M. Fukushima, O. Yamashita, T. Knösche, Masa-aki Sato
{"title":"MEG source reconstruction constrained by diffusion MRI based whole brain dynamical model","authors":"M. Fukushima, O. Yamashita, T. Knösche, Masa-aki Sato","doi":"10.1109/ISBI.2013.6556646","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556646","url":null,"abstract":"Previous studies have shown that MEG source reconstruction is improved by temporal constraints from local current source dynamics. Extending these constraints, we have developed a source reconstruction method that is spatiotemporally constrained by a whole brain dynamical model. The source dynamics are represented by a multivariate autoregressive (MAR) model whose matrix entries are constrained by connectivity estimates based on diffusion MRI. The MAR model parameters are jointly estimated with the source amplitude to infer source-space effective connectivity. Through simulation at low signal-to-noise ratio, we confirmed that the proposed method suppresses spurious sources and, unlike the non-dynamical sparse Bayesian method, can recover a low amplitude source. Furthermore, effective connectivity estimated by the proposed joint approach was more accurate than that obtained from the two stage approach, in which the current sources are first reconstructed by the non-dynamical method, followed by MAR model fitting to the resulting sources.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116076798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Efficient GRAPPA reconstruction using random projection","authors":"Jingyuan Lyu, Yuchou Chang, L. Ying","doi":"10.1109/ISBI.2013.6556571","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556571","url":null,"abstract":"As a data-driven technique, GRAPPA has been widely used for parallel MRI reconstruction. In GRAPPA, a large amount of calibration data is desirable for accurate calibration and thus estimation. However, the computational time increases with the large number of equations to be solved, which is especially serious in 3-D reconstruction. To address this issue, a number of approaches have been developed to compress the large number of physical channels to fewer virtual channels. In this paper, we tackle the complexity problem from a different prospective. We propose to use random projections to reduce the dimension of the problem in the calibration step. Experimental results show that randomly projecting the data onto a lower-dimensional subspace yields results comparable to those of traditional GRAPPA, but is computationally significantly less expensive.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117042967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Mahapatra, A. Vezhnevets, P. Schüffler, J. Tielbeek, F. Vos, J. Buhmann
{"title":"Weakly supervised semantic segmentation of Crohn's disease tissues from abdominal MRI","authors":"D. Mahapatra, A. Vezhnevets, P. Schüffler, J. Tielbeek, F. Vos, J. Buhmann","doi":"10.1109/ISBI.2013.6556607","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556607","url":null,"abstract":"We address the problem of weakly supervised segmentation (WSS) of medical images which is more challenging and has potentially greater applications in the medical imaging community. Training images are labeled only by the classes they contain, and not by the pixel labels. We make use of the Multi Image Model (MIM) for weakly supervised segmentation which exploits superpixel features and assigns labels to every pixel. MIM connects superpixels from all training images in a data driven fashion. Test images are integrated into the MIM for predicting their labels, thus making full use of the training samples. Experimental results on abdominal magnetic resonance (MR) images of patients with Crohn's disease show that WSS performs close to fully supervised methods and given sufficient samples can perform on par with fully supervised methods.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"105 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116348702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Siyamalan Manivannan, Ruixuan Wang, E. Trucco, A. Hood
{"title":"Automatic normal-abnormal video frame classification for colonoscopy","authors":"Siyamalan Manivannan, Ruixuan Wang, E. Trucco, A. Hood","doi":"10.1109/ISBI.2013.6556557","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556557","url":null,"abstract":"Two novel schemes are proposed to represent intermediate-scale features for normal-abnormal classification of colonoscopy images. The first scheme works on the full-resolution image, the second on a multi-scale pyramid space. Both schemes support any feature descriptor; here we use multi-resolution local binary patterns which outperformed other features reported in the literature in our comparative experiments. We also compared experimentally two types of features not previously used in colonoscopy image classification, bag of features and sparse coding, each with and without spatial pyramid matching (SPM). We find that SPM improves performance, therefore supporting the importance of intermediate-scale features as in the proposed schemes for classification. Within normal-abnormal frame classification, we show that our representational schemes outperforms other features reported in the literature in leave-N-out tests with a database of 2100 colonoscopy images.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"119 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116614294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A new similarity measure for deformable image registration based on intensity matching","authors":"Yongning Lu, Ying Sun, Rui Liao, S. Ong","doi":"10.1109/ISBI.2013.6556455","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556455","url":null,"abstract":"Deformable image registration plays an important role in medical image analysis. Multi-modal image registration remains a challenging research topic due to the complexity of modeling the relationship between two images. Mutual information (MI) is widely used in the field of multi-modal image registration, however, it suffers from problems such as interpolation artifacts and/or statistical insufficiency. The problem is worsened when bias field and noise are present. There have been attempts to map images to a common modality before image registration process, but the error introduced by the mapping may be detrimental to the registration. In this paper, instead of explicitly mapping the images to a common modality, we introduce a new similarity measure based on intensity matching information, which can be learnt from the existing registered training pairs or images pairs registered by performing MI based registration. Experiments on simulated brain MRI and real myocardial perfusion MR image sequences indicate that our proposed similarity measure outperforms the conventional MI and Kroon and Slump's method [1].","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115454810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sparse component selection with application to MEG source localization","authors":"Martin Luessi, M. Hämäläinen, V. Solo","doi":"10.1109/ISBI.2013.6556535","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556535","url":null,"abstract":"In several applications, the observed signal can be modeled as the projection of a sparse signal with constant support over time plus additive noise. In this paper, we develop a sparse component selection method which models the latent signal to be sparse and to be composed of a number unknown basis signals. The estimation is based on the maximization of the penalized log-likelihood, for which we develop an efficient minorization-maximization (MM) algorithm. We use simulations with synthetic data and real data from a magnetoencephalography (MEG) experiment to demonstrate the performance of the method.