7T MRI subthalamic nucleus atlas for use with 3T MRI.
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ABSTRACT:
SUBMITTER: Milchenko M
PROVIDER: S-EPMC5757662 | biostudies-literature | 2018 Jan
REPOSITORIES: biostudies-literature
Publications
7T MRI subthalamic nucleus atlas for use with 3T MRI.
Milchenko Mikhail M Norris Scott A SA Poston Kathleen K Campbell Meghan C MC Ushe Mwiza M Perlmutter Joel S JS Snyder Abraham Z AZ
Journal of medical imaging (Bellingham, Wash.) 20180108 1
Deep brain stimulation (DBS) of the subthalamic nucleus (STN) reduces motor symptoms in most patients with Parkinson disease (PD), yet may produce untoward effects. Investigation of DBS effects requires accurate localization of the STN, which can be difficult to identify on magnetic resonance images collected with clinically available 3T scanners. The goal of this study is to develop a high-quality STN atlas that can be applied to standard 3T images. We created a high-definition STN atlas derive ...[more]
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Project description:In the recent MRI scanning, ultra-high-field (7T) MR imaging provides higher resolution and better tissue contrast compared to routine 3T MRI, which may help in more accurate and early brain diseases diagnosis. However, currently, 7T MRI scanners are more expensive and less available at clinical and research centers. These motivate us to propose a method for the reconstruction of images close to the quality of 7T MRI, called 7T-like images, from 3T MRI, to improve the quality in terms of resolution and contrast. By doing so, the post-processing tasks, such as tissue segmentation, can be done more accurately and brain tissues details can be seen with higher resolution and contrast. To do this, we have acquired a unique dataset which includes paired 3T and 7T images scanned from same subjects, and then propose a hierarchical reconstruction based on group sparsity in a novel multi-level Canonical Correlation Analysis (CCA) space, to improve the quality of 3T MR image to be 7T-like MRI. First, overlapping patches are extracted from the input 3T MR image. Then, by extracting the most similar patches from all the aligned 3T and 7T images in the training set, the paired 3T and 7T dictionaries are constructed for each patch. It is worth noting that, for the training, we use pairs of 3T and 7T MR images from each training subject. Then, we propose multi-level CCA to map the paired 3T and 7T patch sets to a common space to increase their correlations. In such space, each input 3T MRI patch is sparsely represented by the 3T dictionary and then the obtained sparse coefficients are used together with the corresponding 7T dictionary to reconstruct the 7T-like patch. Also, to have the structural consistency between adjacent patches, the group sparsity is employed. This reconstruction is performed with changing patch sizes in a hierarchical framework. Experiments have been done using 13 subjects with both 3T and 7T MR images. The results show that our method outperforms previous methods and is able to recover better structural details. Also, to place our proposed method in a medical application context, we evaluated the influence of post-processing methods such as brain tissue segmentation on the reconstructed 7T-like MR images. Results show that our 7T-like images lead to higher accuracy in segmentation of white matter (WM), gray matter (GM), cerebrospinal fluid (CSF), and skull, compared to segmentation of 3T MR images.
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Project description:ObjectiveInjuries to the wrist are, due to its small size and complex anatomical structures, difficult to assess by MR, and surgical interventions such as diagnostic arthroscopy are often necessary. Therefore, improved visualization using non-invasive methods could be of clinical value. As a first step of improvement, the purpose of this study was to evaluate visualization of anatomical structures at 7T compared with 3T MR.MethodsEighteen healthy volunteers (three males and three females from each age decade between 20 and 49 years) were examined with 7T and 3T MR. Four musculoskeletal radiologists graded 2D and 3D images on a five-level grading scale for visibility of ligaments, cartilage, nerves, trabecular bone, and tendons, as well as overall image quality (i.e., edge sharpness, perceived tissue contrast, and presence of artefacts). Statistical analysis was done using a visual grading characteristics (VGC) analysis.ResultsVisibility of cartilage, trabecular bone, tendons, nerves, and ligaments was graded significantly higher at 7T with an area under the curve (AUCVGC) of 0.62-0.88 (95% confidence interval [CI] 0.50-0.97, p = < 0.0001-0.03) using either 2D or 3D imaging. Imaging with 3T was not graded as superior to 7T for any structure. Image quality was also significantly superior at 7T, except for artefacts, where no significant differences were found.ConclusionsTendons, trabecular bone, nerves, and ligaments were all significantly better visualized at 7T compared to 3T.Key points• MRI of the wrist at 7T with a commercially available wrist coil is feasible at similar acquisition times as for 3T MRI. • The current study showed 7T to be superior to 3T in the visualization of anatomical structures of the wrist, including ligaments, tendons, nerves, and trabecular bone. • Image quality was significantly superior at 7T, except for artefacts, where no significant differences were found.
