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Labelled as DIAN_Pet

Description: Pipeline to process PET scans

Algorithm and tools developed by: Dr. Yi Su, Contact: suy@mir.wustl.edu

Talk by Yi Su on PET Processing

How to add a pipeline to a project

Add screen
addPet.jpg

Input Parameters:
Name

Description
CSV Value
Schema Link
fwhm

Full-width-half-max (fwhm) of the assumed PET scanner point spread function to be used
for partial volume correction.The fwhm is for partial volume correction only, we traditionally
do not apply PVC, to be consistent with Jon's manual processing you need to use the
non-corrected version.
0.6

mst:

Model Starting Time in Minutes from time of injection and scan for dynamic scans.
40

mdt

Model Duration in Minutes for dynamic scans.
30

t1

The name of the MR data file in FreeSurfer space (T1.mgz is used)
T1.mgz

wmparc

The FreeSurfer segmentation output file (wmparc.mgz is used)
wmparc.mgz

isstat

Whether is scan is a static or a dynamic . If the difference between the Injection
Starttime and the Scan start time is more than 2minutes, its assumed to be a static scan,
else its a dynamic scan.
For a PET session, while launching the pipeline, appropriate value can be selected.


isecat

Whether is scan is an ECAT or a DICOM scan. This is populated for the user.


roisfn

Path to ROI file name (Default: /nrgpackages/tools/pib_proc/ROIs)
/nrgpackages/tools/pib_proc/ROIs

fslut

Path to the Freesurfer LUT file (Default: /nrgpackages/tools/freesurfer5/FreeSurferColorLUT.txt )
/nrgpackages/tools/freesurfer5/
FreeSurferColorLUT.txt






NOTE: The parameters mst and mdt are to determine which portion of data is used for logan analysis to calculate binding potentials (BP). For our local projects we traditionally used 30-60 minutes post injection, so mst would be 30 and mdt would also be 30. DIAN is a special case where 40-70 minutes is used to do the modeling.

Pre-requisites:

  • Freesurfer processed data of the T1 scan. (Link to setup the Freesurfer pipeline for a project)

Launch a pipeline for a session

If the injection start time and or scan start time is not included in the PET Session, the radio buttons labelled 'Is a Static Scan" "Is a Dynamic Scan are not selected". Before launching the pipeline, make sure appropriate value is selected.

PetLaunch.png