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1.
Biomed Eng Online ; 22(1): 113, 2023 Dec 03.
Article in English | MEDLINE | ID: mdl-38044423

ABSTRACT

BACKGROUND: Understanding the hemodynamics of an abdominal aortic aneurysm (AAA) is crucial for risk assessment and treatment planning. This study introduces a low-cost, patient-specific in vitro AAA model to investigate hemodynamics using particle image velocimetry (PIV) and flow-simulating circuit, validated through fluid-structure interaction (FSI) simulations. METHODS: In this study, 3D printing was employed to manufacture a flexible patient-specific AAA phantom using a lost-core casting technique. A pulsatile flow circuit was constructed using off-the-shelf components. A particle image velocimetry (PIV) setup was built using an affordable laser source and global shutter camera, and finally, the flow field inside the AAA was analyzed using open-source software. Fluid-structure interaction (FSI) simulations were performed to enhance our understanding of the flow field, and the results were validated by PIV analysis. Both steady-state and transient flow conditions were investigated. RESULTS: Our experimental setup replicated physiological conditions, analyzing arterial wall deformations and flow characteristics within the aneurysm. Under constant flow, peak wall deformations and flow velocities showed deviations within - 12% to + 27% and - 7% to + 5%, respectively, compared to FSI simulations. Pulsatile flow conditions further demonstrated a strong correlation (Pearson coefficient 0.85) in flow velocities and vectors throughout the cardiac cycle. Transient phenomena, particularly the formation and progression of vortex structures during systole, were consistently depicted between experimental and numerical models. CONCLUSIONS: By bridging high-fidelity experimental observations with comprehensive computational analyses, this study underscores the potential of integrated methodologies in enhancing our understanding of AAA pathophysiology. The convergence of realistic AAA phantoms, precise PIV measurements at affordable cost point, and validated FSI models heralds a new paradigm in vascular research, with significant implications for personalized medicine and bioengineering innovations.


Subject(s)
Aortic Aneurysm, Abdominal , Hemodynamics , Humans , Blood Flow Velocity , Arteries/physiology , Rheology , Models, Cardiovascular
2.
J Digit Imaging ; 34(3): 717-730, 2021 06.
Article in English | MEDLINE | ID: mdl-34159419

ABSTRACT

In medical devices, nonconformance with Digital Imaging and Communications in Medicine (DICOM) standard is a serious risk. DICOM nonconformance radiology devices could cause undetected image loss, increasing examination time, and costs in health centers and could even result in the wrong patient treatment. However, there is a rich literature on medical standards that identify the best practices for producing safe and effective medical software. However, these standards do not expressly provide tools to deal with all the relevant DICOM compatibility issues in a specific case. This study aims to introduce a systematic software development workflow that complies with medical standards and ensures DICOM conformance of a new or upgraded radiology software project. In this approach, DICOM conformance gets the highest priority, and the whole software project is organized around it. Software requirement analysis, risk evaluation, and test management tasks are arranged systematically to make the final device DICOM conformant. This conceptual framework was developed during the R&D work towards a novel radiography device, and it could be employed as a roadmap in other medical imaging software projects. The proposed methodology controls the DICOM compatibility risk of the final software, and its systematic evaluation complied with medical standards.


Subject(s)
Radiology Information Systems , Humans , Radiography , Software , Workflow
3.
IEEE J Transl Eng Health Med ; 8: 1800311, 2020.
Article in English | MEDLINE | ID: mdl-32617198

ABSTRACT

BACKGROUND: Digital radiography devices are still the gold standard for diagnosis or therapy guidance in medicine. Despite the similarities between all direct digital x-ray systems, researchers and new companies face significant challenges during the development phase of innovative x-ray devices; each component is manufactured independently, guidance towards device integration from manufacturers is limited, global standards for device integration is lacking. METHOD: In scope of this study a plug-integrate-play (PIP) conceptual model for x-ray imaging system is introduced and implemented as an open hardware platform, SyncBox. The researchers are free to select each individual device component from different vendors based on their intended application and target performance are utilized in criteria. RESULT: As its first implementation, SyncBox and its platform a full body high resolution radiographic scanner that employs a novel TDI digital detector. CONCLUSION: We believe that SyncBox has a potential for introducing an open source hardware platform to x-ray equipment design.

