). The method accounts for random noise, intensity overlapping, partial volume effect (PVE), and intensity shading artifacts, which always appear in DT-MR images. The proposed method was applied to 20 patients with clinically diagnosed brain infarction by DT-MRI scans. The accuracy and reproducibility in terms of identifying the infarction lesion have been confirmed by clinical experts. This automatic segmentation method is promising not only in detecting the location and the size of infarction lesion in stroke patient but also in quantitatively analyzing diffusion anisotropy of lesion to guide clinical diagnoses and therapy.     

PET成像中部分容积效应的成因及影响因素

部分容积效应(Partial volume effect,PVE)是影响医学影像设备图像分析的重要因素.PET成像系统有限的分辨率使PVE更加明显,造成大病灶图像边缘模糊,小病灶图像模糊暗淡;在定量分析上使标准化摄取值(SUV)降低,影响对病灶性质的判定及放化疗等治疗效果的评估.本文对PVE的成因、影响因素、实际影响进行初步的探讨. 1 PVE的成因 PVE是由两个效应共同作用下形成的,即点源扩展及组织分数效应.点源扩展是PET分辨率较低造成的[1],组织分数效应主要和PET采集图像信号的方式有关[2],下面进行详细的叙述.     

Infant cerebral ventricle volume: a comparison of 3-D ultrasound and magnetic resonance imaging

Enlargement of the cerebral lateral ventricles is observed in several neuropsychiatric disorders with origins in early brain development. Lateral ventricle size is also predictive of poor neurodevelopmental outcome in premature infants. Three-dimensional (3-D) ultrasound (US) offers an improved methodology for the study of lateral ventricle volume in neonates and infants. To assess the validity of ventricle volume measures obtained with 3-D US, we compared the volumes obtained by 3-D US with magnetic resonance imaging (MRI) in seven infants. Ventricle volumes were determined using a computer-assisted image analysis program, IRIS. There was excellent correlation between ventricle volumes obtained with 3-D US and those obtained with MRI (intraclass correlation coefficient 0.92, F = 23.28, p = 0.00027), indicating that 3-D US provides valid measures of overall lateral ventricle volume compared to the "gold standard" of MRI. 3-D US can provide an economical and practical means of studying lateral ventricle volume in neonates, a neurostructural marker of abnormal brain development.     

Differentiation of breast masses using 3-D sonographic and echo-enhancer-based evaluation of the vascular pattern: initial experiences

To evaluate the potential of combined 3-D B-mode and color Doppler (CD) data sets in the differentiation of breast masses, in 50 patients with histologically proven solid breast lesions, 3-D datasets were acquired. A 3-D display was created and volume calculation of tumors, their periphery and vasculature was performed. Time-intensity curves of enhancement after administration of a contrast agent were analyzed. Volumetry of tumor vasculature yielded no significant differences between malignant and benign tumors regarding vascularization of the center (2.60 vs. 2.88%) and periphery (6.66 vs. 3.78%). Only the mean values for the rise time in the center of the tumor, fibroadenoma (FA): 5.7 s and ductal invasive carcinoma (DIC): 15.8s; p = 0.05, and the time to peak in the periphery, FA: 21.0 s and DIC: 31.6 s; p = 0.03, differed significantly. The 3-D ultrasound (US) technique was of no additional value in differentiating breast masses. The calculation of time-intensity curves after administration of a contrast agent may be helpful in differentiating FA and DIC.     

Investigation of spatial resolution, partial volume effects and smoothing in functional MRI using artificial 3D time series

This work addresses the balance between temporal signal-to-noise ratio (tSNR) and partial volume effects (PVE) in functional magnetic resonance imaging (fMRI) and investigates the impact of the choice of spatial resolution and smoothing. In fMRI, since physiological time courses are monitored, tSNR is of greater importance than image SNR. Improving SNR by an increase in voxel volume may be of negligible benefit when physiological fluctuations dominate the noise. Furthermore, at large voxel volumes, PVE are more pronounced, leading to an overall loss in performance. Artificial fMRI time series, based on high-resolution anatomical data, were used to simulate BOLD activation in a controlled manner. The performance was subsequently quantified as a measure of how well the resulted activation matched the simulated activation. The performance was highly dependent on the spatial resolution. At high contrast-to-noise ratio (CNR), the optimal voxel volume was small, i.e. in the region of 2(3) mm(3). It was also shown that using a substantially larger voxel volume in this case could potentially negate the CNR benefits. The optimal smoothing kernel width was dependent on the CNR, being larger at poor CNR. At CNR >1, little or no smoothing proved advantageous. The use of artificial time series gave an opportunity to quantitatively investigate the effects of partial volume and smoothing in single subject fMRI. It was shown that a proper choice of spatial resolution and smoothing kernel width is important for fMRI performance.     

