Local extraction of extra-axial CSF from structural MRI

The quantification of cerebrospinal fluid (CSF), specifically the extra-axial cerebrospinal fluid (EA-CSF), which is the CSF in the subarachnoid space surrounding the cortical surface of the brain, has recently been shown to play an important role in the neuropathology of autism spectrum disorder (ASD) in infants. While prior work addressed measuring the global volume of EA-CSF, there was no available tool that quantifies the local, anatomical distribution of the EA-CSF. A localized EA-CSF quantification would provide more accurate and interpretable measurements. In our recent work, we proposed such a local EA-CSF extraction by using a pipeline that combines probabilistic brain tissue segmentation, cortical surface reconstruction and streamline-based local EA-CSF quantification. Yet, that system had several shortcomings, in particular a lack of available software tools, as well as a quantification where EA-CSF portions are counted multiple times. The purpose of this article is to present a novel, graphical user interface based, publicly available software tool, called LocalEACSF, which allows the user to easily run an adapted version of this pipeline and provide a set of straightforward quality control visualizations to assess the quality of the EA-CSF quantification. This tool further adds improvements and optimizations to the prior assessment. The LocalEACSF tool allows neuroimaging labs to compute a local extraction of extra-axial CSF in their neuroimaging studies in order to investigate its role in normal and atypical brain development, without the need for extensive technical knowledge.