4. PET data extraction

This step involves the extraction of regional time-activity curves (TAC's) from the dynamic PET images and that of the geometric transfer matrices (GTM's) from the simulated PET images (RSF's). command: 
pvc_extract_matrix [options] simuPET.mnc real_PET.mnc atlas.mnc \
matrix_slice tac_slice list_ROI
where:
  • simuPET.mnc and atlas.mnc are respectively the simulated regional spread functions (RSF's), and the corresponding ROI templates generated by the previous step (step 3)
  • matrix_slice and tac_slice are respectively the geometric transfer matrix (GTM) for each PET slice, and the time-activity curves (TAC's) extracted from the real PET images, both using atlas.mnc as anatomical masks (ROI's).
  • listROI is an output file containing useful information about the area of each ROI (volume-of-interest), etc... -for further data analysis. For now, one option is actually not one: -label label_file where label_file is a tracer-dependent transformation file that indicates which of the 90+ regions identified in the ICBM atlas need to be merged into functionnally distinct tissue components. An exemple of such file is given below in the case of the tracer [18F]fluoro-L-dopa:

    12 12 white
    10 10 gray
    21 21 caudate
    23 23 putamen



    This table may contain a restrictred number of tissue components as shown in this exemple, or can be a translation label file that lists all existing labels in Talairach space, with their corresponding value in the brain phantom (i.e., labeled MRI in PET native space). You can see another exemple of such translation file in /usr/local/mni/data/PVCcorrect/standard_labels.dat You should follow this exemple to create your own tracer-dependent label translation file.

    <olivier@bic.mni.mcgill.ca>
    last updated: Dec. 3, 1998