Recommendations for Processing Head CT Data

John Muschelli
2019 Frontiers in Neuroinformatics  
Many research applications of neuroimaging use magnetic resonance imaging (MRI). As such, recommendations for image analysis and standardized imaging pipelines exist. Clinical imaging, however, relies heavily on X-ray computed tomography (CT) scans for diagnosis and prognosis. Currently, there is only one image processing pipeline for head CT, which focuses mainly on head CT data with lesions. We present tools and a complete pipeline for processing CT data, focusing on open-source solutions,
more » ... t focus on head CT but are applicable to most CT analyses. We describe going from raw DICOM data to a spatially normalized brain within CT presenting a full example with code. Overall, we recommend anonymizing data with Clinical Trials Processor, converting DICOM data to NIfTI using dcm2niix, using BET for brain extraction, and registration using a publicly-available CT template for analysis.
doi:10.3389/fninf.2019.00061 pmid:31551745 pmcid:PMC6738271 fatcat:lnbjkk6qvnfahbn5qdd4akzleq