title: sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping.
abstract: A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility.
authors: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA. ; Department of Radiology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.
authors: Rafael
authors: R
authors: Ceschin
authors: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA. ; Department of Radiology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.
authors: Ashok
authors: A
authors: Panigrahy
authors: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA. ; Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA. ; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
authors: Vanathi
authors: V
authors: Gopalakrishnan
keywords: brain tumors; diffusion MR; open source; parametric mapping