4.
J Digit Imaging ; 33(3): 708-721, 2020 06.
Article in English | MEDLINE | ID: mdl-31845123

ABSTRACT

A device-independent software package, named iBEX, is developed to accelerate the research and development efforts for X-ray imaging setups such as chest radiography, linear and multidirectional tomography, and dental and skeletal radiography. Its extension mechanism makes the software adaptable for a wide range of digital X-ray imaging hardware combinations and provides capabilities for researchers to develop image processing plug-ins. Independent of the X-ray sensor technology, iBEX could integrate with heterogeneous communication channels of digital detectors. iBEX is a freeware option for preclinical and early clinical testing of radiography devices. It provides tools to calibrate the device, integrate to health information infrastructure, acquire image, store studies on local storage, and send them to Picture Archiving and Communication System (PACS). iBEX is a unique open-source project bringing X-ray imaging devices' software into the scope of the open-source community to reduce the X-ray scanners' research effort, potentially increase the image quality, and cut down the production and testing costs of radiography devices.


Subject(s)
Radiographic Image Enhancement , Radiology Information Systems , Humans , Image Processing, Computer-Assisted , Software , Tomography, X-Ray Computed
5.
J Biomech ; 57: 69-78, 2017 05 24.
Article in English | MEDLINE | ID: mdl-28433388

ABSTRACT

Sarcomere length changes are central to force production and excursion of skeletal muscle. Previous modeling indicates non-uniformity of that if mechanical interaction of muscle with its surrounding muscular and connective tissues is taken into account. Hence, quantifying length changes along the fascicles of activated human muscle in vivo is crucial, but this is lacking due to technical complexities. Combining magnetic resonance imaging deformation analyses and diffusion tensor imaging tractography, the aim was to test the hypothesis that submaximal plantar flexion activity at 15% MVC causes heterogeneous length changes along the fascicles of human medial gastrocnemius (GM) muscle. A general fascicle strain distribution pattern shown for all subjects indicates that proximal track segments are shortened, whereas distal ones are lengthened (e.g., by 13% and 29%, respectively). Mean fiber direction strains of different tracts also shows heterogeneity (for up to 57.5% of the fascicles). Inter-subject variability of amplitude and distribution of fascicle strains is notable. These findings confirm the hypothesis and are solid indicators for the functionally dependent mechanics of human muscle, in vivo. Heterogeneity of fascicle strains can be explained by epimuscular myofascial force transmission. To the best of our knowledge, this is the first study, which quantified local deformations along human skeletal muscle fascicles caused by sustained submaximal activation. The present approach and indicated fascicle strain heterogeneity has numerous implications for muscle function in health and disease to estimate the muscle's contribution to the joint moment and excursion and to evaluate mechanisms of muscle injury and several treatment techniques.


Subject(s)
Muscle, Skeletal/diagnostic imaging , Muscle, Skeletal/physiology , Adult , Biomechanical Phenomena , Diffusion Tensor Imaging , Female , Humans , Magnetic Resonance Imaging
6.
J Magn Reson Imaging ; 46(6): 1718-1727, 2017 12.
Article in English | MEDLINE | ID: mdl-28294455

