MRI Institute for Biomedical Research

Detroit, MI, United States

MRI Institute for Biomedical Research

Detroit, MI, United States
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Buch S.,MRI Institute for Biomedical Research | Ye Y.,Wayne State University | Haacke E.M.,MRI Institute for Biomedical Research | Haacke E.M.,Wayne State University
Journal of Cerebral Blood Flow and Metabolism | Year: 2017

A quantitative estimate of cerebral blood oxygen saturation is of critical importance in the investigation of cerebrovascular disease. We aimed to measure the change in venous oxygen saturation (Y v) before and after the intake of the vaso-dynamic agents caffeine and acetazolamide with high spatial resolution using susceptibility mapping. Caffeine and acetazolamide were administered on separate days to five healthy volunteers to measure the change in oxygen extraction fraction. The internal streaking artifacts in the susceptibility maps were reduced by giving an initial susceptibility value uniformly to the structure-of-interest, based on a priori information. Using this technique, Y v for normal physiological conditions, post-caffeine and post-Acetazolamide was measured inside the internal cerebral veins as Y Normal = 69.1 ± 3.3%, Y Caffeine = 60.5 ± 2.8%, and Y Acet = 79.1 ± 4.0%. This suggests that susceptibility mapping can serve as a sensitive biomarker for measuring reductions in cerebro-vascular reserve through abnormal vascular response. The percentage change in oxygen extraction fraction for caffeine and acetazolamide were found to be +27.0 ± 3.8% and â '32.6 ± 2.1%, respectively. Similarly, the relative changes in cerebral blood flow in the presence of caffeine and acetazolamide were found to be â '30.3% and + 31.5%, suggesting that the cerebral metabolic rate of oxygen remains stable between normal and challenged brain states for healthy subjects. © The Author(s) 2016.


Liu S.,MRI Institute for Biomedical Research | Zheng H.,Uber | Feng Y.,LinkedIn | Li W.,USAA
Progress in Biomedical Optics and Imaging - Proceedings of SPIE | Year: 2017

A novel deep learning architecture (XmasNet) based on convolutional neural networks was developed for the classification of prostate cancer lesions, using the 3D multiparametric MRI data provided by the PROSTATEx challenge. End-to-end training was performed for XmasNet, with data augmentation done through 3D rotation and slicing, in order to incorporate the 3D information of the lesion. XmasNet outperformed traditional machine learning models based on engineered features, for both train and test data. For the test data, XmasNet outperformed 69 methods from 33 participating groups and achieved the second highest AUC (0.84) in the PROSTATEx challenge. This study shows the great potential of deep learning for cancer imaging. © 2017 SPIE.


Habib C.A.,Wayne State University | Liu M.,Wayne State University | Bawany N.,Wayne State University | Garbern J.,Wayne State University | And 7 more authors.
American Journal of Neuroradiology | Year: 2012

BACKGROUND AND PURPOSE: It is well known that patients with MS tend to have abnormal iron deposition in and around the MS plaques, in the basal ganglia and the THA. In this study, we used SWI to quantify iron content in patients with MS and healthy volunteers. MATERIALS AND METHODS: Fifty-two patients with MS were recruited to assess abnormal iron content in their basal ganglia and THA structures. One hundred twenty-two healthy subjects were recruited to establish a baseline of normal iron content in deep GM structures. Each structure was separated into 2 regions: a low-iron-content region and a high-iron-content region. The average phase, the percentage area, and the total phase of the high-iron-content region were evaluated. A weighting was also assigned to each subject depending on the level of iron content and its deviation from the normal range. RESULTS: A clear separation between iron content in healthy subjects versus patients with MS was seen. For healthy subjects 13% and for patients with MS 65% showed an iron-weighting factor >3 SDs from the normal mean (P < .05). The results for those patients younger than 40 years are even more impressive. In these cases, only 1% of healthy subjects and 67% of patients with RRMS showed abnormally high iron content. CONCLUSIONS: Iron-weighting factors in the basal ganglia, THA, and the midbrain appeared to be abnormal in roughly two-thirds of patients with MS as measured by SWI.


