Jun Lian - Academia.edu (original) (raw)

Papers by Jun Lian

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2012

IEEE Transactions on Medical Imaging, 2021

Accurate segmentation of the prostate and organs at risk (OARs, e.g., bladder and rectum) in male... more Accurate segmentation of the prostate and organs at risk (OARs, e.g., bladder and rectum) in male pelvic CT images is a critical step for prostate cancer radiotherapy. Unfortunately, the unclear organ boundary and large shape variation make the segmentation task very challenging. Previous studies usually used representations defined directly on unclear boundaries as context information to guide segmentation. Those boundary representations may not be so discriminative, resulting in limited performance improvement. To this end, we propose a novel boundary coding network (BCnet) to learn a discriminative representation for organ boundary and use it as the context information to guide the segmentation. Specifically, we design a two-stage learning strategy in the proposed BCnet: 1) Boundary coding representation learning. Two sub-networks under the supervision of the dilation and erosion masks transformed from the manually delineated organ mask are first separately trained to learn the spatial-semantic context near the organ boundary. Then we encode the organ boundary based on the predictions of these two sub-networks and design a multi-atlas based refinement strategy by transferring the knowledge from training data to inference. 2) Organ segmentation. The boundary coding representation as context information, in addition to the image patches, are used to train the final segmentation network. Experimental results on a large and diverse male pelvic CT dataset show that our method achieves superior performance compared with several state-of-the-art methods.

Biomedical Physics & Engineering Express, 2019

Helical TomoTherapy has unique challenges in handling intrafractional motion compared to a 30 con... more Helical TomoTherapy has unique challenges in handling intrafractional motion compared to a 30 conventional LINAC. In this study, we analyzed the impact of intrafractional motion on cumulative dosimetry using actual patient motion data from clinically treated patients and investigated real time jaw and multileaf collimator (MLC) compensation approaches to minimize the motioninduced dose discrepancy in clinically acceptable TomoTherapy lung SBRT treatments. Intrafractional motion traces from eight fiducial tracking CyberKnife lung tumor treatment cases 35 were used in this study. These cases were re-planned on TomoTherapy for SBRT, with 18 Gy × 3 fractions to a planning target volume (PTV) defined on the breath-hold CT without ITV expansion. Each case was planned with four different jaw settings: 1 cm static, 2.5 cm static, 2.5 cm dynamic and 5 cm dynamic. In-house 4D dose accumulation software was used to compute the dose distributions with tumor motion and then compensate for that motion by modifying the 40 original jaw and MLC positions to track the trajectory of the tumor. The impact of motion and effectiveness of compensation on the PTV coverage depends on the motion type and plan settings. On average, the PTV V100% (the percent volume of the PTV receiving the prescription dose) accumulated from three fractions changed from 96.6% (motion-free) to 83.1% (motionincluded), 97.5% to 93.0%, 97.7% to 92.1%, and 98.1% to 93.7% for the 1 cm static jaw, 2.5 cm 45 static jaw, 2.5 cm dynamic jaw and 5 cm dynamic jaw setting, respectively. When the jaw and MLC compensation algorithm was engaged, the PTV V100% was restored back to 92.2%, 95.9%, 96.6% and 96.4%, for the four jaw settings mentioned above respectively. TomoTherapy lung tumor SBRT treatments using a field width of 2.5 cm or larger are less sensitive to motion than treatments using a 1 cm field width. For 1 cm field width plans, PTV coverage can be greatly 50

IEEE Transactions on Medical Robotics and Bionics, 2019

In this paper, we describe a method for recovering the tissue properties directly from medical im... more In this paper, we describe a method for recovering the tissue properties directly from medical images and study the correlation of tissue (i.e. prostate) elasticity with the aggressiveness of prostate cancer using medical image analysis. Methods: We present a novel method that uses geometric and physical constraints to deduce the relative tissue elasticity parameters. Although elasticity reconstruction, or elastograph, can be used to estimate tissue elasticity, it is less suited for invivo measurements or deeply seated organs like prostate. We develop a method to estimate tissue elasticity values based on pairs of images, using a finite-element based biomechanical model derived from an initial set of images, local displacements and an optimization-based framework. Results: We demonstrate the feasibility of a statistically based classifier that automatically provides a clinical T-stage and Gleason score based on the elasticity values reconstructed from computed tomography (CT) images. Conclusions: We study the relative elasticity parameters by performing cancer Grading/Staging prediction and achieve up to 85% accuracy for cancer Staging prediction and up to 77% accuracy for cancer Grading prediction using feature set which includes recovered relative elasticity parameters and patient age information.

IEEE transactions on bio-medical engineering, Jan 9, 2018

Medical imaging plays a critical role in various clinical applications. However, due to multiple ... more Medical imaging plays a critical role in various clinical applications. However, due to multiple considerations such as cost and radiation dose, the acquisition of certain image modalities may be limited. Thus, medical image synthesis can be of great benefit by estimating a desired imaging modality without incurring an actual scan. In this paper, we propose a generative adversarial approach to address this challenging problem. Specifically, we train a fully convolutional network (FCN) to generate a target image given a source image. To better model a nonlinear mapping from source to target and to produce more realistic target images, we propose to use the adversarial learning strategy to better model the FCN. Moreover, the FCN is designed to incorporate an image-gradient-difference based loss function to avoid generating blurry target images. Long-term residual unit is also explored to help the training of the network. We further apply Auto-Context Model (ACM) to implement a context...