ABSTRACT

PURPOSE: To test whether the combined use of 4D arterial spin labeling angiography (4D ASL) and contrast-enhanced magnetic resonance angiography (4D CE-MRA) can work as a prospective alternative to digital subtraction angiography (DSA) for the delineation of the arteriovenous malformation (AVM) nidus in stereotactic radiosurgery (SRS) planning. MATERIALS AND METHODS: A custom 4D ASL sequence and a proof-of-concept software tool to integrate 4D ASL data to SRS planning were implemented. Ten AVM patients were scanned at 3T. Two observers independently contoured niduses in two separate sessions. Reference niduses were contoured using DSA, 4D ASL, and 4D CE-MRA. Test niduses were contoured using 4D ASL and 4D CE-MRA only. Reference and test niduses from both observers were compared in terms of volume, distance between centers of volumes (dCOV), and the Jaccard index (JI). RESULTS: In volume comparisons, excellent intraobserver and interobserver agreements were obtained (intraclass correlation coefficients: 0.99 and 0.98, respectively). Median dCOV, JIs between reference and test niduses were 0.55 mm, 0.78 for Observer 1 and were 0.6 mm, 0.78 for Observer 2. None of the dCOV and JI parameters varied significantly among the delineation methods or the observers (P = 0.84, P = 0.39). CONCLUSION: Our preliminary results indicate that reproducibility of the target volumes with high agreement levels is achievable without using DSA. The combined use of high temporal resolution 4D ASL and high spatial resolution and vessel-to-background contrast 4D CE-MRA provided sufficient spatiotemporal angiographic information for the delineation of AVM niduses. LEVEL OF EVIDENCE: 2 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017;46:1718-1727.


Subject(s)
Angiography, Digital Subtraction/methods , Imaging, Three-Dimensional/methods , Intracranial Arteriovenous Malformations/diagnostic imaging , Intracranial Arteriovenous Malformations/surgery , Magnetic Resonance Angiography/methods , Radiosurgery/methods , Adolescent , Adult , Child , Female , Humans , Male , Middle Aged , Reproducibility of Results , Spin Labels , Young Adult
7.
J Mech Behav Biomed Mater ; 63: 207-219, 2016 10.
Article in English | MEDLINE | ID: mdl-27429070

ABSTRACT

Muscle fiber direction strain provides invaluable information for characterizing muscle function. However, methods to study this for human muscles in vivo are lacking. Using magnetic resonance (MR) imaging based deformation analyses and diffusion tensor (DT) imaging based tractography combined, we aimed to assess muscle fiber direction local tissue deformations within the human medial gastrocnemius (GM) muscle. Healthy female subjects (n=5, age=27±1 years) were positioned prone within the MR scanner in a relaxed state with the ankle angle fixed at 90°. The knee was brought to flexion (140.8±3.0°) (undeformed state). Sets of 3D high resolution MR, and DT images were acquired. This protocol was repeated at extended knee joint position (177.0±1.0°) (deformed state). Tractography and Demons nonrigid registration algorithm was utilized to calculate local deformations along muscle fascicles. Undeformed state images were also transformed by a synthetic rigid body motion to calculate strain errors. Mean strain errors were significantly smaller then mean fiber direction strains (lengthening: 0.2±0.1% vs. 8.7±8.5%; shortening: 3.3±0.9% vs. 7.5±4.6%). Shortening and lengthening (up to 23.3% and 116.7%, respectively) occurs simultaneously along individual fascicles despite imposed GM lengthening. Along-fiber shear strains confirm the presence of much shearing between fascicles. Mean fiber direction strains of different tracts also show non-uniform distribution. Inhomogeneity of fiber strain indicates epimuscular myofascial force transmission. We conclude that MR and DT imaging analyses combined provide a powerful tool for quantifying deformation along human muscle fibers in vivo. This can help substantially achieving a better understanding of normal and pathological muscle function and mechanisms of treatment techniques.


