Publications by authors named "Daniel J Blezek"

20 Publications

  • Page 1 of 1

Fast super-resolution ultrasound microvessel imaging using spatiotemporal data with deep fully convolutional neural network.

Phys Med Biol 2021 Mar 2. Epub 2021 Mar 2.

Department of Radiology, Mayo Clinic, Rochester, UNITED STATES.

Ultrasound localization microscopy (ULM) has been proposed to image microvasculature beyond the ultrasound diffraction limit. Although ULM can attain microvascular images with a sub-diffraction resolution, long data acquisition time and processing time are the critical limitations. Deep learning-based ULM (deep-ULM) has been proposed to mitigate these limitations. However, microbubble (MB) localization used in deep-ULMs is currently based on spatial information without the use of temporal information. The highly spatiotemporally coherent MB signals provide a strong feature that can be used to differentiate MB signals from background artifacts. In this study, a deep neural network was employed and trained with spatiotemporal ultrasound datasets to better identify the MB signals by leveraging both the spatial and temporal information of the MB signals. Training, validation and testing datasets were acquired from MB suspension to mimic the realistic intensity-varying and moving MB signals. The performance of the proposed network was first demonstrated in the chicken embryo chorioallantoic membrane dataset with an optical microscopic image as the reference standard. Substantial improvement in spatial resolution was shown for the reconstructed super-resolved images compared with power Doppler images. The full-width-half-maximum (FWHM) of a microvessel was improved from 133 µm to 35 µm, which is smaller than the ultrasound wavelength (73 µm). The proposed method was further tested in an in vivo human liver data. Results showed the reconstructed super-resolved images could resolve a microvessel of nearly 170 µm (FWHM). Adjacent microvessels with a distance of 670 µm, which cannot be resolved with power Doppler imaging, can be well-separated with the proposed method. Improved contrast ratios using the proposed method were shown compared with that of the conventional deep-ULM method. Additionally, the processing time to reconstruct a high-resolution ultrasound frame with an image size of 1024 × 512 pixels was around 16 ms, comparable to state-of-the-art deep-ULMs.
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http://dx.doi.org/10.1088/1361-6560/abeb31DOI Listing
March 2021

Development of a volumetric pancreas segmentation CT dataset for AI applications through trained technologists: a study during the COVID 19 containment phase.

Abdom Radiol (NY) 2020 12 16;45(12):4302-4310. Epub 2020 Sep 16.

Department of Radiology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

Purpose: To evaluate the performance of trained technologists vis-à-vis radiologists for volumetric pancreas segmentation and to assess the impact of supplementary training on their performance.

Methods: In this IRB-approved study, 22 technologists were trained in pancreas segmentation on portal venous phase CT through radiologist-led interactive videoconferencing sessions based on an image-rich curriculum. Technologists segmented pancreas in 188 CTs using freehand tools on custom image-viewing software. Subsequent supplementary training included multimedia videos focused on common errors, which were followed by second batch of 159 segmentations. Two radiologists reviewed all cases and corrected inaccurate segmentations. Technologists' segmentations were compared against radiologists' segmentations using Dice-Sorenson coefficient (DSC), Jaccard coefficient (JC), and Bland-Altman analysis.

Results: Corrections were made in 71 (38%) cases from first batch [26 (37%) oversegmentations and 45 (63%) undersegmentations] and in 77 (48%) cases from second batch [12 (16%) oversegmentations and 65 (84%) undersegmentations]. DSC, JC, false positive (FP), and false negative (FN) [mean (SD)] in first versus second batches were 0.63 (0.15) versus 0.63 (0.16), 0.48 (0.15) versus 0.48 (0.15), 0.29 (0.21) versus 0.21 (0.10), and 0.36 (0.20) versus 0.43 (0.19), respectively. Differences were not significant (p > 0.05). However, range of mean pancreatic volume difference reduced in the second batch [- 2.74 cc (min - 92.96 cc, max 87.47 cc) versus - 23.57 cc (min - 77.32, max 30.19)].

Conclusion: Trained technologists could perform volumetric pancreas segmentation with reasonable accuracy despite its complexity. Supplementary training further reduced range of volume difference in segmentations. Investment into training technologists could augment and accelerate development of body imaging datasets for AI applications.
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http://dx.doi.org/10.1007/s00261-020-02741-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493700PMC
December 2020

MRI and tractography techniques to localize the ventral intermediate nucleus and dentatorubrothalamic tract for deep brain stimulation and MR-guided focused ultrasound: a narrative review and update.