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Project description:BackgroundMulti-atlas segmentation, a popular technique implemented in the Automated Segmentation of Hippocampal Subfields (ASHS) software, utilizes multiple expert-labelled images ("atlases") to delineate medial temporal lobe substructures. This multi-atlas method is increasingly being employed in early Alzheimer's disease (AD) research, it is therefore becoming important to know how the construction of the atlas set in terms of proportions of controls and patients with mild cognitive impairment (MCI) and/or AD affects segmentation accuracy.ObjectiveTo evaluate whether the proportion of controls in the training sets affects the segmentation accuracy of both controls and patients with MCI and/or early AD at 3T and 7T.MethodsWe performed cross-validation experiments varying the proportion of control subjects in the training set, ranging from a patient-only to a control-only set. Segmentation accuracy of the test set was evaluated by the Dice similarity coeffiecient (DSC). A two-stage statistical analysis was applied to determine whether atlas composition is linked to segmentation accuracy in control subjects and patients, for 3T and 7T.ResultsThe different atlas compositions did not significantly affect segmentation accuracy at 3T and for patients at 7T. For controls at 7T, including more control subjects in the training set significantly improves the segmentation accuracy, but only marginally, with the maximum of 0.0003 DSC improvement per percent increment of control subject in the training set.ConclusionASHS is robust in this study, and the results indicate that future studies investigating hippocampal subfields in early AD populations can be flexible in the selection of their atlas compositions.
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Project description:Recent technological progress enables MRI recordings at ultra-high fields of 7 T and above leading to brain images of higher resolution and increased signal-to-noise ratio. Despite these benefits, imaging at 7 T exhibits distinct challenges due to B1 field inhomogeneities, causing decreased image quality and problems in data analysis. Although several strategies have been proposed, a systematic investigation of bias-corrected 7 T data for voxel-based morphometry (VBM) is still missing and it is an ongoing matter of debate if VBM at 7 T can be carried out properly. Here, an optimized VBM study was conducted, evaluating the impact of field strength (3T vs. 7 T) and pulse sequence (MPRAGE vs. MP2RAGE) on gray matter volume (GMV) estimates. More specifically, twenty-two participants were measured under the conditions 3T MPRAGE, 7 T MPRAGE and 7 T MP2RAGE. Due to the fact that 7 T MPRAGE data exhibited strong intensity inhomogeneities, an alternative preprocessing pipeline was proposed and applied for that data. VBM analysis revealed higher GMV estimates for 7 T predominantly in superior cortical areas, caudate nucleus, cingulate cortex and the hippocampus. On the other hand, 3T yielded higher estimates especially in inferior cortical areas of the brain, cerebellum, thalamus and putamen compared to 7 T. Besides minor exceptions, these results were observed for 7 T MPRAGE as well for the 7 T MP2RAGE measurements. Results gained in the inferior parts of the brain should be taken with caution, as native GM segmentations displayed misclassifications in these regions for both 7 T sequences. This was supported by the test-retest measurements showing highest variability in these inferior regions of the brain for 7 T and also for the advanced MP2RAGE sequence. Hence, our data support the use of 7 T MRI for VBM analysis in cortical areas, but direct comparison between field strengths and sequences requires careful assessment. Similarly, analysis of the inferior cortical regions, cerebellum and subcortical regions still remains challenging at 7 T even if the advanced MP2RAGE sequence is used.