Subject(s)
Diffusion Tensor Imaging , Magnetic Resonance Imaging , Muscle Fibers, Skeletal/pathology , Muscle, Skeletal/diagnostic imaging , Adult , Female , Humans
8.
J Peripher Nerv Syst ; 21(3): 128-33, 2016 09.
Article in English | MEDLINE | ID: mdl-27117347

ABSTRACT

Paclitaxel (PTX) is among the most commonly used cancer drugs that cause chemotherapy-induced peripheral neuropathy (CIPN), a debilitating and serious dose-limiting side effect. Currently, no drugs exist to prevent CIPN, and symptomatic therapy is often ineffective. In order to identify therapeutic candidates to prevent axonal degeneration induced by PTX, we carried out a phenotypic drug screening using primary rodent dorsal root ganglion sensory neurons. We identified fluocinolone acetonide as a neuroprotective compound and verified it through secondary screens. Furthermore, we showed its efficacy in a mouse model of PTX-induced peripheral neuropathy and confirmed with four different cancer cell lines that fluocinolone acetonide does not interfere with PTX's antitumor activity. Our study identifies fluocinolone acetonide as a potential therapy to prevent CIPN caused by PTX.


Subject(s)
Anti-Inflammatory Agents/therapeutic use , Fluocinolone Acetonide/therapeutic use , Paclitaxel/adverse effects , Peripheral Nervous System Diseases/chemically induced , Peripheral Nervous System Diseases/prevention & control , Animals , Animals, Newborn , Anti-Inflammatory Agents/pharmacology , Antineoplastic Agents, Phytogenic/adverse effects , Axons/drug effects , Axons/pathology , Cell Line, Tumor , Cells, Cultured , Disease Models, Animal , Dose-Response Relationship, Drug , Embryo, Mammalian , Female , Fluocinolone Acetonide/pharmacology , Ganglia, Spinal/cytology , Mice , Nerve Fibers/drug effects , Nerve Fibers/pathology , Neurons/drug effects , Rats , Rats, Sprague-Dawley
9.
IEEE Trans Biomed Circuits Syst ; 9(1): 12-20, 2015 Feb.
Article in English | MEDLINE | ID: mdl-24893369

ABSTRACT

In this work, a fully optical Complementary Metal Oxide Semiconductor (CMOS) based catheter tracking system designed for 3 T Magnetic Resonance Imaging (MRI) environment is presented. The system aims to solve the Radio Frequency (RF) induced heating problem present in conventional wired catheter tracking systems used in MRI. It is based on an integrated circuit, consisting of a receiver and an optical power supply unit. The optical power supply unit includes a single on-chip photodiode and a DC-DC converter that boosts the low photodiode voltage output to voltages greater than 1.5 V. Through an optically driven switch, the accumulated charge on an a storage capacitor is transferred to the rest of the system. This operation is novel in the way that it is fully optical and the switch control is done through modulation of the applied light. An on-chip local oscillator signal for the receiver is avoided by application of an RF signal that is generated by the MRI machine at the receiving period. The signals received by a micro-coil antenna are processed by the on-chip direct conversion receiver. The processed signal is then transferred, also optically, to the outside world for tracking purposes. The frequency encoding method is used for MRI tracking. Operation with various levels of external optical power does not generate noticeble temperature increase in the system. The overall system is successfully tested in a 3 T MRI machine to demonstrate its full operation.


Subject(s)
Magnetic Resonance Imaging/instrumentation , Equipment Design , Metals/chemistry , Oxides/chemistry , Semiconductors , Signal-To-Noise Ratio
10.
Med Biol Eng Comput ; 52(10): 885-94, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25173518

ABSTRACT

We describe a new method for frequency down-conversion of MR signals acquired with the radio-frequency projections method for device localization. A low-amplitude, off-center RF pulse applied simultaneously with the echo signal is utilized as the reference for frequency down-conversion. Because of the low-amplitude and large offset from the Larmor frequency, the RF pulse minimally interfered with magnetic resonance of protons. We conducted an experiment with the coil placed at different positions to verify this concept. The down-converted signal was transformed into optical signal and transmitted via fiber-optic cable to a receiver unit placed outside the scanner room. The position of the coil could then be determined by the frequency analysis of this down-converted signal and superimposed on previously acquired MR images for comparison. Because of minimal positional errors (≤ 0.8 mm), this new device localization method may be adequate for most interventional MRI applications.