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, 2017

Computed tomography (CT) is critical for various clinical applications, e.g., radiation treatment... more Computed tomography (CT) is critical for various clinical applications, e.g., radiation treatment planning and also PET attenuation correction in MRI/PET scanner. However, CT exposes radiation during acquisition, which may cause side effects to patients. Compared to CT, magnetic resonance imaging (MRI) is much safer and does not involve radiations. Therefore, recently researchers are greatly motivated to estimate CT image from its corresponding MR image of the same subject for the case of radiation planning. In this paper, we propose a data-driven approach to address this challenging problem. Specifically, we train a fully convolutional network (FCN) to generate CT given the MR image. To better model the nonlinear mapping from MRI to CT and produce more realistic images, we propose to use the adversarial training strategy to train the FCN. Moreover, we propose an image-gradient-difference based loss function to alleviate the blurriness of the generated CT. We further apply Auto-Cont...

International Journal of Radiation Oncology*Biology*Physics, 2016

The objective of this study is to evaluate weekly primary tumor regression rates (PTRR) and nodal... more The objective of this study is to evaluate weekly primary tumor regression rates (PTRR) and nodal tumor regression rates (NTRR) of head and neck cancers (HNC) during radiation (RT) as a prognostic indicator of oncologic outcomes and survival. Image guided radiation therapy (IGRT), specifically computed tomography (CT)-on-Rails (CToR), increases the accuracy of daily RT and additionally affords the opportunity for intratreatment response evaluation. Materials/Methods: A single-institution retrospective review from 2008 to 2013 was completed for patients with HNC who received RT with CToR. Forty-three patients with 70 measurable targets, 43 primary lesions and 27 metastatic lymph nodes, met inclusion criteria. Patients without radiographically evident primary tumors and those with surgical intervention prior to RT were excluded. Results: The analysis included 43 patients with a median age of 56 years (21-78), and 91% of them were male. The majory of patients were diagnosed with oropharynx cancers (63%), 26% nasopharynx and 11% sinonasal. Fifty-eight percent of patients received definitive chemoradiation, and 26% received induction followed by chemoradiation. The mean primary and nodal gross tumor volume (GTV) pre-RT was 38.5 mL (standard deviation [SD] 34.9) and 13.6 mL (SD 10.3), respectively. PTRR of 25% at fraction 15 (nZ26) was associated with superior 5-year local control (LC) (100% vs 70%, PZ.003), relapse-free survival (RFS; 84% vs 45%, PZ.007), and overall survival (OS; 88% vs 50%, PZ.005). On both univariate and multivariate analysis, PTRR <25% was associated with increased hazard of local failure compared to 25% (PZ.001 for both). There was not a strong independent correlation of NTRR with regional control, distant control or RFS. Further characterization of tracked lymph nodes revealed that 70% (nZ19) were purely cystic or had a cystic component. Many of the highly cystic nodes demonstrated an initial increase in size, likely secondary to RT induced inflammation, before later regression. Conclusion: CToR enables accurate GTV tracking during treatment which carries prognostic value. PTRR of 25% at midtreatment can be used as an indicator for LC, RFS, and OS. NTRR does not appear to carry the same prognostic value as PTRR due to variations in nodal architecture, an initial paradoxical size increase, especially in cystic nodes, and treatment response often continuing up to 4 months post-RT. The clinical implication of TRR appears to be of most value when tracking the primary lesion, and specifically if PTRR <25% treatment plan modification may be warranted given a higher likelihood of treatment failure.

Frontiers in oncology, 2017

Computed tomography (CT), combined positron emitted tomography and CT (PET/CT), and magnetic reso... more Computed tomography (CT), combined positron emitted tomography and CT (PET/CT), and magnetic resonance imaging (MRI) are commonly used in head and neck radiation planning. Hybrid PET/MRI has garnered attention for potential added value in cancer staging and treatment planning. Herein, we compare PET/MRI vs. planning CT for head and neck cancer gross tumor volume (GTV) delineation. We prospectively enrolled patients with head and neck cancer treated with definitive chemoradiation to 60-70 Gy using IMRT. We performed pretreatment contrast-enhanced planning CT and gadolinium-enhanced PET/MRI. Primary and nodal volumes were delineated on planning CT (GTV-CT) prospectively before treatment and PET/MRI (GTV-PET/MRI) retrospectively after treatment. GTV-PET/MRI was compared to GTV-CT using separate rigid registrations for each tumor volume. The Dice similarity coefficient (DSC) metric evaluating spatial overlap and modified Hausdorff distance (mHD) evaluating mean orthogonal distance diffe...

