Joint Head and Neck Radiotherapy-MRI Development Cooperative, Travis Salzillo, M. Alex Dresner, Ashley Way, Kareem Wahid, Brigid McDonald, Sam Mulder, Mohamed Naser, Renjie He, Yao Ding, Alison Yoder, Sara Ahmed, Kelsey Corrigan, Gohar Manzar, Lauren Andring, Chelsea Pinnix, R. Jason Stafford, Abdallah S. Mohamed, John Christodouleas, Jihong Wang, Clifton David Fuller
PurposeTo improve segmentation accuracy in head and neck cancer (HNC) radiotherapy treatment planning for the 1.5T hybrid magnetic resonance imaging/linear accelerator (MR-Linac), three-dimensional (3D), T2-weighted, fat-suppressed magnetic resonance imaging sequences were developed and optimized.ApproachAfter initial testing, spectral attenuated inversion recovery (SPAIR) was chosen as the fat suppression technique. Five candidate SPAIR sequences and a nonsuppressed, T2-weighted sequence were acquired for five HNC patients using a 1.5T MR-Linac. MR physicists identified persistent artifacts in two of the SPAIR sequences, so the remaining three SPAIR sequences were further analyzed. The gross primary tumor volume, metastatic lymph nodes, parotid glands, and pterygoid muscles were delineated using five segmentors. A robust image quality analysis platform was developed to objectively score the SPAIR sequences on the basis of qualitative and quantitative metrics.ResultsSequences were analyzed for the signal-to-noise ratio and the contrast-to-noise ratio and compared with fat and muscle, conspicuity, pairwise distance metrics, and segmentor assessments. In this analysis, the nonsuppressed sequence was inferior to each of the SPAIR sequences for the primary tumor, lymph nodes, and parotid glands, but it was superior for the pterygoid muscles. The SPAIR sequence that received the highest combined score among the analysis categories was recommended to Unity MR-Linac users for HNC radiotherapy treatment planning.ConclusionsOur study led to two developments: an optimized, 3D, T2-weighted, fat-suppressed sequence that can be disseminated to Unity MR-Linac users and a robust image quality analysis pathway that can be used to objectively score SPAIR sequences and can be customized and generalized to any image quality optimization protocol. Improved segmentation accuracy with the proposed SPAIR sequence will potentially lead to improved treatment outcomes and reduced toxicity for patients by maximizing the target coverage and minimizing the radiation exposure of organs at risk.
MR diffusion tensor imaging (DTI) technique together with traditional T1 or T2 weighted MRI scans supplies rich information sources for brain cancer diagnoses. These images form large-scale, high-dimensional data sets. Due to the fact that significant correlations exist among these images, we assume low-dimensional geometry data structures (manifolds) are embedded in the high-dimensional space. Those manifolds might be hidden from radiologists because it is challenging for human experts to interpret high-dimensional data. Identification of the manifold is a critical step for successfully analyzing multimodal MR images.
We have developed various manifold learning algorithms (Tran et al. 2011; Tran et al. 2013) for medical image analysis. This paper presents a comparative study of an incremental manifold learning scheme (Tran. et al. 2013) versus the deep learning model (Hinton et al. 2006) in the application of brain tumor progression prediction. The incremental manifold learning is a variant of manifold learning algorithm to handle large-scale datasets in which a representative subset of original data is sampled first to construct a manifold skeleton and remaining data points are then inserted into the skeleton by following their local geometry. The incremental manifold learning algorithm aims at mitigating the computational burden associated with traditional manifold learning methods for large-scale datasets. Deep learning is a recently developed multilayer perceptron model that has achieved start-of-the-art performances in many applications. A recent technique named "Dropout" can further boost the deep model by preventing weight coadaptation to avoid over-fitting (Hinton et al. 2012).
We applied the two models on multiple MRI scans from four brain tumor patients to predict tumor progression and compared the performances of the two models in terms of average prediction accuracy, sensitivity, specificity and precision. The quantitative performance metrics were calculated as average over the four patients. Experimental results show that both the manifold learning and deep neural network models produced better results compared to using raw data and principle component analysis (PCA), and the deep learning model is a better method than manifold learning on this data set. The averaged sensitivity and specificity by deep learning are comparable with these by the manifold learning approach while its precision is considerably higher. This means that the predicted abnormal points by deep learning are more likely to correspond to the actual progression region.