MRI evaluation of complex renal cysts using the Bosniak classification: a comparison to CT

Purpose

The purpose of this study was to compare the ability of magnetic resonance imaging (MRI) and computed tomography (CT) to discriminate between benign and malignant cystic renal lesions utilizing the Bosniak classification.

Materials and Methods

We retrospectively searched our Radiological Information System using renal/kidney cysts as entries. The search retrieved 2929 patients and 525 complex renal cysts. After exclusions, 42 complex cysts, from 37 patients, with CT and MRI, up to six months apart, were included. Surgery and pathology report and follow-up of at least 24 months were used as a standard of reference.

Results

The mean age of patients was 51.4 years, ranging from 11 to 82 years old. Twenty-nine lesions were classified as Bosniak I, II or II-F by CT and/or MRI and 13 as Bosniak III or IV, by one of the methods. The interobserver agreement for Bosniak classification for CT was 0.87 and 0.93 for MRI. Fifteen lesions had higher Bosniak categories on MRI, included six with change in management. Only two lesions had a higher category on CT, one with change in management. The frequency of malignancy for Bosniak III was 50 % (2/4) for CT and 20% for MRI (1/5), as Bosniak upgrades by MRI resulted in surgery for benign lesions. Both methods had 100 % frequency of malignancy for category 4.

Conclusion

MRI led to category migration and management change of complex renal cysts in a significant proportion of cases, likely due to its superior soft tissue and contrast resolution. The impact of MRI on detection and outcomes of malignant complex renal cysts still requires further investigation.

     

Investigation of cortical thickness and volume during spontaneous attacks of migraine without aura: a 3-Tesla MRI study

BackgroundStructural imaging has revealed changes in cortical thickness in migraine patients compared to healthy controls is reported, but presence of dynamic cortical and subcortical changes during migraine attack versus inter-ictal phase is unknown. The aim of the present study was to investigate possible changes in cortical thickness during spontaneous migraine attacks. We hypothesized that pain-related cortical area would be affected during the attack compared to an inter-ictal phase.MethodsTwenty-five patients with migraine without aura underwent three-dimensional T1-weighted imaging on a 3-Tesla MRI scanner during spontaneous and untreated migraine attacks. Subsequently, 20 patients were scanned in the inter-ictal phase, while 5 patients did not show up for the inter-ictal scan. Four patients were excluded from the analysis because of bilateral migraine pain and another one patient was excluded due to technical error in the imaging. Longitudinal image processing was done using FreeSurfer. Repeated measures ANOVA was used for statistical analysis and to control for multiple comparison the level of significance was set at p = 0.025.ResultsIn a total of 15 patients, we found reduced cortical thickness of the precentral (p = 0.023), pericalcarine (p = 0.024), and temporal pole (p = 0.017) cortices during the attack compared to the inter-ictal phase. Cortical volume was reduced in prefrontal (p = 0.018) and pericalcarine (p = 0.017) cortices. Hippocampus volume was increased during attack (p = 0.007). We found no correlations between the pain side or any other clinical parameters and the reduced cortical size.ConclusionSpontaneous migraine attacks are accompanied by transient reduced cortical thickness and volume in pain-related areas. The findings constitute a fingerprint of acute pain in migraine patients, which can be used as a possible biomarker to predict antimigraine treatment effect in future studies.Trial registrationThe study was registered at ClinicalTrials.gov ({"type":"clinical-trial","attrs":{"text":"NCT02202486","term_id":"NCT02202486"}}NCT02202486).     

Automated Visualization and Quantification of Spiral Artery Blood Flow Entering the First-Trimester Placenta,Using 3-D Power Doppler Ultrasound

