Works with XNAT versions:

  • 1.5
  • 1.6


Uploaded By:


Tags: , , , ,

  • Version: 1
  • License:
  • Upload Date: September 17, 2012

This Plugin Accesses:

  • Database
  • Credits:

    Yi Su, Avi Snyder
  • Description:

    fspet is a package for processing amyloid imaging data (PIB PET) to obtain quantitative information about amyloid load in the brain. Regional quantification is achieved by utilizing FreeSurfer segmentation results (the wmparc.mgz file). The output of this analysis are binding potential and SUVR measurements of cortical gray matter regions, subcortical regions, and white matter regions. Global index of amyloid load is presented as a mean cortical binding potential (MCBP) or an all cortical mean (CALL) measure. The data processing stream requires an input file (see example in the tst folder). The input file specifies the location and name of the PET data (can be both ecat file or dicom file), and the FreeSurfer file (T1.mgz or orig.mgz, and wmparc.mgz). It also asks for the fwhm of the PET data, time range used for quantification.

    For additional information contact Yi Su, PhD (suy@mir.wustl.edu)

    The 4dfp package is adapted from Avi Snyder’s 4dfp package (avi@npg.wustl.edu)


    $ cd $FSPET (location of this package)
    $ cd 4dfp (enter the 4dfp folder)
    $ ./comp4dfp (compile 4dfp package)
    $ ./install4dfp (copy 4dfp executables into the bin directory)
    $ cd ..
    $ cd src (enter the src directory)
    $ make ALL
    $ cd ..

    After these steps, all the binaries should have been generated, the executables are in three locations: 4dfp/bin, scripts, and src. They can be put into user defined executable locations, or these three folders can be added into the path. For installations with existing 4dfp packages, please ignore the 4dfp portion of the installation. The 4dfp folder and the atlas folder can be removed.

    After installation the environmental variable FSPET need to be set to run the package.

    $ setenv FSPET /location/of/fspet (csh)
    $ export FSPET=/location/of/fspet (bash)


    $ cd $FSPET/tst pib_fs_proc bertpib_params.txt

    This will generate a pib_proc directory within the tst folder, and perform the analysis there. When the job is done (in a couple of hours), text output will be generated that contains quantification result. Compare the results with the .txt files in the pib_proc_ref directory. The results should be similar.

  • Environment where add-on is currently running:

    XNAT Pipeline Engine

Add-on Screenshots