Brain Infarct Segmentation and Registration on MRI or CT for Lesion-symptom Mapping

Summary

Provided here is a practical tutorial for an open-access, standardized image processing pipeline for the purpose of lesion-symptom mapping. A step-by-step walkthrough is provided for each processing step, from manual infarct segmentation on CT/MRI to subsequent registration to standard space, along with practical recommendations and illustrations with exemplary cases.

Abstract

In lesion-symptom mapping (LSM), brain function is inferred by relating the location of acquired brain lesions to behavioral or cognitive symptoms in a group of patients. With recent advances in brain imaging and image processing, LSM has become a popular tool in cognitive neuroscience. LSM can provide fundamental insights into the functional architecture of the human brain for a variety of cognitive and non-cognitive functions. A crucial step in performing LSM studies is the segmentation of lesions on brains scans of a large group of patients and registration of each scan to a common stereotaxic space (also called standard space or a standardized brain template). Described here is an open-access, standardized method for infarct segmentation and registration for the purpose of LSM, as well as a detailed and hands-on walkthrough based on exemplary cases. A comprehensive tutorial for the manual segmentation of brain infarcts on CT scans and DWI or FLAIR MRI sequences is provided, including criteria for infarct identification and pitfalls for different scan types. The registration software provides multiple registration schemes that can be used for processing of CT and MRI data with heterogeneous acquisition parameters. A tutorial on using this registration software and performing visual quality checks and manual corrections (which are needed in some cases) is provided. This approach provides researchers with a framework for the entire process of brain image processing required to perform an LSM study, from gathering of the data to final quality checks of the results.

Introduction

Lesion-symptom mapping (LSM), also called lesion-behavior mapping, is an important tool for studying the functional architecture of the human brain¹. In lesion studies, brain function is inferred and localized by studying patients with acquired brain lesions. The first case studies linking neurological symptoms to specific brain locations performed in the nineteenth century already provided fundamental insights into the anatomical correlates of language and several other cognitive processes². Yet, the neuroanatomical correlates of many aspects of cognition and other brain functions remained elusive. In the past decades, ....

Protocol

This protocol follows the guidelines of our institutions human research ethics committee.

1. Collection of Scans and Clinical Data

1. Collect brain CT or MRI scans of patients with ischemic stroke. Most scanners save the scans as DICOM (Digital Imaging and Communications in Medicine) files that can be copied to a hard disk or server.
   NOTE: Scans from every scanner type, scan protocol, and MRI field strength can be used, as long as 1) the time window requirements for the used scan type are met (see Table 1) and 2) there are no artifacts that hamper accurate infarct delineatio....

Results

Exemplar cases of brain infarct segmentations on CT (Figure 3), DWI (Figure 5), and FLAIR (Figure 6) images, and subsequent registration to the MNI-152 template are provided here. The registration results shown in Figure 3B and Figure 5C were not entirely successful, as there was misalignment near the frontal horn of the ventricle. The regis.......

Discussion

LSM is a powerful tool to study the functional architecture of the human brain. A crucial step in any lesion-symptom mapping study is the preprocessing of imaging data, segmentation of the lesion and registration to a brain template. Here, we report a standardized pipeline for lesion segmentation and registration for the purpose of lesion-symptom mapping. This method can be performed with freely available image processing tools, can be used to process both CT and structural MRI scans, and covers the entire process of pre.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
dcm2niix	N/A	N/A	free download https://github.com/rordenlab/dcm2niix
ITK-SNAP	N/A	N/A	free download www.itksnap.org
MATLAB	MathWorks	N/A	Version 2015a or higher
MRIcron	N/A	N/A	free download https://www.nitrc.org/projects/mricron
RegLSM	N/A	N/A	free download www.metavcimap.org/support/software-tools
SPM12b	N/A	N/A	free download https://www.fil.ion.ucl.ac.uk/spm/