Neurosurg Focus 2020 07;49(1):E8

Departments of1Radiology.

The thalamic ventral intermediate nucleus (VIM) can be targeted for treatment of tremor by several procedures, including deep brain stimulation (DBS) and, more recently, MR-guided focused ultrasound (MRgFUS). To date, such targeting has relied predominantly on coordinate-based or atlas-based techniques rather than directly targeting the VIM based on imaging features. While general regional differences of features within the thalamus and some related white matter tracts can be distinguished with conventional imaging techniques, internal nuclei such as the VIM are not discretely visualized. Advanced imaging methods such as quantitative susceptibility mapping (QSM) and fast gray matter acquisition T1 inversion recovery (FGATIR) MRI and high-field MRI pulse sequences that improve the ability to image the VIM region are emerging but have not yet been shown to have reliability and accuracy to serve as the primary method of VIM targeting. Currently, the most promising imaging approach to directly identify the VIM region for clinical purposes is MR diffusion tractography.In this review and update, the capabilities and limitations of conventional and emerging advanced methods for evaluation of internal thalamic anatomy are briefly reviewed. The basic principles of tractography most relevant to VIM targeting are provided for familiarization. Next, the key literature to date addressing applications of DTI and tractography for DBS and MRgFUS is summarized, emphasizing use of direct targeting. This literature includes 1-tract (dentatorubrothalamic tract [DRT]), 2-tract (pyramidal and somatosensory), and 3-tract (DRT, pyramidal, and somatosensory) approaches to VIM region localization through tractography.The authors introduce a 3-tract technique used at their institution, illustrating the oblique curved course of the DRT within the inferior thalamus as well as the orientation and relationship of the white matter tracts in the axial plane. The utility of this 3-tract tractography approach to facilitate VIM localization is illustrated with case examples of variable VIM location, targeting superior to the anterior commissure-posterior commissure plane, and treatment in the setting of pathologic derangement of thalamic anatomy. Finally, concepts demonstrated with these case examples and from the prior literature are synthesized to highlight several potential advantages of tractography for VIM region targeting.
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http://dx.doi.org/10.3171/2020.4.FOCUS20170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8032505PMC
July 2020

Current concepts of cross-sectional and functional anatomy of the cerebellum: a pictorial review and atlas.

Br J Radiol 2020 Feb 8;93(1106):20190467. Epub 2020 Jan 8.

Department of Radiology, Mayo Clinic, Rochester, Minnesota, United States.

Recognition of key concepts of structural and functional anatomy of the cerebellum can facilitate image interpretation and clinical correlation. Recently, the human brain mapping literature has increased our understanding of cerebellar anatomy, function, connectivity with the cerebrum, and significance of lesions involving specific areas.Both the common names and numerically based Schmahmann classifications of cerebellar lobules are illustrated. Anatomic patterns, or signs, of key fissures and white matter branching are introduced to facilitate easy recognition of the major anatomic features. Color-coded overlays of cross-sectional imaging are provided for reference of more complex detail. Examples of exquisite detail of structural and functional cerebellar anatomy at 7 T MRI are also depicted.The functions of the cerebellum are manifold with the majority of areas involved with non-motor association function. Key concepts of lesion-symptom mapping which correlates lesion location to clinical manifestation are introduced, emphasizing that lesions in most areas of the cerebellum are associated with predominantly non-motor deficits. Clinical correlation is reinforced with examples of intrinsic pathologic derangement of cerebellar anatomy and altered functional connectivity due to pathology of the cerebral hemisphere. The purpose of this pictorial review is to illustrate basic concepts of these topics in a cross-sectional imaging-based format that can be easily understood and applied by radiologists.
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http://dx.doi.org/10.1259/bjr.20190467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055440PMC
February 2020

Remote ischemic preconditioning for elective endovascular intracranial aneurysm repair: a feasibility study.

Neuroradiol J 2019 Jun 3;32(3):166-172. Epub 2019 Apr 3.