Journal of applied clinical medical physics, Jul 8, 2015

Deep inspiration breath-hold (DIBH) radiotherapy for left-sided breast cancer can reduce cardiac ... more Deep inspiration breath-hold (DIBH) radiotherapy for left-sided breast cancer can reduce cardiac exposure and internal motion. We modified our in-house treatment planning system (TPS) to retrospectively analyze breath-hold motion log files to calculate the dosimetric effect of the motion during breath hold. Thirty left-sided supine DIBH breast patients treated using AlignRT were studied. Breath-hold motion was recorded - three translational and three rotational displacements of the treatment surface - the Real Time Deltas (RTD). The corresponding delivered dose was estimated using the beam-on portions of the RTDs. Each motion was used to calculate dose, and the final estimated dose was the equally weighted average of the multiple resultant doses. Ten of thirty patients had internal mammary nodes (IMN) purposefully included in the tangential fields, and we evaluated the percentage of IMN covered by 40 Gy. The planned and delivered heart mean dose, lungs V20 (volume of the lungs recei...

Medical physics, 2016

Prostate brachytherapy is an important treatment technique for patients with localized prostate c... more Prostate brachytherapy is an important treatment technique for patients with localized prostate cancer. An inflatable rectal ultrasound probe cover is frequently utilized during the procedure to adjust for unfavorable prostate position relative to the implant grid. However, the inflated cover causes prostate deformation, which is not accounted for during dosimetric planning. Most of the therapeutic dose is delivered after the procedure when the prostate and surrounding organs-at-risk are less deformed. The aim of this study is to quantify the potential dosimetry changes between the initial plan (prostate deformed) and the more realistic dosimetry when the prostate is less deformed without the cover. The authors prospectively collected the ultrasound images of the prostate immediately preceding and just after inflation of the rectal probe cover from thirty-four consecutive patients undergoing real-time planning of I-125 permanent seed implant. Manual segmentations of the deformed and...

Lecture Notes in Computer Science, 2016

IEEE transactions on medical imaging, Jun 18, 2016

Segmenting male pelvic organs from CT images is a prerequisite for prostate cancer radiotherapy. ... more Segmenting male pelvic organs from CT images is a prerequisite for prostate cancer radiotherapy. The efficacy of radiation treatment highly depends on segmentation accuracy. However, accurate segmentation of male pelvic organs is challenging due to low tissue contrast of CT images, as well as large variations of shape and appearance of the pelvic organs. Among existing segmentation methods, deformable models are the most popular, as shape prior can be easily incorporated to regularize the segmentation. Nonetheless, the sensitivity to initialization often limits their performance, especially for segmenting organs with large shape variations. In this paper, we propose a novel approach to guide deformable models, thus making them robust against arbitrary initializations. Specifically, we learn a displacement regressor, which predicts 3D displacement from any image voxel to the target organ boundary based on the local patch appearance. This regressor provides a nonlocal external force f...

IEEE Transactions on Medical Imaging, 2016

Computed tomography (CT) imaging is an essential tool in various clinical diagnoses and radiother... more Computed tomography (CT) imaging is an essential tool in various clinical diagnoses and radiotherapy treatment planning. Since CT image intensities are directly related to positron emission tomography (PET) attenuation coefficients, they are indispensable for attenuation correction (AC) of the PET images. However, due to the relatively high dose of radiation exposure in CT scan, it is advised to limit the acquisition of CT images. In addition, in the new PET and magnetic resonance (MR) imaging scanner, only MR images are available, which are unfortunately not directly applicable to AC. These issues greatly motivate the development of *

Physical Review E, 2001

Time-series methods for estimating Lyapunov exponents may give a positive exponent when they are ... more Time-series methods for estimating Lyapunov exponents may give a positive exponent when they are applied to the time series of strange nonchaotic systems. Strange nonchaotic systems are characterized by expanding and contracting regions in phase space that result in repeatedly expanding or contracting trajectories. Using time-series methods, the maximum time-series Lyapunov exponent is calculated as an average of the locally most expanding exponents that characterize the divergence of nearby trajectories following a reconstructed attractor over time. A positive exponent is reported by time-series methods for trajectories in an expanding region. While in a converging region, the most expanding dynamics are related to the quasiperiodic driving force. Statistically, a zero exponent related to the quasiperiodic force is obtained through time-series methods within converging regions. As a result, the calculated maximum Lyapunov exponent is positive.

Journal of applied clinical medical physics / American College of Medical Physics, Jan 6, 2014

Direct aperture optimization (DAO) has been used to produce high dosimetric quality intensity-mod... more Direct aperture optimization (DAO) has been used to produce high dosimetric quality intensity-modulated radiotherapy (IMRT) treatment plans with fast treatment delivery by directly modeling the multileaf collimator segment shapes and weights. To improve plan quality and reduce treatment time for our in-house treatment planning system, we implemented a new DAO approach without using a global objective function (GFO). An index concept is introduced as an inverse form of back-projection used in the CT multiplicative algebraic reconstruction technique (MART). The index, introduced for IMRT optimization in this work, is analogous to the multiplicand in MART. The index is defined as the ratio of the optima over the current. It is assigned to each voxel and beamlet to optimize the fluence map. The indices for beamlets and segments are used to optimize multileaf collimator (MLC) segment shapes and segment weights, respectively. Preliminary data show that without sacrificing dosimetric quali...