Subject(s)
Magnetic Resonance Imaging/instrumentation , Radio Waves , Humans , Phantoms, Imaging , Time Factors
11.
Bioinformatics ; 30(6): 860-7, 2014 Mar 15.
Article in English | MEDLINE | ID: mdl-24215027

ABSTRACT

MOTIVATION: Reverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event 'gene interaction' and is used to calculate the probability of a candidate graph (G) in the structure learning process. RESULTS: Our simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods. AVAILABILITY: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP. CONTACT: hasan.otu@bilgi.edu.tr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Gene Regulatory Networks , Software , Bayes Theorem , Carcinoma, Renal Cell/genetics , Gene Expression , Genomics , Humans , Kidney Neoplasms/genetics , Probability
12.
Article in English | MEDLINE | ID: mdl-23061528

ABSTRACT

The complicated muscle activity of the human tongue and the resultant surface shapes can give us important clues about speech motor control and pathological tongue motion. This study uses tagged magnetic resonance imaging to provide a 2D surface deformation analysis of the tongue, as well as a 4D compression-expansion analysis, during utterances of four different syllables (/ba/, /ta/, /sha/ and /ga/). All speech tasks were performed several times to confirm the repeatability of the motion analysis. The results showed that the tongue has unique motion patterns for utterances of different syllables, and these differences, which may not be observed by a simple surface analysis, can be examined thoroughly by a 4D motion model-based analysis of the tongue muscles.


Subject(s)
Speech/physiology , Tongue/physiology , Adult , Humans , Magnetic Resonance Imaging, Cine , Male , Motion , Tongue/anatomy & histology
13.
J Biomech Eng ; 135(9): 91003, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23722229

ABSTRACT

Evidence on epimuscular myofascial force transmission (EMFT) was shown for undissected muscle in situ. We hypothesize that global length changes of gastrocnemius muscle-tendon complex in vivo will cause sizable and heterogeneous local strains within all muscles of the human lower leg. Our goal is to test this hypothesis. A method was developed and validated using high-resolution 3D magnetic resonance image sets and Demons nonrigid registration algorithm for performing large deformation analyses. Calculation of strain tensors per voxel in human muscles in vivo allowed quantifying local heterogeneous tissue deformations and volume changes. After hip and knee movement (Δ knee angle ≈ 25 deg) but without any ankle movement, local lengthening within m. gastrocnemius was shown to occur simultaneously with local shortening (maximally by +34.2% and -32.6%, respectively) at different locations. Moreover, similar local strains occur also within other muscles, despite being kept at constant muscle-tendon complex length. This is shown for synergistic m. soleus and deep flexors, as well as for antagonistic anterior crural and peroneal muscle groups: minimum peak lengthening and shortening equaled 23.3% and 25.54%, respectively despite global isometric conditions. These findings confirm our hypothesis and show that in vivo, muscles are in principle not independent mechanically.


Subject(s)
Leg/physiology , Magnetic Resonance Imaging , Mechanical Phenomena , Muscles/physiology , Adult , Algorithms , Artifacts , Biomechanical Phenomena , Humans , Male , Muscles/cytology , Stress, Mechanical
14.
J Cardiovasc Magn Reson ; 14: 38, 2012 Jun 21.
Article in English | MEDLINE | ID: mdl-22720758