At various stage of progression, most brain tumors are not homogenous. In this presentation, we retrospectively studied
the distribution of ADC values inside tumor volume during the course of tumor treatment and progression for a selective
group of patients who underwent an anti-VEGF trial. Complete MRI studies were obtained for this selected group of
patients including pre- and multiple follow-up, post-treatment imaging studies. In each MRI imaging study, multiple
scan series were obtained as a standard protocol which includes T1, T2, T1-post contrast, FLAIR and DTI derived
images (ADC, FA etc.) for each visit. All scan series (T1, T2, FLAIR, post-contrast T1) were registered to the
corresponding DTI scan at patient's first visit. Conventionally, hyper-intensity regions on T1-post contrast images are
believed to represent the core tumor region while regions highlighted by FLAIR may overestimate tumor size. Thus we
annotated tumor regions on the T1-post contrast scans and ADC intensity values for pixels were extracted inside tumor
regions as defined on T1-post scans. We fit a mixture Gaussian (MG) model for the extracted pixels using the
Expectation-Maximization (EM) algorithm, which produced a set of parameters (mean, various and mixture coefficients)
for the MG model. This procedure was performed for each visits resulting in a series of GM parameters. We studied the
parameters fitted for ADC and see if they can be used as indicators for tumor progression. Additionally, we studied the
ADC characteristics in the peri-tumoral region as identified by hyper-intensity on FLAIR scans. The results show that
ADC histogram analysis of the tumor region supports the two compartment model that suggests the low ADC value subregion
corresponding to densely packed cancer cell while the higher ADC value region corresponding to a mixture of
viable and necrotic cells with superimposed edema. Careful studies of the composition and relative volume of the two
compartments in tumor region may provide some insights in the early assessment of tumor response to therapy for
recurrence brain cancer patients.
In a recent study [1], we investigated the feasibility of predicting brain tumor progression based on multiple MRI series
and we tested our methods on seven patients' MRI images scanned at three consecutive visits A, B and C. Experimental
results showed that it is feasible to predict tumor progression from visit A to visit C using a model trained by the
information from visit A to visit B. However, the trained model failed when we tried to predict tumor progression from
visit B to visit C, though it is clinically more important. Upon a closer look at the MRI scans revealed that histograms of
MRI scans such as T1, T2, FLAIR etc taken at different times have slight shifts or different shapes. This is because those
MRI scans are qualitative instead of quantitative so MRI scans taken at different times or by different scanners might
have slightly different scales or have different homogeneities in the scanning region. In this paper, we proposed a
method to overcome this difficulty. The overall goal of this study is to assess brain tumor progression by exploring seven
patients' complete MRI records scanned during their visits in the past two years. There are ten MRI series in each visit,
including FLAIR, T1-weighted, post-contrast T1-weighted, T2-weighted and five DTI derived MRI volumes: ADC, FA,
Max, Min and Middle Eigen Values. After registering all series to the corresponding DTI scan at the first visit, we
applied a histogram matching algorithm to non-DTI MRI scans to match their histograms to those of the corresponding
MRI scans at the first visit. DTI derived series are quantitative and do not require the histogram matching procedure. A
machine learning algorithm was then trained using the data containing information from visit A to visit B, and the
trained model was used to predict tumor progression from visit B to visit C. An average of 72% pixel-wise accuracy was
achieved for tumor progression prediction from visit B to visit C.
A machine learning technique is presented for assessing brain tumor progression by exploring six patients' complete
MRI records scanned during their visits in the past two years. There are ten MRI series, including diffusion tensor image
(DTI), for each visit. After registering all series to the corresponding DTI scan at the first visit, annotated normal and
tumor regions were overlaid. Intensity value of each pixel inside the annotated regions were then extracted across all of
the ten MRI series to compose a 10 dimensional vector. Each feature vector falls into one of three categories:normal,
tumor, and normal but progressed to tumor at a later time. In this preliminary study, we focused on the trend of brain
tumor progression during three consecutive visits, i.e., visit A, B, and C. A machine learning algorithm was trained using
the data containing information from visit A to visit B, and the trained model was used to predict tumor progression from
visit A to visit C. Preliminary results showed that prediction for brain tumor progression is feasible. An average of
80.9% pixel-wise accuracy was achieved for tumor progression prediction at visit C.
Purpose: Diffusion tensor imaging (DTI) is an inherently quantitative imaging technique that measures the
diffusivities of water molecules in tissue. However, the accuracy of DTI measurements depends on many
factors such S/N ratio and magnet field strength. Therefore, before quantitative assessment of tumor
progression based on DTI metric changes can be made with confidence, one have to assess the accuracy or
variance in the DTI metrics. This is especially important for multi-institutional clinical trials or for large
institutions where patients may be imaged on multiple MR scanners at multiple times in follow up studies.
In this presentation, we studied the feasibility of using CSF as an internal QC marker for data acquisition
and processing qualities. Method: ADC and FA of CSF for brain tumor patients' DTI studies (total of 85
scans over three years) were analyzed. In addition, a phantom was used to check the inherent variations of
the MR systems. Results: The results show that the coefficient of variations for ADC and FA are 8.4% and
13.2% in CSF among all patients. For all DTI scans done on 1.5 T scanners, they are 7.4% and 9.1%, while
for 3T they are 9.8% and 18% respectively. Conclusion: CSF can be used as an internal QC measure of the
DTI acquisition accuracy and consistency among longitude studies on patients, making it a potentially
useful in multi-institutional trials.
An interactive, easy-to-use computer program has been developed to assess the quality of softcopy display by measuring the contrast sensitivity, spatial resolution and spatial uniformity at different backgrounds and object types. The program features random variation of the test object location, which minimizes the guessing error often associated with psychophysical measurements. It operates on a Microsoft Window/NT platform and is intended for routine quality assurance (QA) as well as for acceptance testing of PACS. The QA data obtained with this program can be plotted chronologically and centrally managed so as to detect trends in monitor deterioration. The principal motivation for developing this program was to provide an indirect yet sensitive and accurate measure of monitor characteristics with a minimum of specialized equipment.
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