The Journal of Physiology, 2003

Preparation of hippocampal slices and perfusion All experiments were performed in the CA1 or CA3 ... more Preparation of hippocampal slices and perfusion All experiments were performed in the CA1 or CA3 regions of hippocampal brain slices prepared from Sprague-Dawley rats (175-250 g). Rats were anaesthetized with ethyl ether and decapitated. The experimental protocol was reviewed and approved by the Institution Animal Care and Use Committee. The brain was rapidly removed and one hemisphere glued to the stage of a Vibroslicer (Vibroslice, Campden Instruments Ltd, London, UK) Slicing was carried out in cold (3-4°C), oxygenated sucrose-based artificial cerebrospinal fluid (ACSF) consisting of (mM): sucrose 220, KCl 3, NaH 2 PO 4 1.25, MgSO 4 2, NaHCO 3 26, CaCl 2 2, dextrose 10. The resulting 350 mm thick slices were immediately transferred to a holding chamber with 'normal' ACSF consisting of (mM): NaCl 124, KCl 3.75, KH 2 PO 4 1.25, CaCl 2 2, MgSO 4 2, NaHCO 3 26, dextrose 10, held at room temperature and bubbled with 95 % O 2-5 % CO 2 .

The Journal of Physiology, 2001

High frequency deep brain stimulation (DBS) of certain brain structures can alleviate or complete... more High frequency deep brain stimulation (DBS) of certain brain structures can alleviate or completely suppress the symptoms of several neuronal disorders including Parkinson's disease (Benabid et al. 1994), epilepsy (Velasco et al. 1995, 1997) and intractable pain (Kumar et al. 1997). It has been

The Journal of Physiology, 2001

1. Spontaneous non-synaptic epileptiform activity was induced by bathing rat hippocampal slices i... more 1. Spontaneous non-synaptic epileptiform activity was induced by bathing rat hippocampal slices in low-Ca 2+ solution. Extracellular recordings from electrodes placed on both sides of a complete cut showed that non-synaptic activity was synchronized across the lesion. 2. Ion-selective electrode recordings showed that each event was accompanied by a transient increase in extracellular potassium that diffused across the lesion. The synchrony was destroyed when a thin film was inserted into the lesion site. 3. Local pressure ejection of KCl evoked an event that subsequently propagated across the lesion. 4. After a complete lesion was made, afterdischarges evoked on one half of a slice were not detected on the other half. 5. Voltage-sensitive dye imaging methods showed that epileptic activity propagated across the mechanical lesion without significant attenuation or additional delays. The velocity of the activity was consistent with that of the slow diffusion of a potassium wave. 6. Since field effects were significantly attenuated across the lesion and all gap junctions and cell processes across the lesion would be cut, these data show that extracellular diffusion, most probably potassium, is sufficient to synchronize populations of neurons and propagate slow frequency epileptiform activity.

Medical Physics, 2004

The endorectal coil is being increasingly used in magnetic resonance imaging (MRI) and MR spectro... more The endorectal coil is being increasingly used in magnetic resonance imaging (MRI) and MR spectroscopic imaging (MRSI) to obtain anatomic and metabolic images of the prostate with high signal-to-noise ratio (SNR). In practice, however, the use of endorectal probe inevitably distorts the prostate and other soft tissue organs, making the analysis and the use of the acquired image data in treatment planning difficult. The purpose of this work is to develop a deformable image registration algorithm to map the MRI/MRSI information obtained using an endorectal probe onto CT images and to verify the accuracy of the registration by phantom and patient studies. A mapping procedure involved using a thin plate spline (TPS) transformation was implemented to establish voxel-tovoxel correspondence between a reference image and a floating image with deformation. An elastic phantom with a number of implanted fiducial markers was designed for the validation of the quality of the registration. Radiographic images of the phantom were obtained before and after a series of intentionally introduced distortions. After mapping the distorted phantom to the original one, the displacements of the implanted markers were measured with respect to their ideal positions and the mean error was calculated. In patient studies, CT images of three prostate patients were acquired, followed by 3 Tesla ͑3 T͒ MR images with a rigid endorectal coil. Registration quality was estimated by the centroid position displacement and image coincidence index (CI). Phantom and patient studies show that TPS-based registration has achieved significantly higher accuracy than the previously reported method based on a rigid-body transformation and scaling. The technique should be useful to map the MR spectroscopic dataset acquired with ER probe onto the treatment planning CT dataset to guide radiotherapy planning.

Medical Physics, 2004

Radiobiological treatment planning depends not only on the accuracy of the models describing the ... more Radiobiological treatment planning depends not only on the accuracy of the models describing the dose-response relation of different tumors and normal tissues but also on the accuracy of tissue specific radiobiological parameters in these models. Whereas the general formalism remains the same, different sets of model parameters lead to different solutions and thus critically determine the final plan. Here we describe an inverse planning formalism with inclusion of model parameter uncertainties. This is made possible by using a statistical analysis-based frameset developed by our group. In this formalism, the uncertainties of model parameters, such as the parameter a that describes tissue-specific effect in the equivalent uniform dose (EUD) model, are expressed by probability density function and are included in the dose optimization process. We found that the final solution strongly depends on distribution functions of the model parameters. Considering that currently available models for computing biological effects of radiation are simplistic, and the clinical data used to derive the models are sparse and of questionable quality, the proposed technique provides us with an effective tool to minimize the effect caused by the uncertainties in a statistical sense. With the incorporation of the uncertainties, the technique has potential for us to maximally utilize the available radiobiology knowledge for better IMRT treatment.

