Manual Segmentation of the Human Choroid Plexus Using Brain MRI

Summary

Despite the crucial role of the choroid plexus in the brain, neuroimaging studies of this structure are scarce due to the lack of reliable automated segmentation tools. The present protocol aims to ensure gold-standard manual segmentation of the choroid plexus that can inform future neuroimaging studies.

Abstract

The choroid plexus has been implicated in neurodevelopment and a range of brain disorders. Evidence demonstrates that the choroid plexus is critical for brain maturation, immune/ inflammatory regulation, and behavioral/cognitive functioning. However, current automated neuroimaging segmentation tools are poor at accurately and reliably segmenting the lateral ventricle choroid plexus. Furthermore, there is no existing tool that segments the choroid plexus located in the third and fourth ventricles of the brain. Thus, a protocol delineating how to segment the choroid plexus in the lateral, third, and fourth ventricle is needed to increase the reliability and replicability of studies examining the choroid plexus in neurodevelopmental and brain disorders. This protocol provides detailed steps to create separately labeled files in 3D Slicer for the choroid plexus based on DICOM or NIFTI images. The choroid plexus will be manually segmented using the axial, sagittal, and coronal planes of T1w images making sure to exclude voxels from gray or white matter structures bordering the ventricles. Windowing will be adjusted to assist in the localization of the choroid plexus and its anatomical boundaries. Methods for assessing accuracy and reliability will be demonstrated as part of this protocol. Gold standard segmentation of the choroid plexus using manual delineations can be used to develop better and more reliable automated segmentation tools that can be openly shared to elucidate changes in the choroid plexus across the lifespan and within various brain disorders.

Introduction

Choroid plexus function
The choroid plexus is a highly vascularized structure in the brain consisting of fenestrated capillaries and a monolayer of choroid plexus epithelial cells¹. The choroid plexus projects into the lateral, third, and fourth cerebral ventricles and produces cerebrospinal fluid (CSF), which plays an important role in neural patterning² and brain physiology^3,4. The choroid plexus secretes neurovascular substances, encompasses a stem-cell like repository, and acts as a physical barrier to impede the entrance of toxic metab....

Protocol

The present protocol was approved by the Institutional Review Board at Beth Israel Deaconess Medical Center. A healthy subject with a brain MRI scan that was free of artifacts or movement was used for this protocol demonstration, and written informed consent was obtained. A 3.0 T MRI scanner with a 32-channel head coil (see Table of Materials) was used to acquire 3D-T1 images with a 1 mm x 1 mm x 1.2 mm resolution. The MP-RAGE ASSET sequence with a 256 x 256 field of view, TR/TE/TI=7.38/3.06/400 ms, and .......

Discussion

Critical steps of the protocol
Three critical steps require special attention when implementing this protocol. First, checking the quality and contrast of MR images is key to ensuring accurate segmentation. If the quality of the image is too poor, or the contrast is too low or too high, it may lead to the inaccurate delineation of the choroid plexus. The contrast for the image can be adjusted by viewing the image's grayscale value or by calibrating the values to enhance the contrast between the.......

Materials

Name	Company	Catalog Number	Comments
3D Slicer	3D Slicer	https://www.slicer.org/	A free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures.
FreeSurfer	FreeSurfer	https://surfer.nmr.mgh.harvard.edu/	An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images
ITK-SNAP	ITK-SNAP	http://www.itksnap.org/pmwiki/pmwiki.php	A free, open-source, multi-platform software application used to segment structures in 3D and 4D biomedical images.
Monai Package	Monai Consortium	https://docs.monai.io/en/stable/metrics.html	Use for Dice Coefficient and DeepMind average Surface Distance.
MRI scanner	GE	Discovery MR750
Psych Package	R-Project	https://cran.r-project.org/web/packages/psych/index.html	A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology.
R Software	R-Project	https://www.r-project.org/	R is a free software environment for statistical computing and graphics.
RStudio	Posit	https://posit.co/	An RStudio integrated development environment (IDE) is a set of tools built to help you be more productive with R and Python.
Windows or Apple OS Desktop or Laptop	Any company	n/a	Needed for running the software used in this protocol.