Haacke E.M.,Wayne State University | Haacke E.M.,MRI Institute for Biomedical Research | Haacke E.M.,McMaster University | Tang J.,McMaster University | And 2 more authors.
Journal of Magnetic Resonance Imaging | Year: 2010

Purpose: To create an orientation-independent, 3D reconstruction of the veins in the brain using susceptibility mapping. Materials and Methods: High-resolution, high-pass filtered phase images usually used for susceptibility weighted imaging (SWI) were used as a source for local magnetic field behavior. These images were subsequently postprocessed using an inverse procedure to generate susceptibility maps of the veins. Regularization and interpolation of the data in k-space of the phase images were used to reduce reconstruction artifacts. To understand the effects of artifacts, and to fine-tune the methodology, simulations of blood vessels were performed with and without noise. Results: With sufficient resolution, major veins in the brain could be visualized with this approach. The usual geometry-dependent phase dipole effects are removed by this processing, leaving basically images of the veins. Different sized vessels show a different level of contrast depending on their partial volume effects. Vessels that are 8 mm or 16 mm in size show quantitative values expected for normal oxygen saturation levels. Smaller vessels show smaller values due to errors in the methodology and due to partial volume effects. Larger vessels show a bias toward a reduced susceptibility approaching 90% of the expected value. Limitations of the method and artifacts related to different sources of errors are demonstrated. Conclusion: Susceptibility maps can successfully create venograms of the brain with varying levels of contrast-to-noise depending on the size of the vessel. Partial volume effects render this approach more useful as an imaging tool or a visualization tool, although certain larger vessels have measured susceptibilities close to expected values associated with normal blood oxygen saturation levels. © 2010 Wiley-Liss, Inc.


Wu Z.,McMaster University | Li S.,Capital Medical University | Lei J.,Tianjin Huan Hu Hospital | An D.,Capital Medical University | And 3 more authors.
American Journal of Neuroradiology | Year: 2010

BACKGROUND AND PURPOSE: SWI is an MR imaging technique that is very sensitive to hemorrhage. Our goal was to compare SWI and CT to determine if SWI can show traumatic SAH in different parts of the subarachnoid space. MATERIALS AND METHODS: Twenty acute TBI patients identified by CT with SAH underwent MR imaging scans. Two neuroradiologists analyzed the CT and SWI data to decide whether there were SAHs in 8 anatomical parts of the subarachnoid space. RESULTS: Fifty-five areas with SAH were identified by both CT and SWI. Ten areas were identified by CT only and 13 by SWI only. SAH was recognized on SWI by its very dark signal intensity surrounded by CSF signal intensity in the sulci or cisterns. Compared with the smooth-looking veins, SAH tended to have a rough boundary and inhomogeneous signal intensity. In many instances, blood in the sulcus left an area of signal intensity loss that had a "triangle" shape. SWI showed 5 more cases of intraventricular hemorrhage than did CT. CONCLUSIONS: SAH can be recognized by SWI through its signal intensity and unique morphology. SWI can provide complementary information to CT in terms of small amounts of SAH and hemorrhage inside the ventricles.


Tang J.,McMaster University | Liu S.,McMaster University | Neelavalli J.,Wayne State University | Cheng Y.C.N.,Wayne State University | And 4 more authors.
Magnetic Resonance in Medicine | Year: 2013

To improve susceptibility quantification, a threshold-based k-space/image domain iterative approach that uses geometric information from the susceptibility map itself as a constraint to overcome the ill-posed nature of the inverse filter is introduced. Simulations were used to study the accuracy of the method and its robustness in the presence of noise. In vivo data were processed and analyzed using this method. Both simulations and in vivo results show that most streaking artifacts inside the susceptibility map caused by the ill-defined inverse filter were suppressed by the iterative approach. In simulated data, the bias toward lower mean susceptibility values inside vessels has been shown to decrease from around 10% to 2% when choosing an appropriate threshold value for the proposed iterative method. Typically, three iterations are sufficient for this approach to converge and this process takes less than 30 s to process a 512 × 512 × 256 dataset. This iterative method improves quantification of susceptibility inside vessels and reduces streaking artifacts throughout the brain for data collected from a single-orientation acquisition. This approach has been applied to vessels alone as well as to vessels and other structures with lower susceptibility to generate whole brain susceptibility maps with significantly reduced streaking artifacts. © 2012 Wiley Periodicals, Inc.


Ayaz M.,MRI Institute for Biomedical Research | Ayaz M.,Massachusetts General Hospital | Boikov A.S.,MRI Institute for Biomedical Research | Boikov A.S.,Wayne State University | And 4 more authors.
Journal of Magnetic Resonance Imaging | Year: 2010

Purpose: To monitor changes in the number of cerebral microbleeds (CMBs) in a longitudinal study of healthy controls (HC) and mild-cognitively impaired (MCI) patients using susceptibility weighted imaging (SWI). Materials and Methods: SWI was used to image 28 HC and 75 MCI patients annually at 1.5 Tesla over a 4-year period. Magnitude and phase data were used to visualize CMBs for the first and last scans of 103 subjects. Results: Preliminary analysis revealed that none of the 28 HC had more than three CMBs. In the 75 MCI patients, five subjects had more than three CMBs in both first and last scans, while one subject had more than three bleeds only in the last scan. In five of these six MCI patients, the number of CMBs increased over time and all six went on to develop progressive cognitive impairment (PCI). Of the 130 total CMBs seen in the last scans of the six MCI cases, most were less than 4 mm in diameter. Conclusion: SWI can reveal small CMBs on the order of 1 mm in diameter and this technique can be used to follow their development longitudinally. Monitoring CMBs may be a means by which to evaluate patients for the presence of microvascular disease that leads to PCI. © 2009 Wiley-Liss, Inc.