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2012

IEEE Transactions on Medical Imaging, 2021

Accurate segmentation of the prostate and organs at risk (OARs, e.g., bladder and rectum) in male... more Accurate segmentation of the prostate and organs at risk (OARs, e.g., bladder and rectum) in male pelvic CT images is a critical step for prostate cancer radiotherapy. Unfortunately, the unclear organ boundary and large shape variation make the segmentation task very challenging. Previous studies usually used representations defined directly on unclear boundaries as context information to guide segmentation. Those boundary representations may not be so discriminative, resulting in limited performance improvement. To this end, we propose a novel boundary coding network (BCnet) to learn a discriminative representation for organ boundary and use it as the context information to guide the segmentation. Specifically, we design a two-stage learning strategy in the proposed BCnet: 1) Boundary coding representation learning. Two sub-networks under the supervision of the dilation and erosion masks transformed from the manually delineated organ mask are first separately trained to learn the spatial-semantic context near the organ boundary. Then we encode the organ boundary based on the predictions of these two sub-networks and design a multi-atlas based refinement strategy by transferring the knowledge from training data to inference. 2) Organ segmentation. The boundary coding representation as context information, in addition to the image patches, are used to train the final segmentation network. Experimental results on a large and diverse male pelvic CT dataset show that our method achieves superior performance compared with several state-of-the-art methods.

Biomedical Physics & Engineering Express, 2019

Helical TomoTherapy has unique challenges in handling intrafractional motion compared to a 30 con... more Helical TomoTherapy has unique challenges in handling intrafractional motion compared to a 30 conventional LINAC. In this study, we analyzed the impact of intrafractional motion on cumulative dosimetry using actual patient motion data from clinically treated patients and investigated real time jaw and multileaf collimator (MLC) compensation approaches to minimize the motioninduced dose discrepancy in clinically acceptable TomoTherapy lung SBRT treatments. Intrafractional motion traces from eight fiducial tracking CyberKnife lung tumor treatment cases 35 were used in this study. These cases were re-planned on TomoTherapy for SBRT, with 18 Gy × 3 fractions to a planning target volume (PTV) defined on the breath-hold CT without ITV expansion. Each case was planned with four different jaw settings: 1 cm static, 2.5 cm static, 2.5 cm dynamic and 5 cm dynamic. In-house 4D dose accumulation software was used to compute the dose distributions with tumor motion and then compensate for that motion by modifying the 40 original jaw and MLC positions to track the trajectory of the tumor. The impact of motion and effectiveness of compensation on the PTV coverage depends on the motion type and plan settings. On average, the PTV V100% (the percent volume of the PTV receiving the prescription dose) accumulated from three fractions changed from 96.6% (motion-free) to 83.1% (motionincluded), 97.5% to 93.0%, 97.7% to 92.1%, and 98.1% to 93.7% for the 1 cm static jaw, 2.5 cm 45 static jaw, 2.5 cm dynamic jaw and 5 cm dynamic jaw setting, respectively. When the jaw and MLC compensation algorithm was engaged, the PTV V100% was restored back to 92.2%, 95.9%, 96.6% and 96.4%, for the four jaw settings mentioned above respectively. TomoTherapy lung tumor SBRT treatments using a field width of 2.5 cm or larger are less sensitive to motion than treatments using a 1 cm field width. For 1 cm field width plans, PTV coverage can be greatly 50

IEEE Transactions on Medical Robotics and Bionics, 2019

In this paper, we describe a method for recovering the tissue properties directly from medical im... more In this paper, we describe a method for recovering the tissue properties directly from medical images and study the correlation of tissue (i.e. prostate) elasticity with the aggressiveness of prostate cancer using medical image analysis. Methods: We present a novel method that uses geometric and physical constraints to deduce the relative tissue elasticity parameters. Although elasticity reconstruction, or elastograph, can be used to estimate tissue elasticity, it is less suited for invivo measurements or deeply seated organs like prostate. We develop a method to estimate tissue elasticity values based on pairs of images, using a finite-element based biomechanical model derived from an initial set of images, local displacements and an optimization-based framework. Results: We demonstrate the feasibility of a statistically based classifier that automatically provides a clinical T-stage and Gleason score based on the elasticity values reconstructed from computed tomography (CT) images. Conclusions: We study the relative elasticity parameters by performing cancer Grading/Staging prediction and achieve up to 85% accuracy for cancer Staging prediction and up to 77% accuracy for cancer Grading prediction using feature set which includes recovered relative elasticity parameters and patient age information.

IEEE transactions on bio-medical engineering, Jan 9, 2018

Medical imaging plays a critical role in various clinical applications. However, due to multiple ... more Medical imaging plays a critical role in various clinical applications. However, due to multiple considerations such as cost and radiation dose, the acquisition of certain image modalities may be limited. Thus, medical image synthesis can be of great benefit by estimating a desired imaging modality without incurring an actual scan. In this paper, we propose a generative adversarial approach to address this challenging problem. Specifically, we train a fully convolutional network (FCN) to generate a target image given a source image. To better model a nonlinear mapping from source to target and to produce more realistic target images, we propose to use the adversarial learning strategy to better model the FCN. Moreover, the FCN is designed to incorporate an image-gradient-difference based loss function to avoid generating blurry target images. Long-term residual unit is also explored to help the training of the network. We further apply Auto-Context Model (ACM) to implement a context...