1 Department of Radiology, Mayo Clinic, Rochester, MN, USA.

Objectives: Remote ischemic preconditioning has been proposed as a possible potential treatment for ischemic stroke. However, neuroprotective benefits of the pre-procedural administration of remote ischemic preconditioning have not been investigated in patients undergoing an elective endovascular intracranial aneurysm repair procedure. This study investigated the safety and feasibility of remote ischemic preconditioning in patients with an unruptured intracranial aneurysm who undergo elective endovascular treatment.

Methods: In this single-center prospective study, patients with an unruptured intracranial aneurysm undergoing elective endovascular treatment with flow diverters or coiling were recruited. Patients received three intermittent cycles of 5 minutes arm ischemia followed by reperfusion using manual blood cuff inflation/deflation less than 5 hours prior to endovascular treatment. Patients were monitored and followed up for remote ischemic preconditioning-related adverse events and ischemic brain lesions by diffusion -weighted magnetic resonance imaging within 48 hours following endovascular treatment.

Results: A total of seven patients aged 60 ± 5 years with an unruptured intracranial aneurysm successfully completed a total of 21 sessions of remote ischemic preconditioning and the required procedures. Except for two patients who developed skin petechiae over their arms, no other serious procedure-related adverse events were observed as a result of the remote ischemic preconditioning procedure. On follow-up diffusion -weighted magnetic resonance imaging, a total of 19 ischemic brain lesions with a median (interquartile range) volume of 245 (61-466) mm were found in four out of seven patients.

Conclusions: The application of remote ischemic preconditioning prior to endovascular intracranial aneurysm repair was well tolerated, safe and clinically feasible. Larger sham-controlled clinical trials are required to determine the safety and efficacy of this therapeutic strategy in mitigating ischemic damage following endovascular treatment of intracranial aneurysms.
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http://dx.doi.org/10.1177/1971400919842059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512210PMC
June 2019

MIRMAID: A Content Management System for Medical Image Analysis Research.

Radiographics 2015 Sep-Oct;35(5):1461-8. Epub 2015 Aug 18.

From the Departments of Radiology (P.D.K., T.L.K., S.G.L., B.J.E.) and Information Services (D.J.B., W.J.R.), Mayo Clinic, 200 1st St SW, Rochester, MN 55905.

Today, a typical clinical study can involve thousands of participants, with imaging data acquired over several time points across multiple institutions. The additional associated information (metadata) accompanying these data can cause data management to be a study-hindering bottleneck. Consistent data management is crucial for large-scale modern clinical imaging research studies. If the study is to be used for regulatory submissions, such systems must be able to meet regulatory compliance requirements for systems that manage clinical image trials, including protecting patient privacy. Our aim was to develop a system to address these needs by leveraging the capabilities of an open-source content management system (CMS) that has a highly configurable workflow; has a single interface that can store, manage, and retrieve imaging-based studies; and can handle the requirement for data auditing and project management. We developed a Web-accessible CMS for medical images called Medical Imaging Research Management and Associated Information Database (MIRMAID). From its inception, MIRMAID was developed to be highly flexible and to meet the needs of diverse studies. It fulfills the need for a complete system for medical imaging research management.
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http://dx.doi.org/10.1148/rg.2015140031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4613872PMC
July 2016

Observer Performance in the Detection and Classification of Malignant Hepatic Nodules and Masses with CT Image-Space Denoising and Iterative Reconstruction.

Radiology 2015 Aug 26;276(2):465-78. Epub 2015 May 26.

From the Departments of Radiology (J.G.F., L.Y., Z.L., D.M.H., S.K.V., J.L.F., M.S., D.L., S.L., C.H.M.), Physiology and Biomedical Engineering (A.M., D.S.L., K.E.A., D.R.H.), Information Technology (D.J.B.), and Biomedical Statistics and Informatics (R.E.C.), Mayo Clinic, 200 First St SW, Rochester, MN 55905; Department of Radiology, Mayo Clinic, Eau Claire, Wis (G.C.B.); Department of Radiology, Mayo Clinic, Jacksonville, Fla (J.C.C.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (A.K.H.).

Purpose: To determine if lower-dose computed tomographic (CT) scans obtained with adaptive image-based noise reduction (adaptive nonlocal means [ANLM]) or iterative reconstruction (sinogram-affirmed iterative reconstruction [SAFIRE]) result in reduced observer performance in the detection of malignant hepatic nodules and masses compared with routine-dose scans obtained with filtered back projection (FBP).

