Figure 1.
Flowchart of successive steps of MRI acquisition and processing.
The successive steps are scanning protocol optimizing, MRI acquisition, homogenous axial and coronal MR sequences registering, three-dimensional volume rendering reconstruction, fiducials identifying, and original coordinates of fiducials measuring.
Figure 2.
Homogenous axial and coronal MR sequences before and after registering in Amira software.
The intersection area of axial and coronal images is shown by dotted boxes. (A) Before registering, the spatial mismatches between axial and coronal MR sequences are quite obvious. (B) After registering, the axial MR sequence matches very closely with the coronal MR sequence.
Figure 3.
Flowchart of CVH head image acquisition and processing.
The successive steps are CVH-1, 2, 4, 5 head image acquisition, resampling, three-dimensional volume rendering reconstruction, fiducials and subthalamic nucleus (STN) identifying, original coordinates of fiducials measuring, and original ranges and gravity center coordinates of STN measuring.
Table 1.
General information of the four CVH cadaver specimens and the cross-sectional images parameters of the four CVH datasets.
Figure 4.
Cross lines identify the locations of all fiducials in the MRI (left) and CVH (right).
For AC, PC, OX and RN, the left-side images are the axial (above) and coronal (below) section of T2-weighted MRIs; the right-side images are axial (above) and coronal (below) section of CVH datasets. Two axial sections are shown for PU-A and PU-L, respectively. AC: Center of anterior commissure; PC: Center of posterior commissure; RN: Gravity center of red nucleus; OX: Anterior tip of optic chiasm center; PU-A: Anterior tip of putamen; PU-L: Lateral tip of putamen.
Figure 5.
The 2D morphology of STN and 3D surface rendering reconstruction models of STN.
The 2D morphology of STN and RN in MRI and CVH are shown in A and B; the 3D surface rendering reconstruction models of STN, based on MR sequences (C) and CVH successive cross-sectional images (D), are displayed. RN: Red nucleus; STN: Subthalamic nucleus.
Figure 6.
The original and new 3D coordinate system of head space.
In the original 3D coordinate system, the upper-left corner pixel (0) in the first image is defined as the origin of the three dimensional space of the whole images sequence and the right side(X), posterior(Y), and inferior (Z) to the origin were defined as positive. In the new 3D coordinate system, the midpoint of the anterior commissure and the posterior commissure (AC-PC) is defined as the origin (0′), and the right side(X’), anterior(Y’), and superior(Z’) to the origin are defined as positive.
Table 2.
Ranges/gravity center coordinates of subthalamic nucleus (STN) in CVH head datasets.
Table 3.
Correlations between red nucleus (RN) and fiducials in 30 MRI sequences.
Table 4.
Difference in localization of the gravity center of red nucleus (RN) using fiducials-based MRI-to-CVH registration.
Table 5.
Ranges and mean coordinate values of RNs and fiducials in 30 MRI sequences and the differences in mean coordinate values between MRI and CVH.