Small Animal Imaging Resource Program @ Johns Hopkins



PET is used to obtain functional images, but does not provide precise anatomic information. Thus an MR scan is performed to provide an anatomic image to supplement the PET data. The 2 image sets need to be coregistered. It is generally recommended to reslice the low resolution image (PET) to the high resolution image (MR). The coregistration of choice for realignment or for a static PET scan to MR is the mutual information algorithm in SPM2. For dynamic studies, the procedure is usually to regiser a mean PET to the MR to get the affine transformation matrix. That transformation is then applied to all frames of the dynamic study.

Using SPM



  1. Begin SPM by typing “spm” at the MATLAB command window prompt.  (assumes the spm2 toolbox is in the MATLAB toolbox folder and that the toolbox is in the path – if the toolbox is not in the path, it can be placed in the path by using “pathtool”).
  2. Click on PET/SPECT. 
  3. (skip steps 3-5 if the MRI .img files are already present).  To produce MRI .img files from raw data (D.001, D.002, etc.), click on the “Toolboxes” menu on the upper-left window and select DICOM. 
  4. Find and load the summary file of interest (eg D.0*, which when clicked on expands to 1-124:D.0*).  According to the header files, SPM may not be able to read the files together as a summary file – in this case, the files can be entered by clicking on each file consecutively (eg for old 30 slice data).  If MRI images are stored in two (or more) separate files, click ‘all’ to select all images.
  5. Say “Done” and SPM will load the files as .img and .hdr and save them in the MATLAB/work directory.  You may want to copy these files to your working directory, e.g. where you obtained the original data files.
  6. Check that the PET files are in .hdr and .img format.  If the PET data is in .ie format, use readadvance to convert the files.
  7. On the upper-left window, click on “Coregister.”
  8. In the lower-left window, enter number of subjects.
  9. Choose the “Coregister and Reslice” option.
  10. Lastly, enter the target and source images per the study design.  The source image will be resliced to the target image.  SPM will then write the resliced image in the same directory as the source image with the prefix “r-.” Usually pick the MR as the target, and a mean PET image as the source.

Using Analyze

  1. Load in both the MR and the mean PET image. Also load in the dynamic image if applicable.
  2. First select the MR, then while holding the <Ctrl> key, select the mean PET. 
  3. Select the 3D Voxel Registration tool.
  4. Go to Tools->Manual and do a manual coregistration to get a good starting point.
  5. Go to Generate->Register to do the automated MI coregistration.
  6. If desired, go to Save Transformed to reslice the mean PET
  7. Drag the dynamic study onto the Voxel Registration window and replace the mean PET (Use current matrix).
  8. Apply 'Save Transformed' to the dynamic study and save all volumes in multivolume