Materials And Methods: This study was approved by the institutional review board and was compliant with HIPAA. Informed consent was obtained from patients for the retrospective use of medical records for research purposes. CT projection data from 33 abdominal and 27 liver or pancreas CT examinations were collected (median volume CT dose index, 13.8 and 24.0 mGy, respectively). Hepatic malignancy was defined by progression or regression or with histopathologic findings. Lower-dose data were created by using a validated noise insertion method (10.4 mGy for abdominal CT and 14.6 mGy for liver or pancreas CT) and images reconstructed with FBP, ANLM, and SAFIRE. Four readers evaluated routine-dose FBP images and all lower-dose images, circumscribing liver lesions and selecting diagnosis. The jackknife free-response receiver operating characteristic figure of merit (FOM) was calculated on a per-malignant nodule or per-mass basis. Noninferiority was defined by the lower limit of the 95% confidence interval (CI) of the difference between lower-dose and routine-dose FOMs being less than -0.10.

Results: Twenty-nine patients had 62 malignant hepatic nodules and masses. Estimated FOM differences between lower-dose FBP and lower-dose ANLM versus routine-dose FBP were noninferior (difference: -0.041 [95% CI: -0.090, 0.009] and -0.003 [95% CI: -0.052, 0.047], respectively). In patients with dedicated liver scans, lower-dose ANLM images were noninferior (difference: +0.015 [95% CI: -0.077, 0.106]), whereas lower-dose FBP images were not (difference -0.049 [95% CI: -0.140, 0.043]). In 37 patients with SAFIRE reconstructions, the three lower-dose alternatives were found to be noninferior to the routine-dose FBP.

Conclusion: At moderate levels of dose reduction, lower-dose FBP images without ANLM or SAFIRE were noninferior to routine-dose images for abdominal CT but not for liver or pancreas CT.
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http://dx.doi.org/10.1148/radiol.2015141991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514571PMC
August 2015

Methods for clinical evaluation of noise reduction techniques in abdominopelvic CT.

Radiographics 2014 Jul-Aug;34(4):849-62

From the Departments of Radiology (E.C.E., L.Y., A.M., M.M.S., D.J., M.R.B., C.H.M., D.M.H., J.G.F.) and Biomedical Engineering (D.S.L., D.J.B.), Mayo Clinic, 200 First St SW, Rochester, MN 55905; and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (A.K.H., R.G.P.).

Most noise reduction methods involve nonlinear processes, and objective evaluation of image quality can be challenging, since image noise cannot be fully characterized on the sole basis of the noise level at computed tomography (CT). Noise spatial correlation (or noise texture) is closely related to the detection and characterization of low-contrast objects and may be quantified by analyzing the noise power spectrum. High-contrast spatial resolution can be measured using the modulation transfer function and section sensitivity profile and is generally unaffected by noise reduction. Detectability of low-contrast lesions can be evaluated subjectively at varying dose levels using phantoms containing low-contrast objects. Clinical applications with inherent high-contrast abnormalities (eg, CT for renal calculi, CT enterography) permit larger dose reductions with denoising techniques. In low-contrast tasks such as detection of metastases in solid organs, dose reduction is substantially more limited by loss of lesion conspicuity due to loss of low-contrast spatial resolution and coarsening of noise texture. Existing noise reduction strategies for dose reduction have a substantial impact on lowering the radiation dose at CT. To preserve the diagnostic benefit of CT examination, thoughtful utilization of these strategies must be based on the inherent lesion-to-background contrast and the anatomy of interest. The authors provide an overview of existing noise reduction strategies for low-dose abdominopelvic CT, including analytic reconstruction, image and projection space denoising, and iterative reconstruction; review qualitative and quantitative tools for evaluating these strategies; and discuss the strengths and limitations of individual noise reduction methods.
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http://dx.doi.org/10.1148/rg.344135128DOI Listing
November 2015

DEWEY: the DICOM-enabled workflow engine system.

J Digit Imaging 2014 Jun;27(3):309-13

Department of Radiology, Mayo Clinic, Rochester, MN, USA.