ABSTRACT

BACKGROUND: The field of interventional cardiovascular MRI is hampered by the unavailability of active guidewires that are both safe and conspicuous. Heating of conductive guidewires is difficult to predict in vivo and disruptive to measure using external probes. We describe a clinical-grade 0.035" (0.89 mm) guidewire for MRI right and left heart catheterization at 1.5 T that has an internal probe to monitor temperature in real-time, and that has both tip and shaft visibility as well as suitable flexibility. METHODS: The design has an internal fiberoptic temperature probe, as well as a distal solenoid to enhance tip visibility on a loopless antenna. We tested different tip-solenoid configurations to balance heating and signal profiles. We tested mechanical performance in vitro and in vivo in comparison with a popular clinical nitinol guidewire. RESULTS: The solenoid displaced the point of maximal heating ("hot spot") from the tip to a more proximal location where it can be measured without impairing guidewire flexion. Probe pullback allowed creation of lengthwise guidewire temperature maps that allowed rapid evaluation of design prototypes. Distal-only solenoid attachment offered the best compromise between tip visibility and heating among design candidates. When fixed at the hot spot, the internal probe consistently reflected the maximum temperature compared external probes.Real-time temperature monitoring was performed during porcine left heart catheterization. Heating was negligible using normal operating parameters (flip angle, 45°; SAR, 1.01 W/kg); the temperature increased by 4.2°C only during high RF power mode (flip angle, 90°; SAR, 3.96 W/kg) and only when the guidewire was isolated from blood cooling effects by an introducer sheath. The tip flexibility and in vivo performance of the final guidewire design were similar to a popular commercial guidewire. CONCLUSIONS: We integrated a fiberoptic temperature probe inside a 0.035" MRI guidewire. Real-time monitoring helps detect deleterious heating during use, without impairing mechanical guidewire operation, and without impairing MRI visibility. We therefore need not rely on prediction to ensure safe clinical operation. Future implementations may modulate specific absorption rate (SAR) based on temperature feedback.


Subject(s)
Alloys , Cardiac Catheterization/instrumentation , Cardiac Catheters , Heart Diseases/diagnosis , Magnetic Resonance Imaging, Cine/instrumentation , Magnetic Resonance Imaging, Interventional/instrumentation , Animals , Disease Models, Animal , Equipment Design , Optical Fibers , Pliability , Swine , Temperature
15.
Surg Radiol Anat ; 33(10): 869-79, 2011 Dec.
Article in English | MEDLINE | ID: mdl-21912991

ABSTRACT

PURPOSE: Mechanical interactions between muscles have been shown for in situ conditions. In vivo data for humans is unavailable. Global and local length changes of calf muscles were studied to test the hypothesis that local strains may occur also within muscle for which global strain equals zero. METHODS: For determination of globally induced strain in m. gastrocnemius in dissected human cadavers several knee joint angles were imposed, while keeping ankle joint angle constant and measuring its muscle-tendon complex length changes. In vivo local strains in both gastrocnemius and soleus muscles were calculated using MRI techniques in healthy human volunteers comparing images taken at static knee angles of 173° and 150°. RESULTS: Imposed global strains on gastrocnemius were much smaller than local strains. High distributions of strains were encountered, e.g. overall lengthened muscle contains locally lengthened, as well as shortened areas within it. Substantial strains were not limited to gastrocnemius, but were found also in synergistic soleus muscle, despite the latter muscle-tendon complex length remaining isometric (constant ankle angle: i.e. global strain = 0), as it does not cross the knee. Based on results of animal experiments this effect is ascribed to myofascial connections between these synergistic muscles. The most likely pathway is the neurovascular tract within the anterior crural compartment (i.e. the collagen reinforcements of blood vessels, lymphatics and nerves). However, direct intermuscular transmission of force may also occur via the perimysium shared between the two muscles. CONCLUSIONS: Global strains imposed on muscle (joint movement) are not good estimators of in vivo local strains within it: differing in magnitude, as well as direction of length change. Substantial mechanical interaction occurs between calf muscles, which is mediated by myofascial force transmission between these synergistic muscles. This confirms conclusions of previous in situ studies in experimental animals and human patients, for in vivo conditions in healthy human subjects.


