Publications

2010
Ali Gholipour, Judy A Estroff, and Simon K Warfield. 2010. “Robust super-resolution volume reconstruction from slice acquisitions: application to fetal brain MRI.” IEEE Trans Med Imaging, 29, 10, Pp. 1739-58.Abstract
Fast magnetic resonance imaging slice acquisition techniques such as single shot fast spin echo are routinely used in the presence of uncontrollable motion. These techniques are widely used for fetal magnetic resonance imaging (MRI) and MRI of moving subjects and organs. Although high-quality slices are frequently acquired by these techniques, inter-slice motion leads to severe motion artifacts that are apparent in out-of-plane views. Slice sequential acquisitions do not enable 3-D volume representation. In this study, we have developed a novel technique based on a slice acquisition model, which enables the reconstruction of a volumetric image from multiple-scan slice acquisitions. The super-resolution volume reconstruction is formulated as an inverse problem of finding the underlying structure generating the acquired slices. We have developed a robust M-estimation solution which minimizes a robust error norm function between the model-generated slices and the acquired slices. The accuracy and robustness of this novel technique has been quantitatively assessed through simulations with digital brain phantom images as well as high-resolution newborn images. We also report here successful application of our new technique for the reconstruction of volumetric fetal brain MRI from clinically acquired data.
2008
Ali Gholipour, Nasser Kehtarnavaz, Kaundinya Gopinath, Richard Briggs, and Issa Panahi. 2008. “Average field map image template for Echo-Planar image analysis.” Conf Proc IEEE Eng Med Biol Soc, 2008, Pp. 94-7.Abstract
Magnetic resonance field map images are normally used in characterizing the magnetic field inhomogeneity for distortion correction in Echo-Planar Imaging (EPI) and accurate localization in functional MRI (fMRI). In this paper, the computation and applications of an average field map image template is investigated based on real field maps. The introduced methodology and the obtained field map image templates may be used in EPI and fMRI image analysis, distortion correction, registration, and functional localization when high-resolution field map images are not available for individual datasets. The introduced methodology involves three stages of pre-processing, registration, and spatial normalization. The analysis and results presented in this paper show the impact and usefulness of the investigated methodology in several applications.
On Tsang, Ali Gholipour, Nasser Kehtarnavaz, Kaundinya Gopinath, Richard Briggs, and Issa Panahi. 2008. “Comparison of tissue segmentation algorithms in neuroimage analysis software tools.” Conf Proc IEEE Eng Med Biol Soc, 2008, Pp. 3924-8.Abstract
Accurate segmentation of different brain tissues is of much importance in magnetic resonance imaging. This paper presents a comparison of the existing segmentation algorithms that are deployed in the neuroimaging community as part of two widely used software packages. The results obtained in this comparison can be used to select the appropriate segmentation algorithm for the neuroimaging application of interest. In addition to the entire brain area, a comparison is carried out for the subcortical region of the brain in terms of its gray matter composition.
Ali Gholipour, Nasser Kehtarnavaz, Richard W Briggs, Kaundinya S Gopinath, Wendy Ringe, Anthony Whittemore, Sergey Cheshkov, and Khamid Bakhadirov. 2008. “Validation of non-rigid registration between functional and anatomical magnetic resonance brain images.” IEEE Trans Biomed Eng, 55, 2 Pt 1, Pp. 563-71.Abstract
This paper presents a set of validation procedures for nonrigid registration of functional EPI to anatomical MRI brain images. Although various registration techniques have been developed and validated for high-resolution anatomical MRI images, due to a lack of quantitative and qualitative validation procedures, the use of nonrigid registration between functional EPI and anatomical MRI images has not yet been deployed in neuroimaging studies. In this paper, the performance of a robust formulation of a nonrigid registration technique is evaluated in a quantitative manner based on simulated data and is further evaluated in a quantitative and qualitative manner based on in vivo data as compared to the commonly used rigid and affine registration techniques in the neuroimaging software packages. The nonrigid registration technique is formulated as a second-order constrained optimization problem using a free-form deformation model and mutual information similarity measure. Bound constraints, resolution level and cross-validation issues have been discussed to show the degree of accuracy and effectiveness of the nonrigid registration technique. The analyses performed reveal that the nonrigid approach provides a more accurate registration, in particular when the functional regions of interest lie in regions distorted by susceptibility artifacts.
2007
Ali Gholipour, Nasser Kehtarnavaz, Richard Briggs, Michael Devous, and Kaundinya Gopinath. 2007. “Brain functional localization: a survey of image registration techniques.” IEEE Trans Med Imaging, 26, 4, Pp. 427-51.Abstract
Functional localization is a concept which involves the application of a sequence of geometrical and statistical image processing operations in order to define the location of brain activity or to produce functional/parametric maps with respect to the brain structure or anatomy. Considering that functional brain images do not normally convey detailed structural information and, thus, do not present an anatomically specific localization of functional activity, various image registration techniques are introduced in the literature for the purpose of mapping functional activity into an anatomical image or a brain atlas. The problems addressed by these techniques differ depending on the application and the type of analysis, i.e., single-subject versus group analysis. Functional to anatomical brain image registration is the core part of functional localization in most applications and is accompanied by intersubject and subject-to-atlas registration for group analysis studies. Cortical surface registration and automatic brain labeling are some of the other tools towards establishing a fully automatic functional localization procedure. While several previous survey papers have reviewed and classified general-purpose medical image registration techniques, this paper provides an overview of brain functional localization along with a survey and classification of the image registration techniques related to this problem.

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