Workflow is a widely used term to describe the sequence of steps to accomplish a task. The use of workflow technology in medicine and medical imaging in particular is limited. In this article, we describe the application of a workflow engine to improve workflow in a radiology department. We implemented a DICOM-enabled workflow engine system in our department. We designed it in a way to allow for scalability, reliability, and flexibility. We implemented several workflows, including one that replaced an existing manual workflow and measured the number of examinations prepared in time without and with the workflow system. The system significantly increased the number of examinations prepared in time for clinical review compared to human effort. It also met the design goals defined at its outset. Workflow engines appear to have value as ways to efficiently assure that complex workflows are completed in a timely fashion.
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http://dx.doi.org/10.1007/s10278-013-9661-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026461PMC
June 2014

Adaptive nonlocal means filtering based on local noise level for CT denoising.

Med Phys 2014 Jan;41(1):011908

Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905.

Purpose: To develop and evaluate an image-domain noise reduction method based on a modified nonlocal means (NLM) algorithm that is adaptive to local noise level of CT images and to implement this method in a time frame consistent with clinical workflow.

Methods: A computationally efficient technique for local noise estimation directly from CT images was developed. A forward projection, based on a 2D fan-beam approximation, was used to generate the projection data, with a noise model incorporating the effects of the bowtie filter and automatic exposure control. The noise propagation from projection data to images was analytically derived. The analytical noise map was validated using repeated scans of a phantom. A 3D NLM denoising algorithm was modified to adapt its denoising strength locally based on this noise map. The performance of this adaptive NLM filter was evaluated in phantom studies in terms of in-plane and cross-plane high-contrast spatial resolution, noise power spectrum (NPS), subjective low-contrast spatial resolution using the American College of Radiology (ACR) accreditation phantom, and objective low-contrast spatial resolution using a channelized Hotelling model observer (CHO). Graphical processing units (GPU) implementation of this noise map calculation and the adaptive NLM filtering were developed to meet demands of clinical workflow. Adaptive NLM was piloted on lower dose scans in clinical practice.

Results: The local noise level estimation matches the noise distribution determined from multiple repetitive scans of a phantom, demonstrated by small variations in the ratio map between the analytical noise map and the one calculated from repeated scans. The phantom studies demonstrated that the adaptive NLM filter can reduce noise substantially without degrading the high-contrast spatial resolution, as illustrated by modulation transfer function and slice sensitivity profile results. The NPS results show that adaptive NLM denoising preserves the shape and peak frequency of the noise power spectrum better than commercial smoothing kernels, and indicate that the spatial resolution at low contrast levels is not significantly degraded. Both the subjective evaluation using the ACR phantom and the objective evaluation on a low-contrast detection task using a CHO model observer demonstrate an improvement on low-contrast performance. The GPU implementation can process and transfer 300 slice images within 5 min. On patient data, the adaptive NLM algorithm provides more effective denoising of CT data throughout a volume than standard NLM, and may allow significant lowering of radiation dose. After a two week pilot study of lower dose CT urography and CT enterography exams, both GI and GU radiology groups elected to proceed with permanent implementation of adaptive NLM in their GI and GU CT practices.

Conclusions: This work describes and validates a computationally efficient technique for noise map estimation directly from CT images, and an adaptive NLM filtering based on this noise map, on phantom and patient data. Both the noise map calculation and the adaptive NLM filtering can be performed in times that allow integration with clinical workflow. The adaptive NLM algorithm provides effective denoising of CT data throughout a volume, and may allow significant lowering of radiation dose.
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http://dx.doi.org/10.1118/1.4851635DOI Listing
January 2014

Computer-aided detection of intracranial aneurysms in MR angiography.

J Digit Imaging 2011 Feb 24;24(1):86-95. Epub 2009 Nov 24.

Mayo Clinic, Medical Imaging Informatics Innovation Center, Rochester, MN 55905, USA.

