Chris Flask

Deformable and rigid registration of MRI and microPET images for photodynamic therapy of cancer in mice

We are investigating imaging techniques to study the tumor response to photodynamic therapy (PDT). Positron emission tomography (PET) can provide physiological and functional information. High-resolution magnetic resonance imaging (MRI) can provide anatomical and morphological changes. Image registration can combine MRI and PET images for improved tumor monitoring. In this study, we acquired high-resolution MRI and microPET 18F-fluorodeoxyglucose (FDG) images from C3H mice with RIF-1 tumors that were treated with Pc 4-based PDT. We developed two registration methods for this application. For registration of the whole mouse body, we used an automatic three-dimensional, normalized mutual information algorithm. For tumor registration, we developed a finite element model (FEM)-based deformable registration scheme. To assess the quality of whole body registration, we performed slice-by-slice review of both image volumes; manually segmented feature organs, such as the left and right kidneys and the bladder, in each slice; and computed the distance between corresponding centroids. Over 40 volume registration experiments were performed with MRI and microPET images. The distance between corresponding centroids of organs was 1.5 +/- 0.4 mm which is about 2 pixels of microPET images. The mean volume overlap ratios for tumors were 94.7% and 86.3% for the deformable and rigid registration methods, respectively. Registration of high-resolution MRI and microPET images combines anatomical and functional information of the tumors and provides a useful tool for evaluating photodynamic therapy.

Blood attenuation with SSFP-compatible saturation (BASS)

To investigate a rapid flow‐suppression method for improving the contrast‐to‐noise ratio (CNR) between the vessel wall and the lumen for cardiovascular imaging applications.

Radial Alternating TE Sequence for Faster Fat Suppression

This study describes a steady‐state sequence that uses a radial k‐space trajectory and alternating echo times (TEs) between even and odd k‐space views. The sequence generated a single data set that was used to reconstruct images with inherent fat suppression. This fat suppression results from the fat phase variation in alternate echoes giving rise to cancellation in the central portion of k‐space. This new fat‐suppression method provides inherent fat suppression in half the acquisition time relative to the radial two‐point Dixon method. The improvement in k‐space sampling efficiency is demonstrated in phantom and clinical images, and through measured point‐spread functions (PSFs). As a result, the radial alternating TE sequence offers improved temporal resolution over a radial version of the two‐point Dixon sequence by requiring fewer total projections to obtain the same effective resolution in water‐based tissues. Magn Reson Med 50:1095–1099, 2003.

Rapid dark-blood carotid vessel-wall imaging with random bipolar gradients in a radial SSFP acquisition

To investigate and evaluate a new rapid dark‐blood vessel‐wall imaging method using random bipolar gradients with a radial steady‐state free precession (SSFP) acquisition in carotid applications.

Fast Lipid And Water Levels by Extraction with Spatial Smoothing (FLAWLESS): Three-dimensional volume fat/water separation at 7 Tesla

To quickly and robustly separate fat/water components of 7T MR images in the presence of field inhomogeneity for the study of metabolic disorders in small animals.

MICE : A mouse imaging collaboration environment

With the ever-increasing complexity of science and engineering, many important research problems are being addressed by collaborative, multidisciplinary teams. We present a web-based collaborative environment for small animal imaging research, called the Mouse Imaging Collaboration Environment (MICE). MICE provides an effective and user-friendly tool for managing and sharing of the terabytes of high-resolution and high-dimension image data generated at small animal imaging core facilities. We describe the design of MICE and our experience in the implementation and deployment of a beta-version baseline-MICE. The baseline-MICE provides an integrated solution from image data acquisition to end-user access and long-term data storage at our UH/Case Small Animal Imaging Resource Center. As image data is acquired from scanners, it is pushed to the MICE server which automatically stores it in a directory structure according to its DICOM metadata. The directory structure reflects imaging modality, principle investigators, animal models, scanning dates and study details. Registered end-users access this imaging data through an authenticated web-interface. Thumbnail images are created by custom scripts running on the MICE server while data down-loading is achieved through standard web-browser ftp. MICE provides a security infrastructure that manages user roles, their access privileges such as read/write, and the right to modify the access privileges. Additional data security measures include a two server paradigm with the Web access server residing outside a network firewall to provide access through the Internet, and the imaging data server - a large RAID storage system supporting flexible backup policies - residing behind the protected firewall with a dedicated link to the Web access server. Direct network link to the RAID storage system outside the firewall other than this dedicated link is not permitted. Establishing the initial image directory structure and letting the project leader manage data access through a web-interface represent Phase I implementation. In Phase II, features for uploading image analysis scripts and results back to the MICE server will be implemented, as well as mechanisms facilitating asynchronous and synchronous discussion, annotation, and analysis. Most of MICE features are being implemented in the Plone5 object-oriented database environment which greatly shortens developmental time and effort by the reuse of a variety of Plones open-source modules for Content Management Systems.7, 8 The open-source modules are well suited as an implementation basis of MICE and provide data integration as a built-in primitive.