Subject(s)
Fascia/physiology , Knee Joint/physiology , Leg/physiology , Muscle, Skeletal/physiology , Tendons/physiology , Dissection , Female , Humans , Magnetic Resonance Imaging , Male , Stress, Mechanical
16.
Clin EEG Neurosci ; 42(2): 98-106, 2011 Apr.
Article in English | MEDLINE | ID: mdl-21675599

ABSTRACT

The stability of the steady-state visual evoked potentials (SSVEPs) across trials and subjects makes them a suitable tool for the investigation of the visual system. The reproducible pattern of the frequency characteristics of SSVEPs shows a global amplitude maximum around 10 Hz and additional local maxima around 20 and 40 Hz, which have been argued to represent resonant behavior of damped neuronal oscillators. Simultaneous electroencephalogram/functional magnetic resonance imaging (EEG/fMRI) measurement allows testing of the resonance hypothesis about the frequency-selective increases in SSVEP amplitudes in human subjects, because the total synaptic activity that is represented in the fMRI-Blood Oxygen Level Dependent (fMRI-BOLD) response would not increase but get synchronized at the resonance frequency. For this purpose, 40 healthy volunteers were visually stimulated with flickering light at systematically varying frequencies between 6 and 46 Hz, and the correlations between SSVEP amplitudes and the BOLD responses were computed. The SSVEP frequency characteristics of all subjects showed 3 frequency ranges with an amplitude maximum in each of them, which roughly correspond to alpha, beta and gamma bands of the EEG. The correlation maps between BOLD responses and SSVEP amplitude changes across the different stimulation frequencies within each frequency band showed no significant correlation in the alpha range, while significant correlations were obtained in the primary visual area for the beta and gamma bands. This non-linear relationship between the surface recorded SSVEP amplitudes and the BOLD responses of the visual cortex at stimulation frequencies around the alpha band supports the view that a resonance at the tuning frequency of the thalamo-cortical alpha oscillator in the visual system is responsible for the global amplitude maximum of the SSVEP around 10 Hz. Information gained from the SSVEP/fMRI analyses in the present study might be extrapolated to the EEG/fMRI analysis of the transient event-related potentials (ERPs) in terms of expecting more reliable and consistent correlations between EEG and fMRI responses, when the analyses are carried out on evoked or induced oscillations (spectral perturbations) in separate frequency bands instead of the time-domain ERP peaks.


Subject(s)
Electroencephalography/methods , Evoked Potentials, Visual/physiology , Magnetic Resonance Imaging/methods , Models, Neurological , Thalamus/physiology , Visual Cortex/physiology , Adult , Female , Humans , Male , Nonlinear Dynamics , Visual Pathways/physiology , Young Adult
17.
Bioinformatics ; 27(12): 1667-74, 2011 Jun 15.
Article in English | MEDLINE | ID: mdl-21551144

ABSTRACT

MOTIVATION: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network. RESULTS: Proposed method takes into account the connectivity and relatedness between nodes of the pathway through factoring pathway topology in its model. Our simulations using synthetic data demonstrated robustness of our approach. We tested proposed method, Bayesian Pathway Analysis (BPA), on human microarray data regarding renal cell carcinoma (RCC) and compared our results with gene set enrichment analysis. BPA was able to find broader and more specific pathways related to RCC. AVAILABILITY: Accompanying BPA software (BPAS) package is freely available for academic use at http://bumil.boun.edu.tr/bpa.


Subject(s)
Algorithms , Gene Expression Profiling , Gene Regulatory Networks , Bayes Theorem , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/metabolism , High-Throughput Screening Assays , Humans , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Models, Biological , Software
18.
J Neuroimaging ; 21(2): 145-51, 2011 Apr.
Article in English | MEDLINE | ID: mdl-20040011

ABSTRACT

The aim of the study is to analyze diffusion tensor imaging (DTI) characteristics of the Guillain-Mollaret triangle (GMT) in patients with hypertrophic olivary degeneration (HOD) and to investigate their correlation with previously reported histopathology. DTI was performed in 10 patients diagnosed with HOD. Fractional anisotropy, apparent diffusion coefficient, axial diffusivity, and radial diffusivity were measured in the inferior olivary nucleus (IO), the central tegmental tract, the red and the dentate nuclei, and the superior cerebellar peduncle of HOD patients and compared to age, sex, and side-matched 10 neurologically normal population. The prominent finding on DTI in affected IO was an increase in radial diffusivity compatible with demyelination. While conventional magnetic resonance imaging did not show any sign of involvement in the other components of GMT, DTI demonstrated signal changes in all anatomical components of the GMT. Main DTI findings in GMT of patients with HOD were an increase in radial diffusivity representing demyelination and an increase in axial diffusivity that is reflective of neuronal hypertrophy. DTI parameters can reflect the spatiotemporal evolution of transneuronal degeneration associated with HOD in a manner consistent with the known pathologic stages of HOD.