Liu S.,McMaster University | Neelavalli J.,Wayne State University | Cheng Y.-C.N.,Wayne State University | Tang J.,McMaster University | And 3 more authors.
Magnetic Resonance in Medicine | Year: 2013

Microbleeds have been implicated to play a role in many neurovascular and neurodegenerative diseases. The diameter of each microbleed has been used previously as a possible quantitative measure for grading microbleeds. We propose that magnetic susceptibility provides a new quantitative measure of extravasated blood. Recently, a Fourier-based method has been used that allows susceptibility quantification from phase images for any arbitrarily shaped structures. However, when very small objects, such as microbleeds, are considered, the accuracy of this susceptibility mapping method still remains to be evaluated. In this article, air bubbles and glass beads are taken as microbleed surrogates to evaluate the quantitative accuracy of the susceptibility mapping method. We show that when an object occupies only a few voxels, an estimate of the true volume of the object is necessary for accurate susceptibility quantification. Remnant errors in the quantified susceptibilities and their sources are evaluated. We show that quantifying magnetic moment, rather than the susceptibility of these small structures, may be a better and more robust alternative. Copyright © 2012 Wiley Periodicals, Inc.


Buch S.,McMaster University | Liu S.,McMaster University | Ye Y.,Wayne State University | Cheng Y.-C.N.,Wayne State University | And 4 more authors.
Magnetic Resonance in Medicine | Year: 2015

Purpose To demonstrate the mapping of structures with high susceptibility values, such as the sinuses, bones and teeth, using short echo times. Methods Four in vivo datasets were collected with a gradient-echo sequence (TE1=2.5 ms, TE2=5 ms and TE3=7.5 ms). Complex division was performed to remove the phase offset term and generate the phase at TE=2.5 ms. Susceptibility maps were generated from unwrapped phase images, using a geometry-constrained iterative algorithm, by preserving phase information in the extracerebral tissues. The susceptibility results were improved by updating the missing phase information inside structures with no signal using the predicted phase at each iteration step. Simulated phase images of a three-dimensional brain model and tooth phantom were used to validate the proposed method. Results Improved susceptibility maps were obtained once the phase information in the extracerebral tissue region was incorporated, for both the model and in vivo data. For in vivo data, the average susceptibilities of air (sphenoid sinus), bone and calcium (teeth) were found to be (in ppm): Δχ(sinus-tissue)=+9.2±1.3, Δχ(bone-tissue)=-2.1±0.6 and Δχ(teeth-tissue)=-3.3±1.2, respectively. Conclusion High susceptibility structures with little or no signal can be imaged using quantitative susceptibility mapping and can be used to improve background field removal. Magn Reson Med 73:2185-2194, 2015. © 2014 Wiley Periodicals, Inc.


Hopp K.,University of Saskatchewan | Popescu B.F.Gh.,University of Saskatchewan | McCrea R.P.E.,University of Saskatchewan | Harder S.L.,Loma Linda University | And 5 more authors.
Journal of Magnetic Resonance Imaging | Year: 2010

Purpose: To test the ability of susceptibility weighted images (SWI) and high pass filtered phase images to localize and quantify brain iron. Materials and Methods: Magnetic resonance (MR) images of human cadaver brain hemispheres were collected using a gradient echo based SWI sequence at 1.5T. For X-ray fluorescence (XRF)mapping, each brain was cut to obtain slices that reasonably matched the MR images and iron was mapped at the iron K-edge at 50 or 100 μm resolution. Iron was quantified using XRF calibration foils. Phase and iron XRF were averaged within anatomic regions of one slice, chosen for its range of iron concentrations and nearly perfect anatomic correspondence. X-ray absorption spectroscopy (XAS) was used to determine if the chemical form of iron was different in regions with poorer correspondence between iron and phase. Results: Iron XRF maps, SWI, and high pass filtered phase data in nine brain slices from five subjects were visually very similar, particularly in high iron regions. The chemical form of iron could not explain poor matches. The correlation between the concentration of iron and phase in the cadaver brain was estimated as cFe [μg/g tissue] = 850Δφ + 110. Conclusion: The phase shift Δφ was found to vary linearly with iron concentration with the best correspondence found in regions with high iron content. © 2010 Wiley-Liss, Inc.

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