Custom developed image processing software.




At CIPAC, we have a team of software developers dedicated to building custom applications that best fit the processing pipelines of each research project. Emphasis is made on designing and implementing tools that allow the extraction of key image features, robust and reliable quantitative analysis and longitudinal (4D) and cross-sectional (3D) interactive image visualization and analysis. Below are a few of the software packages developed for specific programs, filling their analysis needs. For more information, please contact us.




Cerebra-WML is a stand-alone custom application developed to perform quantitative analysis of white matter lesions (WML), based on the assumption that these lesions present as white-matter hyper-intensities in T2-weighted magnetic resonance (MR) images. Cerebra-WML is designed to lead the user through a workflow to detect and quantify WMLs while allowing a rapid and consistent evaluation of the MR images.  

The image-processing pipeline in Cerebra-WML combines information from T1-weighted and fluid-attenuated inversion recovery (FLAIR) images. From the T1-weighted images, the skull is stripped, the cerebrospinal fluid is removed, and the brain tissue is then segmented into gray matter and white matter. The WML detection can be done through either an automated or a manual process. Finally, the application automatically generates a quantitative analysis report of the segmented WMLs in a PDF format. 




MR brain perfusion is a widely used imaging technique for quantitative analysis of cerebral microvascular hemodynamics. Cerebra-Perfusion is designed to create high-quality perfusion maps from T1-weighted dynamic contrast enhanced (DCE) or T2*-weighted Dynamic susceptibility contrast (DSC) MR images.

The major features of Cerebra-Perfusion include: a) Fast generation of cerebral blood flow (CBF), cerebral blood volume (CBV) and mean transit time (MTT) maps. b) Choice of image correction tools, such as ringing artifact correction, B1 inhomogeneity correction and image registration. c) Optimize analysis result by performing partial volume effect (PVE) correction. d) Selection of different deconvolution methods. e) Visual inspection of arterial input function (AIF), venous output function (VOF), tissue contrast concentration curve and residue function.




Susceptibility mapping is a useful tool for examining the presence of certain biomarkers related to cerebral microbleeds (iron), cognitive decline (iron), and Multiple Sclerosis (calcium). Susceptibility Weighted Imaging (SWI) has been traditionally used but it has its shortcomings. For instance, cerebral microbleed size estimated from SWI images is dependent upon several factors, including: Field strength, echo time, repetition time and flip angle. Quantitative Susceptibility Mapping (QSM) provides an improvement over SWI by limiting the impact of scanner and sequence parameter variation on the final outcome. 

The Cerebra-QSM package provides tools for generating susceptibility maps from raw DICOM images and extracting region of interest statistics.  The package includes a graphical user interface for processing and viewing data and a set of command line tools, which allow for batch processing data.





Cerebral microbleeds (CMB) are MRI-defined small, rounded hypointense lesions that are commonly observed on susceptibility-weighted images (SWI). Cerebra-CMB offers a semi-automatic tool for quantification of CMBs.

The microbleed segmentation is performed based on a seeded region-growing algorithm, which starts from a seed point picked by the user and identifies connected voxels based on the adjustable intensity threshold and the adjustable upper radius limit from the seed point. Segmented CMBs are labeled and the size of each CMB is automatically calculated. Generated mask images of CMBs can be saved in both DICOM and NIFTI format; also can be reopened and edited by the application. Finally Cerebra-CMB can automatically generate a quantitative analysis report and a .txt file of the detected CMBs that can be easily imported into EXCEL for further analysis.