Intracranial aneurysms represent a significant cause of morbidity and mortality. While the risk factors for aneurysm formation are known, the detection of aneurysms remains challenging. Magnetic resonance angiography (MRA) has recently emerged as a useful non-invasive method for aneurysm detection. However, even for experienced neuroradiologists, the sensitivity to small (<5 mm) aneurysms in MRA images is poor, on the order of 30~60% in recent, large series. We describe a fully automated computer-aided detection (CAD) scheme for detecting aneurysms on 3D time-of-flight (TOF) MRA images. The scheme locates points of interest (POIs) on individual MRA datasets by combining two complementary techniques. The first technique segments the intracranial arteries automatically and finds POIs from the segmented vessels. The second technique identifies POIs directly from the raw, unsegmented image dataset. This latter technique is useful in cases of incomplete segmentation. Following a series of feature calculations, a small fraction of POIs are retained as candidate aneurysms from the collected POIs according to predetermined rules. The CAD scheme was evaluated on 287 datasets containing 147 aneurysms that were verified with digital subtraction angiography, the accepted standard of reference for aneurysm detection. For two different operating points, the CAD scheme achieved a sensitivity of 80% (71% for aneurysms less than 5 mm) with three mean false positives per case, and 95% (91% for aneurysms less than 5 mm) with nine mean false positives per case. In conclusion, the CAD scheme showed good accuracy and may have application in improving the sensitivity of aneurysm detection on MR images.
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http://dx.doi.org/10.1007/s10278-009-9254-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046787PMC
February 2011

Cell accelerated cryoablation simulation.

Comput Methods Programs Biomed 2010 Jun 24;98(3):241-52. Epub 2009 Oct 24.

Department of Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.

Tumor cryoablation is a clinical procedure where supercooled probes are used to destroy cancerous lesions. Cryoablation is a safe and effective palliative treatment for skeletal metastases, providing immediate and long term pain relief, increasing mobility and improving quality of life. Ideally, lesions are encompassed by an ice ball and frozen to a sufficiently low temperature to ensure cell death. "Lethal ice" is the term used to describe regions within the ice ball where cell death occurs. Failure to achieve lethal ice in all portions of a lesion may explain the high recurrence rate currently observed. Tracking growth of lethal ice is critical to success of percutaneous ablations, however, no practical methods currently exist for non-invasive temperature monitoring. Physicians lack planning tools which provide accurate estimation of the ice formation. Simulation of ice formation, while possible, is computationally demanding and too time consuming to be of clinical utility. We developed the computational framework for the simulation, acceleration strategies for multicore Intel x86 and IBM Cell architectures, and performed preliminary validation of the simulation. Our results demonstrate that the streaming SIMD implementation has better performance and scalability. Both accelerated and non-accelerated algorithms demonstrate good agreement between simulation and manually identified ice ball boundaries in phantom and patient images. Our results show promise for the development of novel cryoablation planning tools with real-time monitoring capability for clinical use.
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http://dx.doi.org/10.1016/j.cmpb.2009.09.004DOI Listing
June 2010

Estimating amounts of iron oxide from gradient echo images.

Magn Reson Med 2009 May;61(5):1132-6

General Electric Global Research, Niskayuna, NY 12309, USA.

Rat legs directly injected with superparamagnetic iron oxide (SPIO) were studied by dual-echo, gradient-echo imaging. The amount of iron injected was estimated using a point dipole model for the SPIO injection site. Saturation magnetization of 6:1 PEG/amino modified silane-coated iron oxide particles with 5- to 6-nm core and 20-25 hydrodynamic diameter was approximately 110 emu/g of iron. Estimates of the amount of iron injected made from signal void volumes surrounding SPIO centers yielded erroneous results varying with sample orientation in the scanner and echo time (TE). For example, a 10 microL, 3-microg iron injection produced signal void volumes of 80 and 210 microL at TE of 9.8 and 25 ms, respectively, giving apparent iron contents of 6 +/- 1 and 10 +/- 2 microg respectively. A more effective approach uses the phase difference between two gradient recalled echo images. To estimate iron content, this approach fits the expected (3 cos(2)theta - 1)/(/r/3) spatial phase distribution to the observed phase differences. Extraneous phase effects made fitting phase at a single TE ineffective. With the dual echo method, 18 independent estimates were 2.48 +/- 0.26 microg std, independently of sample orientation. Estimates in empty control regions were -90 and -140 ng. A 1-microg injection indicated 0.5, 1.2, and 1.2 microg.
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http://dx.doi.org/10.1002/mrm.21930DOI Listing
May 2009

128-channel body MRI with a flexible high-density receiver-coil array.

J Magn Reson Imaging 2008 Nov;28(5):1219-25

GE Global Research, Niskayuna, New York 12309, USA.

Purpose: To determine whether the promise of high-density many-coil MRI receiver arrays for enabling highly accelerated parallel imaging can be realized in practice.

