Essential for a quality PET/CT coregistration is that the PET and CT data be in the correct absolute units, and that both image volumes have the same orientation. Unfortunately, Analyze software does not support interfile 3.0 format which is what is used for the Gamma Medica X-Spect SPECT/CT. Thus the images need to be read as raw data. Since each CT image slice is saved to a different file, we need to first load in all files then group together to create a single volume image.

Read in the CT slices:
1: In the main Analyze window select File->Import/Export…
2: In the ImportExport window select Tools->Raw Data…
3: In the Raw Data – ImportExport window select the “Files” tab
In the first file window:
File             *.slice (remember to hit ‘Enter’!)
In the second window
File             desired_filename (ok to leave blank)

select the “Image Parameters” tab and use the following settings:
Byte Offset: 0
Width:         512
Height:        512
Depth:         512 (Check to determine actual number of slices)
Volumes:    1
Data Type:  signed 16-bit
Byte Swap: None
Flip Y!

Voxel Dim: Width=Height=Depth=.17
Select 'Load'

Writing the CT volume:
In the main Analyze window the CT volume image will be named 'RawData' by default. Select the image then go to File->Save As. Select the directory and enter the desired filename.

Note that since the CT data are so large (256 Mb for a complete volume!), it is helpful to truncate the data set so that it excludes most of the data that lie outside the animal. To truncate the data go to File->Save As and select the SubRegion tab. Enter the range of X Y Z voxels, then select 'Preview' to ensure the desired region is included. The first 10 CT slices on either end of the FOV will often have an aliasing artifact, thus Z can almost always be truncated by 10 (e.g. select 11-502, for a 512 slice image). The X and Y truncation depend on the size of the animal and the transaxial centering.

Before coregistration, need to Create a mean PET image

Coregister PET/CT with Analyze
Make sure both the mean PET and the truncated CT are loaded into Analyze. Select the Base image first (usually the CT), then with the Ctrl key pressed, select the Match image (PET). Both CT and PET images will be highlighted, then select 3-D Voxel Registration. If the images look like they are almost lined up then select 'Register'. If registration looks good then 'Save' transformed image. If the images are not lined up well, then they should first be lined up manually to get the registration pretty close. At that point the automated registration can be used.A normalized mutual information algorithm is used for coregistration. Always inspect the coregistration before accepting it. If it's acceptable then 'Save' transformed image.