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, 2017

Computed tomography (CT) is critical for various clinical applications, e.g., radiation treatment... more Computed tomography (CT) is critical for various clinical applications, e.g., radiation treatment planning and also PET attenuation correction in MRI/PET scanner. However, CT exposes radiation during acquisition, which may cause side effects to patients. Compared to CT, magnetic resonance imaging (MRI) is much safer and does not involve radiations. Therefore, recently researchers are greatly motivated to estimate CT image from its corresponding MR image of the same subject for the case of radiation planning. In this paper, we propose a data-driven approach to address this challenging problem. Specifically, we train a fully convolutional network (FCN) to generate CT given the MR image. To better model the nonlinear mapping from MRI to CT and produce more realistic images, we propose to use the adversarial training strategy to train the FCN. Moreover, we propose an image-gradient-difference based loss function to alleviate the blurriness of the generated CT. We further apply Auto-Cont...

International Journal of Radiation Oncology*Biology*Physics, 2016

The objective of this study is to evaluate weekly primary tumor regression rates (PTRR) and nodal... more The objective of this study is to evaluate weekly primary tumor regression rates (PTRR) and nodal tumor regression rates (NTRR) of head and neck cancers (HNC) during radiation (RT) as a prognostic indicator of oncologic outcomes and survival. Image guided radiation therapy (IGRT), specifically computed tomography (CT)-on-Rails (CToR), increases the accuracy of daily RT and additionally affords the opportunity for intratreatment response evaluation. Materials/Methods: A single-institution retrospective review from 2008 to 2013 was completed for patients with HNC who received RT with CToR. Forty-three patients with 70 measurable targets, 43 primary lesions and 27 metastatic lymph nodes, met inclusion criteria. Patients without radiographically evident primary tumors and those with surgical intervention prior to RT were excluded. Results: The analysis included 43 patients with a median age of 56 years (21-78), and 91% of them were male. The majory of patients were diagnosed with oropharynx cancers (63%), 26% nasopharynx and 11% sinonasal. Fifty-eight percent of patients received definitive chemoradiation, and 26% received induction followed by chemoradiation. The mean primary and nodal gross tumor volume (GTV) pre-RT was 38.5 mL (standard deviation [SD] 34.9) and 13.6 mL (SD 10.3), respectively. PTRR of 25% at fraction 15 (nZ26) was associated with superior 5-year local control (LC) (100% vs 70%, PZ.003), relapse-free survival (RFS; 84% vs 45%, PZ.007), and overall survival (OS; 88% vs 50%, PZ.005). On both univariate and multivariate analysis, PTRR <25% was associated with increased hazard of local failure compared to 25% (PZ.001 for both). There was not a strong independent correlation of NTRR with regional control, distant control or RFS. Further characterization of tracked lymph nodes revealed that 70% (nZ19) were purely cystic or had a cystic component. Many of the highly cystic nodes demonstrated an initial increase in size, likely secondary to RT induced inflammation, before later regression. Conclusion: CToR enables accurate GTV tracking during treatment which carries prognostic value. PTRR of 25% at midtreatment can be used as an indicator for LC, RFS, and OS. NTRR does not appear to carry the same prognostic value as PTRR due to variations in nodal architecture, an initial paradoxical size increase, especially in cystic nodes, and treatment response often continuing up to 4 months post-RT. The clinical implication of TRR appears to be of most value when tracking the primary lesion, and specifically if PTRR <25% treatment plan modification may be warranted given a higher likelihood of treatment failure.

Frontiers in oncology, 2017

Computed tomography (CT), combined positron emitted tomography and CT (PET/CT), and magnetic reso... more Computed tomography (CT), combined positron emitted tomography and CT (PET/CT), and magnetic resonance imaging (MRI) are commonly used in head and neck radiation planning. Hybrid PET/MRI has garnered attention for potential added value in cancer staging and treatment planning. Herein, we compare PET/MRI vs. planning CT for head and neck cancer gross tumor volume (GTV) delineation. We prospectively enrolled patients with head and neck cancer treated with definitive chemoradiation to 60-70 Gy using IMRT. We performed pretreatment contrast-enhanced planning CT and gadolinium-enhanced PET/MRI. Primary and nodal volumes were delineated on planning CT (GTV-CT) prospectively before treatment and PET/MRI (GTV-PET/MRI) retrospectively after treatment. GTV-PET/MRI was compared to GTV-CT using separate rigid registrations for each tumor volume. The Dice similarity coefficient (DSC) metric evaluating spatial overlap and modified Hausdorff distance (mHD) evaluating mean orthogonal distance diffe...