Subject(s)
Diffusion Tensor Imaging/methods , Nerve Degeneration/pathology , Olivary Nucleus/pathology , Adolescent , Adult , Aged , Analysis of Variance , Brain Mapping/methods , Female , Humans , Hypertrophy/pathology , Male , Middle Aged
19.
Magn Reson Med ; 64(1): 306-12, 2010 Jul.
Article in English | MEDLINE | ID: mdl-20577983

ABSTRACT

A real-time implementation of self-calibrating Generalized Autocalibrating Partially Parallel Acquisitions (GRAPPA) operator gridding for radial acquisitions is presented. Self-calibrating GRAPPA operator gridding is a parallel-imaging-based, parameter-free gridding algorithm, where coil sensitivity profiles are used to calculate gridding weights. Self-calibrating GRAPPA operator gridding's weight-set calculation and image reconstruction steps are decoupled into two distinct processes, implemented in C++ and parallelized. This decoupling allows the weights to be updated adaptively in the background while image reconstruction threads use the most recent gridding weights to grid and reconstruct images. All possible combinations of two-dimensional gridding weights G(x)(m)G(y)(n) are evaluated for m,n = {-0.5, -0.4, ..., 0, 0.1, ..., 0.5} and stored in a look-up table. Consequently, the per-sample two-dimensional weights calculation during gridding is eliminated from the reconstruction process and replaced by a simple look-up table access. In practice, up to 34x faster reconstruction than conventional (parallelized) self-calibrating GRAPPA operator gridding is achieved. On a 32-coil dataset of size 128 x 64, reconstruction performance is 14.5 frames per second (fps), while the data acquisition is 6.6 fps.


Subject(s)
Algorithms , Magnetic Resonance Imaging/methods , Calibration , Phantoms, Imaging
20.
J Magn Reson Imaging ; 31(4): 1015-9, 2010 Apr.
Article in English | MEDLINE | ID: mdl-20373448

ABSTRACT

PURPOSE: To enhance real-time magnetic resonance (MR)-guided catheter navigation by overlaying colorized multiphase MR angiography (MRA) and cholangiopancreatography (MRCP) roadmaps in an anatomic context. MATERIALS AND METHODS: Time-resolved MRA and respiratory-gated MRCP were acquired prior to real-time imaging in a pig model. MRA and MRCP data were loaded into a custom real-time MRI reconstruction and visualization workstation where they were displayed as maximum intensity projections (MIPs) in distinct colors. The MIPs were rendered in 3D together with real-time multislice imaging data using alpha blending. Interactive rotation allowed different views of the combined data. RESULTS: Fused display of the previously acquired MIP angiography data with real-time imaging added anatomical context during endovascular interventions in swine. The use of multiple MIPs rendered in different colors facilitated differentiation of vascular structures, improving visual feedback during device navigation. CONCLUSION: Interventional real-time MRI may be enhanced by combining with previously acquired multiphase angiograms. Rendered as 3D MIPs together with 2D slice data, this technique provided useful anatomical context that enhanced MRI-guided interventional applications.


Subject(s)
Cholangiopancreatography, Magnetic Resonance/methods , Imaging, Three-Dimensional/methods , Magnetic Resonance Angiography/methods , Magnetic Resonance Imaging, Interventional/methods , Magnetic Resonance Imaging/methods , Animals , Image Processing, Computer-Assisted/methods , Lung/pathology , Models, Anatomic , Swine , Thrombectomy/methods , Time Factors
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