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Description

Processes PET scans

Can be run on

PETUnifiedPipeline.xml runs on all session types that have a PET scan

Project Inputs

NOTE: PUP Configuration file for a project must be manually setup before adding the pipeline to the project.

Instructions are found on the PUP Configuration page. Due to the intricate nature of this setup, users can request that CNDA Helpdesk complete it for them.

When adding the pipeline to a project, the following table will display but it is only for review purposes. Any changes
will need to be made to the configuration file.
Name
Description
Allowed Values
Examples
(as needed)
Notes
mrLabel
Label of the MR scan
text


mrId
ID of the MR scan
text


pet scan id
ID of the PET in the session
text


tracer
Tracer used
alphanumeric
PIB

half life
Default half-life
1223 or 6586


filter
Specify if filtering should be used
0,1
0 = no
1 = yes


filter xy
XY filter parameter
numeric

Scanner Kernel Mappings
filter z
Z filter parameter
numeric

Scanner Kernel Mappings
fwhm
Full width at half maximum
numeric


delay
Time between injection and scan
in minutes
numeric


tbl
Time bin length
numeric


tolmoco
Motion correction tolerance
numeric


refroistr
ROI label string
text
Cerebellum

FS
Indicate if pipeline should process
with Freesurfer ROIs
0, 1
0 = no
1 = yes


fsid
ID of the Freesurfer
numeric


t1
Name of the MR data file in
Freesurfer space
text
T1.mgz

wmparc
Freesurfer segmentation output file name
text
wmparc.mgz

roiimg
ROI image file
text
RSFMask

rsflist
Name of rsf list data file
text
RSFList.txt

pvc2cflag
Indicate if pvc2c flag should be used
0, 1
0 = no
1 = yes


rsfflag
Indicate if rs flag should be used
0, 1
0 = no
1 = yes


tgflag
Indicate if ROIs will be manual or from
template
0, 1, 2
0 = none
1 = template
2 = manual


template name
Name of template to use for ROI
processing
text


maskroot
Name of maskroot
text


mrscanid
For manual processing, the ID of the
MR scan that is atlas-registered
text


atltarg
For manual processing, the
name of target atlas
text


tolreg
Registration tolerance
numeric


rmf
Masking flag for registration of
reference image
text
-rm

mmf
Masking flag for registration of
moving image
text
-mm

rbf escaped
Reference image for registration of
blurring parameter
double escaped text
with quotes
"-rb 8"

mbf escaped
Parameter for registration of
moving image blurring
double escaped text
with quotes
"-mb 6"

modf escaped
Registration flag for
Intramodal or Intermodal
double escaped text
with quotes
""

mst
Start time for model
numeric


mdt
Length of time of model for dynamic scans
numeric


model
Name of model
text
logan

k2
Eflux rate constant to be used for
Logan Analysis
numeric
0.16

suvr
Indicate if SUVR should be performed
0, 1
0 = no
1 = yes


format type
Format of the PET resource
text
DICOM

format
Format of the PET data
0, 1
0 = DICOM
1 = ECAT








Launch Inputs

Name
Description
Allowed Values
Select PET Scan to Process
Pick which PET scan the pipeline will run on
Choose from available values
Default or Custom ROI
Indicate what ROI the pipeline should use
Choose from available values
Select FreeSurfer Assessor
Select from the available FreeSurfers for the Subject
Choose from available values
Send additional emails to
Indicate other users who should be notified
upon successful completion of the pipeline
Valid email addresses separated
by commas
FreeSurfer, manual ROIs, or template
  • FreeSurfer -- there must be some FreeSurfers run for subject, must be an edit of the QC information on the Freesurfer assessor, and the Freesurfer QC must be marked "Passed" or "Passed with edits".
  • Manual ROIs -- set up the MR registration pipeline on project (link to that pipeline page), download the registered MR and draw ROIs.
  • Otherwise use the template.

Manual ROI upload instructions
1. From Project Report page, click on the Manage tab.
2. Scroll down to find the Project Resource Settings section. Click on the Start button.
3. Under Define Resource for:, click the Scan button.
4. Fill in the following information exactly as indicated below:
  • Title: Upload Manual ROIs
  • Description: Upload hand drawn ROIs for a T1
  • Types: Comma-separated list of any T1 scan types for uploading manual ROIs
    eg. MPRAGE, MPRAGE_GRAPPA2, MPRAGE SENSE2
  • Resource Folder: ROI_711-2B
  • Sub-folder: Leave blank
  • Allow overwrite: Check the box
5. Click the Add button.
ManualRoiDefineResource.jpg
6. Close the Project Resource Settings window.
7. On the MR session or PET-MR session report page, there should be an Upload link next to all the T1 scan types indicated.

ROI uploader
  1. Zip all manual ROIs in a FLAT structure -- they must not be in directories.
  2. Click the Upload link next to the scan.
    UploadROI.jpg
  3. Select Upload Manual ROIs as the destination folder.
  4. Click Browse.
  5. Select the zipped file.
  6. Click Upload.
    UPloadManRoiDialog.jpg

Screenshot of structure of a Manual ROI.
ManualRoiStruct.jpg
For a visual walk-through, see launching PUP pipeline.

Outputs

  • PUP Timecourse created, link displays on Session Details page under Assessments heading.
    PUP_timec.jpg

  • Files added and viewable under Manage Files. PUP files display under the directory structure assessors->PUP Timecourse.
    PUP_files.jpg