The goal of our research was to quantify the placental vascularity in 3-D at 11–13?+?6?wk of pregnancy at precise distances from the utero-placental interface (UPI) using 3-D power Doppler ultrasound. With this automated image analysis technique, differences in vascularity between normal and pathologic pregnancies may be observed. The algorithm was validated using a computer-generated image phantom and applied retrospectively in 143 patients. The following features from the PD data were recorded: The number of spiral artery jets into the inter-villous space, total geometric and PD area. These were automatically measured at discrete millimeter distances from the UPI. Differences in features were compared with pregnancy outcomes: Pre-eclamptic versus normal, all small-for-gestational age (SGA) to appropriate-for-gestational age (AGA) patients and AGA versus SGA in normotensives (Mann-Whitney). The Benjamini-Hochberg procedure was used (false discovery rate 10%) for multiple comparison testing. Features decreased with increasing distance from the UPI (Kruskal-Wallis test; p?<0.001). At 2– 3?mm from the UPI, all features were smaller in pre-eclamptic compared with normal patients and for some in SGA compared with AGA patients (p?<0.05). For AGA versus SGA in normotensive patients, no significant differences were found. Number of jets measured at 2–5?mm from the UPI did not vary because of the position of the placenta in the uterus (ANOVA; p?>?0.05). This method provides a new in-vivo imaging tool for examining spiral artery development through pregnancy. Size and number of entrances of blood flow into the UPI could potentially be used to identify high-risk pregnancies and may provide a new imaging biomarker for placental insufficiency.     

Estimation of the human liver volume and configuration using three-dimensional ultrasonography: effect of a high-caloric liquid meal

The aim of this study was to investigate whether or not a magnetic position sensing system for free-hand acquisition of 3-D ultrasound images could be used to estimate liver volumes, and to study the effect of a high-caloric meal on these volumes in healthy subjects. In vitro accuracy was evaluated by scanning porcine and rabbit livers. Ten healthy subjects were examined fasting and 30 min after ingesting a high-caloric liquid meal. Portal and hepatic vein blood flow were measured by 2-D duplex sonography. The 3-D system yielded a strong correlation (r = 0.99) between true and estimated volumes in vitro. No significant increase in liver volume in response to the meal was seen. However, portal and hepatic vein flow volume increased significantly. Experience in human subjects suggests that a complete 3-D study of liver volumes can be obtained from multiple acoustic windows. In healthy subjects, no significant increase in liver volume was seen in response to ingestion of a high-caloric liquid meal.     

Triple rule-out acute chest pain evaluation using a 320-row-detector volume CT: a comparison of the wide-volume and helical modes

The purpose of this study was to investigate the image quality and radiation dose of triple rule-out computed tomography (TROCT) using a 320-row-detector volume CT system to compare the wide-volume and helical modes of this CT system. Sixty-four patients with noncritical chest pain were allocated to one of 2 groups according to the type of CT examination mode used. Group 1 patients were examined using the wide-volume (non-spiral) mode and group 2 patients were examined using the 160-detector row helical mode, with the same contrast injection protocol in both methods [biphasic injection protocol; injection rate of 4 ml/s, median volume, 70 ml (range 65–100 ml)]. Attenuations of the pulmonary trunk, ascending aorta, and coronary arteries were measured in Hounsfield units; a subjective overall patient-based image quality score of 1–3 was awarded to each study. Effective doses, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated. Average effective dose was significantly lower in group 1 than group 2 (9.7 ± 5.1 vs. 16 ± 5.9 mSv, P < 0.001). The mean attenuation of the main pulmonary trunk was significantly higher in group 1 than group 2 (P = 0.04) and mean attenuations in other vessels were not significant different. SNR and CNR were not significantly different between the groups. The proportion of diagnostic image qualities for chest CT angiography (CTA) was similar between the groups (93.5 vs. 93.9 %). In coronary CTA, group 1 showed a higher proportion of diagnostic image qualities than group 2 (100 vs. 87.9 %). The use of wide-volume mode of 320-detector CT reduces the overall effective radiation dose and results in similar attenuation and image quality for TROCT as compared with the helical mode.     

Morphological evaluation of a regurgitant orifice by 3-D echocardiography: applications in the quantification of valvular regurgitation.

The clinical evaluation of blood flow regurgitation through a heart valve or stenotic lesion is an unresolved problem. The proximal flowfield region has been the study focus in the last few years; however, investigators have failed to identify an accurate and reliable calculation scheme due to lack of geometric information about the shape and size of the regurgitating or stenotic orifice. Presented here is a superior method of calculation, by using three-dimensional (3-D) echocardiography combined with Doppler velocimetry. The geometric structure of the orifice in a regurgitating porcine prosthetic valve in vitro was formulated by 3-D image construction of sequentially obtained 2-D images. The velocity flowfield was accessed by color Doppler flow mapping (CD) and continuous-wave Doppler (CW). Two accurate methods of calculation of regurgitant variables were developed. The first method calculated peak regurgitant flow rate from CD and the second method calculated regurgitant flow volume from CW. Both methods showed excellent correlation with the corresponding true values from an electromagnetic flowmeter. The promising preliminary results in such a realistic porcine model indicate the possibility of establishing a routine procedure to be tested in the clinical setting.