Journal of applied clinical medical physics, Jul 8, 2015

Deep inspiration breath-hold (DIBH) radiotherapy for left-sided breast cancer can reduce cardiac ... more Deep inspiration breath-hold (DIBH) radiotherapy for left-sided breast cancer can reduce cardiac exposure and internal motion. We modified our in-house treatment planning system (TPS) to retrospectively analyze breath-hold motion log files to calculate the dosimetric effect of the motion during breath hold. Thirty left-sided supine DIBH breast patients treated using AlignRT were studied. Breath-hold motion was recorded - three translational and three rotational displacements of the treatment surface - the Real Time Deltas (RTD). The corresponding delivered dose was estimated using the beam-on portions of the RTDs. Each motion was used to calculate dose, and the final estimated dose was the equally weighted average of the multiple resultant doses. Ten of thirty patients had internal mammary nodes (IMN) purposefully included in the tangential fields, and we evaluated the percentage of IMN covered by 40 Gy. The planned and delivered heart mean dose, lungs V20 (volume of the lungs recei...

Medical physics, 2016

Prostate brachytherapy is an important treatment technique for patients with localized prostate c... more Prostate brachytherapy is an important treatment technique for patients with localized prostate cancer. An inflatable rectal ultrasound probe cover is frequently utilized during the procedure to adjust for unfavorable prostate position relative to the implant grid. However, the inflated cover causes prostate deformation, which is not accounted for during dosimetric planning. Most of the therapeutic dose is delivered after the procedure when the prostate and surrounding organs-at-risk are less deformed. The aim of this study is to quantify the potential dosimetry changes between the initial plan (prostate deformed) and the more realistic dosimetry when the prostate is less deformed without the cover. The authors prospectively collected the ultrasound images of the prostate immediately preceding and just after inflation of the rectal probe cover from thirty-four consecutive patients undergoing real-time planning of I-125 permanent seed implant. Manual segmentations of the deformed and...

Lecture Notes in Computer Science, 2016

IEEE transactions on medical imaging, Jun 18, 2016

Segmenting male pelvic organs from CT images is a prerequisite for prostate cancer radiotherapy. ... more Segmenting male pelvic organs from CT images is a prerequisite for prostate cancer radiotherapy. The efficacy of radiation treatment highly depends on segmentation accuracy. However, accurate segmentation of male pelvic organs is challenging due to low tissue contrast of CT images, as well as large variations of shape and appearance of the pelvic organs. Among existing segmentation methods, deformable models are the most popular, as shape prior can be easily incorporated to regularize the segmentation. Nonetheless, the sensitivity to initialization often limits their performance, especially for segmenting organs with large shape variations. In this paper, we propose a novel approach to guide deformable models, thus making them robust against arbitrary initializations. Specifically, we learn a displacement regressor, which predicts 3D displacement from any image voxel to the target organ boundary based on the local patch appearance. This regressor provides a nonlocal external force f...

IEEE Transactions on Medical Imaging, 2016

Computed tomography (CT) imaging is an essential tool in various clinical diagnoses and radiother... more Computed tomography (CT) imaging is an essential tool in various clinical diagnoses and radiotherapy treatment planning. Since CT image intensities are directly related to positron emission tomography (PET) attenuation coefficients, they are indispensable for attenuation correction (AC) of the PET images. However, due to the relatively high dose of radiation exposure in CT scan, it is advised to limit the acquisition of CT images. In addition, in the new PET and magnetic resonance (MR) imaging scanner, only MR images are available, which are unfortunately not directly applicable to AC. These issues greatly motivate the development of *

Physical Review E, 2001

Time-series methods for estimating Lyapunov exponents may give a positive exponent when they are ... more Time-series methods for estimating Lyapunov exponents may give a positive exponent when they are applied to the time series of strange nonchaotic systems. Strange nonchaotic systems are characterized by expanding and contracting regions in phase space that result in repeatedly expanding or contracting trajectories. Using time-series methods, the maximum time-series Lyapunov exponent is calculated as an average of the locally most expanding exponents that characterize the divergence of nearby trajectories following a reconstructed attractor over time. A positive exponent is reported by time-series methods for trajectories in an expanding region. While in a converging region, the most expanding dynamics are related to the quasiperiodic driving force. Statistically, a zero exponent related to the quasiperiodic force is obtained through time-series methods within converging regions. As a result, the calculated maximum Lyapunov exponent is positive.

Journal of applied clinical medical physics / American College of Medical Physics, Jan 6, 2014

Direct aperture optimization (DAO) has been used to produce high dosimetric quality intensity-mod... more Direct aperture optimization (DAO) has been used to produce high dosimetric quality intensity-modulated radiotherapy (IMRT) treatment plans with fast treatment delivery by directly modeling the multileaf collimator segment shapes and weights. To improve plan quality and reduce treatment time for our in-house treatment planning system, we implemented a new DAO approach without using a global objective function (GFO). An index concept is introduced as an inverse form of back-projection used in the CT multiplicative algebraic reconstruction technique (MART). The index, introduced for IMRT optimization in this work, is analogous to the multiplicand in MART. The index is defined as the ratio of the optima over the current. It is assigned to each voxel and beamlet to optimize the fluence map. The indices for beamlets and segments are used to optimize multileaf collimator (MLC) segment shapes and segment weights, respectively. Preliminary data show that without sacrificing dosimetric quali...