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121381774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Kaeppler, Wen Wu, Terrence Chen, M. Koch, A. Kiraly, Norbert Strobel, J. Hornegger
{"title":"Semi-automatic catheter model generation using biplane x-ray images","authors":"S. Kaeppler, Wen Wu, Terrence Chen, M. Koch, A. Kiraly, Norbert Strobel, J. Hornegger","doi":"10.1109/ISBI.2013.6556799","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556799","url":null,"abstract":"Recently, techniques for the automatic detection or tracking of surgical instruments in X-ray guided computer-assisted interventions have emerged. The purposes of these methods are to facilitate inter-modality registration, motion compensation, enhanced visualization or automatic landmark generation in augmented-reality applications. Most techniques incorporate a model of the device as prior information to evaluate results obtained from a low-level detector. In this paper, we present novel approaches which are able to generate both 2-D and 3-D models of circular and linear catheters from biplane X-ray images with only minimal user input. We apply these methods in the context of Electrophysiology to generate models of ablation and mapping catheters. An evaluation on clinical data sets yielded promising results.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"384 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123358043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A non-parametric method based on NBNN for automatic detection of liver lesion in CT images","authors":"Wei Yang, Qianjin Feng, Meiyan Huang, Zhentai Lu, Wufan Chen","doi":"10.1109/ISBI.2013.6556488","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556488","url":null,"abstract":"An automatic liver lesion detection method for CT images is presented, which need not learn the model parameters and segment liver region. The lesion detection problem is formulated as finding a region with maximal score. The developed method employs an over-segmentation algorithm to generate the superpixels (small regions) and adapts the Naive Bayes Nearest Neighbor (NBNN) classifier to score the superpixels. Then, the connected superpixels with positive scores are aggregated as the detected regions. The performance of the method is evaluated on a data set consisting of 442 CT slices of 129 patients acquired in portal venous phase of contrast enhancement. The pixel-wise accuracy for classification and recall for detection can achieve 93% and 62%, respectively. The method can work well for hyperdense, hypodense, and heterogeneous liver lesions.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123770924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Drift correction for fluorescence live cell imaging through correlated motion identification","authors":"Minhua Qiu, Ge Yang","doi":"10.1109/ISBI.2013.6556509","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556509","url":null,"abstract":"Fluorescence live cell imaging is an important experimental technique for visualizing and recording dynamic cellular processes under physiological conditions. However, a problem commonly encountered during imaging is sample drift. Without correction, such drift will cause bias or even error in subsequent image analysis of intracellular movement. Traditional area-based and feature-based image registration techniques often fail to correct such drift because, in addition to whole cell drift, intracellular features of interest also undergo separate and complex motion. To address this problem, we developed an image registration technique based on identifying clusters of features that undergo highly correlated motion. Sample drift is determined from movement of these features and corrected. Experiments confirmed that this technique can effectively remove translational drift with sub-pixel accuracy. For drift that also involves rotation, an extension of the technique is developed to determine rotation angles both within and out of the image plane so that rotational drift can be corrected. The technique is general and can be used for drift correction in a broad range of biological studies.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125250368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Group sparse dictionary learning and inference for resting-state fMRI analysis of Alzheimer'S disease","authors":"Jeonghyeon Lee, Y. Jeong, J. C. Ye","doi":"10.1109/ISBI.2013.6556531","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556531","url":null,"abstract":"A novel group analysis tool for data-driven resting state fMRI analysis using group sparse dictionary learning and mixed model is presented along with the promising indications of Alzheimer's disease progression. Instead of using independency assumption as in popular ICA approaches, the proposed approach is based on the sparse graph assumption such that a temporal dynamics at each voxel position is a sparse combination of global brain dynamics. In estimating the unknown global dynamics and local network structures, we perform sparse dictionary learning for the concatenated temporal data across the subjects by constraining that the network structures within a group are similar. Under the homoscedasticity variance assumption across subjects and groups, we show that the mixed model group inference can be easily performed using second level GLM with summary statistics. Using extensive resting fMRI data set obtained from normal, Mild Cognitive Impairment (MCI), Clinical Dementia Rating scale (CDR) 0.5, CDR 1.0, and CDR 2.0 of Alzheimer's disease patients groups, we demonstrated that the changes of default mode network extracted by the proposed method is more closely correlated with the progression of Alzheimer's disease.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122392854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}