The Stereology and 3D Volume Analyses in Nervous Tissue - Animal Models of Acute Neurological Injuries: Injury and Mechanistic Assessments - page 40

7. 3D Volume
Analysis

Now let us shift our focus from quantifying an object of interest or
signal in the nervous system to analyzing the volume or shape
features of brain regions. Thanks to the advances in imaging
techniques, such as magnetic resonance imaging (MRI) and com-
puted tomography (CT), 3D image stacks of the brain or other
anatomical structures can be routinely collected. Depending on
the goal of the practice, various types of processing pipelines are
available for analyzing these images. This section discusses three
widely used approaches:

1. Volumetric analysis: This method is based on measuring the
volume of a structure of interest. For example, an MRI study
using this method quantifi ed the hippocampal volume in the
brain image and identifi ed bilateral volumetric reduction of
the hippocampus in schizophrenia ( 12 ).
2. Voxel-based morphometry (VBM): VBM is a neuroimaging
analysis method that allows for the investigation of focal differ-
ences in brain anatomy. VBM registers every brain to a template
to make them comparable across individuals. After that, the
image volume is compared across brains at every voxel (i.e.,
every volume element in the image). Figure 5 shows a sample
study using VBM, where signifi cant regions of gray matter loss
in Alzheimer's disease were identifi ed in the brain ( 13 ).
3. Surface-based morphometry (SBM): SBM is similar to VBM
but performs a comparison on a surface instead of in a 3D
image space. SBM registers every surface along with its measure-
ments (e.g., thickness, curvature, etc.) to a template surface,
and then a comparison of these surface measurements is
performed across individuals at every location on the template
surface. Figure 6 shows a sample study using SBM, where
patterns of gray matter loss in Alzheimer's disease were charac-
terized on the cortical surface ( 14 ).

Segmentation and registration are two key operations used in
these methods. Segmentation refers to the operation of partition-
ing a digital image into two or more regions, and registration is the
process of transforming different image data into one coordinate
system. A list of typical software tools for image computing is
shown in Table 3 . The rest of this section discusses how to use
these tools for analyzing 3D volumetric images.

7.1. Segmentation and
Volumetric Analysis

To perform quantitative analysis, a region of interest (ROI) needs
to be extracted from 3D image sets, and this is done by image seg-
mentation. Segmentation involves labeling an image so that the labels
correspond to real world objects. Extensive work has been done on