The Journal of Physiology, 2003

Preparation of hippocampal slices and perfusion All experiments were performed in the CA1 or CA3 ... more Preparation of hippocampal slices and perfusion All experiments were performed in the CA1 or CA3 regions of hippocampal brain slices prepared from Sprague-Dawley rats (175-250 g). Rats were anaesthetized with ethyl ether and decapitated. The experimental protocol was reviewed and approved by the Institution Animal Care and Use Committee. The brain was rapidly removed and one hemisphere glued to the stage of a Vibroslicer (Vibroslice, Campden Instruments Ltd, London, UK) Slicing was carried out in cold (3-4°C), oxygenated sucrose-based artificial cerebrospinal fluid (ACSF) consisting of (mM): sucrose 220, KCl 3, NaH 2 PO 4 1.25, MgSO 4 2, NaHCO 3 26, CaCl 2 2, dextrose 10. The resulting 350 mm thick slices were immediately transferred to a holding chamber with 'normal' ACSF consisting of (mM): NaCl 124, KCl 3.75, KH 2 PO 4 1.25, CaCl 2 2, MgSO 4 2, NaHCO 3 26, dextrose 10, held at room temperature and bubbled with 95 % O 2-5 % CO 2 .

The Journal of Physiology, 2001

High frequency deep brain stimulation (DBS) of certain brain structures can alleviate or complete... more High frequency deep brain stimulation (DBS) of certain brain structures can alleviate or completely suppress the symptoms of several neuronal disorders including Parkinson's disease (Benabid et al. 1994), epilepsy (Velasco et al. 1995, 1997) and intractable pain (Kumar et al. 1997). It has been

The Journal of Physiology, 2001

1. Spontaneous non-synaptic epileptiform activity was induced by bathing rat hippocampal slices i... more 1. Spontaneous non-synaptic epileptiform activity was induced by bathing rat hippocampal slices in low-Ca 2+ solution. Extracellular recordings from electrodes placed on both sides of a complete cut showed that non-synaptic activity was synchronized across the lesion. 2. Ion-selective electrode recordings showed that each event was accompanied by a transient increase in extracellular potassium that diffused across the lesion. The synchrony was destroyed when a thin film was inserted into the lesion site. 3. Local pressure ejection of KCl evoked an event that subsequently propagated across the lesion. 4. After a complete lesion was made, afterdischarges evoked on one half of a slice were not detected on the other half. 5. Voltage-sensitive dye imaging methods showed that epileptic activity propagated across the mechanical lesion without significant attenuation or additional delays. The velocity of the activity was consistent with that of the slow diffusion of a potassium wave. 6. Since field effects were significantly attenuated across the lesion and all gap junctions and cell processes across the lesion would be cut, these data show that extracellular diffusion, most probably potassium, is sufficient to synchronize populations of neurons and propagate slow frequency epileptiform activity.

Medical Physics, 2004

The endorectal coil is being increasingly used in magnetic resonance imaging (MRI) and MR spectro... more The endorectal coil is being increasingly used in magnetic resonance imaging (MRI) and MR spectroscopic imaging (MRSI) to obtain anatomic and metabolic images of the prostate with high signal-to-noise ratio (SNR). In practice, however, the use of endorectal probe inevitably distorts the prostate and other soft tissue organs, making the analysis and the use of the acquired image data in treatment planning difficult. The purpose of this work is to develop a deformable image registration algorithm to map the MRI/MRSI information obtained using an endorectal probe onto CT images and to verify the accuracy of the registration by phantom and patient studies. A mapping procedure involved using a thin plate spline (TPS) transformation was implemented to establish voxel-tovoxel correspondence between a reference image and a floating image with deformation. An elastic phantom with a number of implanted fiducial markers was designed for the validation of the quality of the registration. Radiographic images of the phantom were obtained before and after a series of intentionally introduced distortions. After mapping the distorted phantom to the original one, the displacements of the implanted markers were measured with respect to their ideal positions and the mean error was calculated. In patient studies, CT images of three prostate patients were acquired, followed by 3 Tesla ͑3 T͒ MR images with a rigid endorectal coil. Registration quality was estimated by the centroid position displacement and image coincidence index (CI). Phantom and patient studies show that TPS-based registration has achieved significantly higher accuracy than the previously reported method based on a rigid-body transformation and scaling. The technique should be useful to map the MR spectroscopic dataset acquired with ER probe onto the treatment planning CT dataset to guide radiotherapy planning.

Medical Physics, 2004

Radiobiological treatment planning depends not only on the accuracy of the models describing the ... more Radiobiological treatment planning depends not only on the accuracy of the models describing the dose-response relation of different tumors and normal tissues but also on the accuracy of tissue specific radiobiological parameters in these models. Whereas the general formalism remains the same, different sets of model parameters lead to different solutions and thus critically determine the final plan. Here we describe an inverse planning formalism with inclusion of model parameter uncertainties. This is made possible by using a statistical analysis-based frameset developed by our group. In this formalism, the uncertainties of model parameters, such as the parameter a that describes tissue-specific effect in the equivalent uniform dose (EUD) model, are expressed by probability density function and are included in the dose optimization process. We found that the final solution strongly depends on distribution functions of the model parameters. Considering that currently available models for computing biological effects of radiation are simplistic, and the clinical data used to derive the models are sparse and of questionable quality, the proposed technique provides us with an effective tool to minimize the effect caused by the uncertainties in a statistical sense. With the incorporation of the uncertainties, the technique has potential for us to maximally utilize the available radiobiology knowledge for better IMRT treatment.