Materials And Methods: A 128-channel body receiver-coil array and custom MRI system were developed. The array comprises two clamshells containing 64 coils each, with the posterior array built to maximize signal-to-noise ratio (SNR) and the anterior array design incorporating considerations of weight and flexibility as well. Phantom imaging and human body imaging were performed using a variety of reduction factors and 2D and 3D pulse sequences.

Results: The ratio of SNR relative to a 32-element array of similar footprint was 1.03 in the center of an elliptical loading phantom and 1.7 on average in the outer regions. Maximum g-factors dropped from 5.5 (for 32 channels) to 2.0 (for 128 channels) for 4x4 acceleration and from 25 to 3.3 for 5x5 acceleration. Residual aliasing artifacts for a right/left (R/L) reduction factor of 8 in human body imaging were significantly reduced relative to the 32-channel array.

Conclusion: MRI with a large number of receiver channels enables significantly higher acceleration factors for parallel imaging and improved SNR, provided losses from the coils and electronics are kept negligible.
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http://dx.doi.org/10.1002/jmri.21463DOI Listing
November 2008

Automatic repositioning of MRSI voxels in longitudinal studies: impact on reproducibility of metabolite concentration measurements.

J Magn Reson Imaging 2008 May;27(5):1188-93

Massachusetts General Hospital, A.A. Martinos Center for Biomedical Imaging, Department of Radiology and Neuroradiology Division, Charlestown, Massachusetts 02129, USA.

Purpose: To study an automatic repositioning method to reduce variability in longitudinal MRSI exams based on a priori image registration. Longitudinal proton MR spectroscopic imaging ((1)H MRSI) exams to study the effects of disease or treatment are becoming increasingly common. However, one source of variability in such exams arises from imperfect relocalization of the MRSI grid in the follow-up exams.

Materials And Methods: Six healthy subjects were each scanned three times during the course of 1 day. In each follow-up exam a manually placed MRSI grid was acquired in addition to the automatically repositioned MRSI grid. Then coefficients of variance between baseline and follow-up scans were calculated for N-acetylaspartate, creatine, and choline. In addition, the overall MRSI grid overlap and individual voxel overlaps were also calculated for both the visually and automatically repositioned voxels.

Results: Streamlined workflow, reduced variability of metabolite concentration measurements, and increased voxel overlaps are noted when this automatic repositioning procedure is compared to the visual MRSI grid repositioning approach.

Conclusion: Our results suggest that this approach is able to improve reproducibility in longitudinal MRS exams.
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http://dx.doi.org/10.1002/jmri.21365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679165PMC
May 2008

Atlas stratification.

Med Image Anal 2007 Oct 25;11(5):443-57. Epub 2007 Jul 25.

GE Research, 1 Research Circle, Niskayuna, NY 12309, USA.

The process of constructing an atlas typically involves selecting one individual from a sample on which to base or root the atlas. If the individual selected is far from the population mean, then the resulting atlas is biased towards this individual. This, in turn, may bias any inferences made with the atlas. Unbiased atlas construction addresses this issue by either basing the atlas on the individual which is the median of the sample or by an iterative technique whereby the atlas converges to the unknown population mean. In this paper, we explore the question of whether a single atlas is appropriate for a given sample or whether there is sufficient image based evidence from which we can infer multiple atlases, each constructed from a subset of the data. We refer to this process as atlas stratification. Essentially, we determine whether the sample, and hence the population, is multi-modal and is best represented by an atlas per mode. In this preliminary work, we use the mean shift algorithm to identify the modes of the sample and multidimensional scaling to visualize the clustering process on clinical MRI neurological image datasets.
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http://dx.doi.org/10.1016/j.media.2007.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2042991PMC
October 2007

Automatic prospective registration of high-resolution trabecular bone images of the tibia.

Ann Biomed Eng 2007 Nov 17;35(11):1924-31. Epub 2007 Aug 17.

Department of Radiology, University of California, 1700 4th St., Suite 203, Box 2520, San Francisco, CA 94107, USA.

