Routine clinical imaging studies were used without any special patient positioning during imaging. All the machine parameters and scaling information (e.g. pixel size, field o f view, zoom factor) were obtained from each imaging system itself. These parameters were examined, initially, using a well-defined phantom with known size information. Each imaging system has a specific and known coordinate system which defines the image coordinates based on the patient
directional position inside the imaging system. A typical imaging coordinate system is shown in figure 3.8.
Different images can be made available from any imaging modality by applying different imaging parameters (e.g. different slice thicknesses, or different pulse sequences in M/?7). The following are two main criteria based on which an imaging modality and in turn its images are chosen in the fitting process.
viewing sc reen
( 2 0 slices) Viewing direction
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Transform ation
Potient coordinote system
Figure 3.8- A typical imaging coordinate system showing the transformation from patient to image coordinate system. This image coordinate system is used throughout thesis.
1) The 3-D surface model (objective data) is usually taken from the scan having higher resolution, smaller slice thickness, and the one which covers a larger volume of the patient. On the other hand, the transforming points are sampled, only at slice level, from the contours of the image which have coarser resolution and worse slice thickness.
2) Both the external surface of scalp and brain surface might be visible and thus formed by different segmentation techniques. The external surface of the scalp (skin surface) is the most commonly used object for surface fitting process, and is readily outlined on most images such as CT and MR. Using this external scalp surface is also well suited for automating edge detection methods and thus requires little user interface (see section 4.3.3). In general, an effort is also made to employ skin surfaces instead of brain surfaces where there is a substantial brain surface
deformity (such as a hole) in one o f the images.
The technique was used to register the MR with MR, PET with MR, SPECT (HMPAO)
with MR, and CT with MR brain images o f a number o f patients. Skin surfaces were used for registration o f MR with MR, MR with PET and MR with CT images. Brain surfaces were usually used for the registration o f MR with HMPAO brain images. The characteristics o f the imaging systems and the routine imaging parameters used in the current project are as follow.
MR scans were performed with a 1.5 Tesla Siemens system operated by a VAX host computer. Both 3-D FLASH (Fast Low Angle Shot) images and 2-D slices were used and dealt with separately. Different imaging sequences and parameters were used, creating T2-weighted, T1-weighted or/and STIR (Short Tau Inversion Recovery) images o f a pixel size typically in the order o f 0.70-1 mm (300 mm field o f view, 256*256 matrix size and zoom factor o f 1.2-1.6). Acquisition was typically done with TR=4.0 sec and TE=90 msec for T2, and TR=600 msec and TE=15 msec for T1-weighted images, slice thickness o f 5-6 mm and a gap o f 2-2.5 mm (when STIR sequence is used). Transversal slices were usually obtained starting few millimetres (about 10 mm) from the top o f the head, down to the base o f skull. MR images obtained by a short echo time were used for the detection o f skin surfaces. A STIR sequence was used to create 2-D fat-suppressed MR image which makes the detection o f the brain surfaces easier.
PET images were generated from a PET scanner having eight rings of BGO (bismuth germanate) detectors (512/ring) o f width 5.6 mm (transaxial). This is a CTI system operating at MRC cyclotron unit (in Hammersmith hospital, London). Scans were performed after inhalation o f C for the measurement o f cerebral blood flow. Three other different studies were routinely done using O, or CO for emissional tomography, and ^G e (Germanium) for transmissional information which is used for attenuation correction. 2-D transversal slices o f 6.75 mm thickness and 4.69 mm pixel size were reconstructed, on a 128*128 matrix, from the vertex to the base o f skull. The physical resolution o f the machine corresponds to a full width half maximum (FWHM) o f 6 mm (Spinks et al 1988). The surface o f PET data was obtained from the transmission data set which are usually acquired during scanning for attenuation correction purpose. The external surface can also be defined from emission data as the outer envelope o f the emission distribution detected under a threshold-based segmentation technique.
SPECT images were created by an Elscint SP4 SPECT system using (Technetium) labelled radiopharmaceuticals. The actual resolution of the system is about 7-10 mm at FWHM (at 10 cm in depth). The data were acquired after injection of HMPAO (hexamethylpropylene amine oxime) and the transverse scans were reconstructed with a slice thickness o f the same pixel size. A matrix size of 64*64 gives a pixel size of about 6 mm at a zoom factor o f 1, which was used to obtain 2-D slices. External surfaces from the SPECT can be defined as the outer envelope o f the emission distribution detected by setting o f a threshold value. However, decisions on threshold value and the type o f threshold selection technique are very important factors in the accuracy o f the detected objects (brain surface). Our experiments to achieve the best result are outlinec. in section 4.3.5.
Contiguous CT transverse scans were performed with a T60 Toshiba CT machine using system setting o f 240 mm field o f view and 5 or 10 mm slice thickness. Using a matrix size 320*320 and zoom factor o f 1 gives 2-D slices having a pixel size o f 0.75 mm. For viewing purpose, the original high-grey-level data (represented by a 16-bits value) were scaled to a grey level o f only 256 (correspond to 8 bits) due to the limitation o f our system. CT images are characterized by a distinct skin tissue image adjacent to a low noisy background. Therefore, surface detection is usually easy and relatively trivial on the CT data.