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Project description:BackgroundSimultaneous positron emission tomography (PET)/magnetic resonance imaging (MRI) scanners and inserts are valuable tools for accurate diagnosis, treatment planning, and monitoring due to their complementary information. However, the integration of a PET system into an MRI scanner presents technical challenges for a distortion-free operation.PurposeWe aim to develop a PET insert dedicated to breast imaging in combination with the 3T PET/MRI scanner Biograph mMR (Siemens Healthineers) as well as a brain PET insert for the 7T MRI scanner MAGNETOM Terra (Siemens Healthineers). For this development, we selected as a basis the C13500 series PET modules (Hamamatsu Photonics K.K.) as they offer an all-in-one solution with a scalable, modular design for compact integration with state-of-the-art performance. The original PET modules were not designed to be operated with an MRI scanner, therefore we implemented several modifications such as signal transmission via plastic optical fiber, radio frequency (RF) shielding of the front-end electronics, and filter for the power supply lines. In this work, we evaluated the mutual MRI compatibility between the modified PET modules and the 3T and 7T MRI scanner.MethodsWe used a proof-of-concept setup with two detectors to comprehensively evaluate a potential distortion of the performance of the modified PET modules whilst exposing them to a variety of MR sequences up to the peak operation conditions of the Biograph mMR. A method using the periodicity of the sequences to identify distortions of the PET events in the phase of RF pulse transmission was introduced. Vice versa, the potential distortion of the Biograph mMR was evaluated by vendor proprietary MRI compatibility test sequences. Afterwards, these studies were extended to the MAGNETOM Terra.ResultsNo distortions were introduced by gradient field switching (field strength up to 20 mT/m at a slew rate of 66.0 T/ms-1 ). However, RF pulse transmission induced a reduction of the single event rate from 33.0 kcounts/s to 32.0 kcounts/s and a degradation of the coincidence resolution time from 251 to 299 ps. Further, the proposed method revealed artifacts in the energy and timing histograms. Finally, by using the front-end filters it was possible to prevent any RF pulse induced distortion of event rate, energy, or time stamps even for a 700° flip angle (45.5 μT) sequence. The evaluations to assess potential distortions of the MRI scanner showed that carefully designed RF shielding boxes for the PET modules were required to prevent distortion of the RF spectra. The increase in B0 field inhomogeneity of 0.254 ppm and local changes of the B1 field of 12.5% introduced by the PET modules did not qualitatively affect the MR imaging with a spin echo and MPRAGE sequence for the Biograph mMR and the MAGNETOM Terra, respectively.ConclusionOur study demonstrates the feasibility of using a modified version of the PET modules in combination with 3T and 7T MRI scanners. Building upon the encouraging MRI compatibility results from our proof-of-concept detectors, we will proceed to develop PET inserts for breast and brain imaging using these modules.
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Project description:This study aimed to evaluate the diagnostic value of ultrahigh-field magnetic resonance imaging (MRI) for brain tumors in clinical practice. Thirty patients with brain tumors underwent 7- and 3-T MRI. The performance and diagnostic confidence of 7- and 3-T MRI in the visualization of tumor details such as internal structure and feeding artery were evaluated by radiologists. Contrast-enhanced region performance and tumor detail diagnostic confidence score (DCS) were calculated and compared between 7 and 3T using Wilcoxon rank sum test. In 19 with obvious enhancement and 11 cases without obvious enhancement, 7- and 3-T MRI showed similar performance. The tumors' internal structure and feeding artery were more clearly depicted by 7-T MRI (62.2% and 54.4%, respectively) than by 3-T MRI (2.2% and 6.7%, respectively). Furthermore, the mean DCSs of both internal structure and feeding artery were higher at 7T than at 3T (internal structure: 16.29 ± 9.67 vs. -5.79 ± 4.12, p = 0.028; feeding artery: 21.96 ± 6.93 vs. 4.46 ± 7.07, p = 0.028). The DCS was more significantly improved in the senior radiologist group. Better visualization of brain tumor details and higher tumor detail diagnostic confidence can be obtained with 7-T MRI.
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