Magnetic Resonance Imaging (MRI) longitudinal studies conducted to assess changes in tibia bone quality impose strict requirements on the reproducibility of the prescribed region acquired. Registration, the process of aligning two images, is commonly performed on the images after acquisition. However, techniques to improve image registration precision by adjusting scanning parameters prospectively, prior to image acquisition, would be preferred. We have adapted an automatic prospective mutual information based registration algorithm to a MRI longitudinal study of trabecular bone of the tibia and compared it to a post-scan manual registration. Qualitatively, image alignment due to the prospective registration is shown in 2D subtraction images and 3D surface renderings. Quantitatively, the registration performance is demonstrated by calculating the sum of the squares of the subtraction images. Results show that the sum of the squares is lower for the follow up images with prospective registration by an average of 19.37% +/- 0.07 compared to follow up images with post-scan manual registration. Our study found no significant difference between the trabecular bone structure parameters calculated from the post-scan manual registration and the prospective registration images (p > 0.05). All coefficient of variation values for all trabecular bone structure parameters were within a 2-4.5% range which are within values previously reported in the literature. Results suggest that this algorithm is robust enough to be used in different musculoskeletal imaging applications including the hip as well as the tibia.
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http://dx.doi.org/10.1007/s10439-007-9365-zDOI Listing
November 2007

Atlas stratification.

Med Image Comput Comput Assist Interv 2006 ;9(Pt 1):712-9

GE Research, Niskayuna, NY 12309, USA.

The process of constructing an atlas typically involves selecting one individual from a sample on which to base or root the atlas. If the individual selected is far from the population mean, then the resulting atlas is biased towards this individual. This, in turn, can bias any inferences made with the atlas. Unbiased atlas construction addresses this issue by either basing the atlas on the individual which is the median of the sample or by an iterative technique whereby the atlas converges to the unknown population mean. In this paper, we explore the question of whether a single atlas is appropriate for a given sample or whether there is sufficient image based evidence from which we can infer multiple atlases, each constructed from a subset of the data. We refer to this process as atlas stratification. Essentially, we determine whether the sample, and hence the population, is multi-modal and is best represented by an atlas per mode. We use the mean shift algorithm to identify the modes of the sample and multidimensional scaling to visualize the clustering process.
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http://dx.doi.org/10.1007/11866565_87DOI Listing
April 2007

Automatic repositioning of single voxels in longitudinal 1H MRS studies.

NMR Biomed 2005 Oct;18(6):352-61

GE Global Research Center, Niskayuna, NY 12309, USA.

An automatic procedure, allowing the prospective registration of brain MRI images and the acquisition of nearly identical brain volumes (coverage and orientation) in longitudinal exams, is presented. This procedure, based on a fast registration algorithm and a tailored pulse sequence, is used to reposition single voxels for 1H MRS data acquired in vivo. The impact of the repositioning method on the extent of voxel overlap and on the reproducibility of metabolite concentration measurements is studied. A statistically significant increase in voxel overlap and generally decreased short-term measurement variability (decreased coefficients of variation and increased reproducibility coefficients) are observed. Differences in the long-term variances of metabolite concentrations and concentration ratios measured using the eye and automatic repositioning scheme, however, do not reach statistical significance. The improved workflow associated with the use of the automatic repositioning process, which obviates the need for skilled operator intervention for voxel repositioning, suggests that approaches similar to the one presented here may be a standard element in tomorrow's longitudinal MRI and MRS exams.
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http://dx.doi.org/10.1002/nbm.965DOI Listing
October 2005

MR lymphangiography: imaging strategies to optimize the imaging of lymph nodes with ferumoxtran-10.

Radiographics 2004 May-Jun;24(3):867-78

Department of Radiology, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114, USA.

Detection of local or regional metastases to lymph nodes is clinically important in virtually any type of primary tumor. Current imaging techniques rely heavily on the size criterion for characterization of nodal disease. However, size can be an ineffective parameter for diagnosis of tumor spread to lymph nodes. Magnetic resonance (MR) imaging performed before and after administration of ferumoxtran-10 is a promising technique for characterization of lymph nodes in patients with various primary tumors. Normal homogeneous uptake of ferumoxtran-10 in nonmetastatic nodes shortens the T2 and T2*, turning these nodes dark, whereas malignant nodes lack uptake and remain hyperintense. To optimize acquisition strategies, the following factors should be considered: the timing of contrast material-enhanced imaging, the section thickness, the imaging plane, and the imaging parameters for T2*-weighted sequences. In addition, MR imaging with ferumoxtran-10 allows presurgical mapping of lymph nodes and quantitative estimation of T2*.
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http://dx.doi.org/10.1148/rg.243035190DOI Listing
August 2004