PET Unified Pipeline
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4dfp Update README Oct 17, 2018
AVtemplate Added brainmask to the AVtemplate folder. Feb 5, 2014
IDAIF Added tools to create TAC files from combined regions and updated Feb 11, 2015
matlabcode Added matlab code for IDAIF processing. Jun 6, 2014
scripts Included individual 4dfp tool subfolders with modified makefile and i… Oct 16, 2018
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1406pib1_LOGAN.txt sample output Jan 9, 2014
1406pib1_LOGANLR.txt sample output Jan 9, 2014
1406pib1_LOGANLR_PVC2C.txt sample output Jan 9, 2014
1406pib1_LOGANLR_RSF.txt sample output Jan 9, 2014
1406pib1_LOGAN_PVC2C.txt sample output Jan 9, 2014
1406pib1_LOGAN_RSF.txt sample output Jan 9, 2014
1406pib1_Left-Cerebellum-Cortex.mdl sample output Jan 9, 2014
1406pib1_msum_Left-Cerebellum-Cortex.suvr sample output Jan 9, 2014
1406pib1_msum_SUVR.txt sample output Jan 9, 2014
1406pib1_msum_SUVRLR.txt sample output Jan 9, 2014
1406pib1_msum_SUVRLR_PVC2C.txt sample output Jan 9, 2014
1406pib1_msum_SUVRLR_RSF.txt sample output Jan 9, 2014
1406pib1_msum_SUVR_PVC2C.txt sample output Jan 9, 2014
1406pib1_msum_SUVR_RSF.txt sample output Jan 9, 2014
LICENSE Included individual 4dfp tool subfolders with modified makefile and i… Oct 16, 2018
PUP.docx Doc first commit Jan 9, 2014
README.md Update README.md Oct 17, 2018
ROIs Added ROIs file for FS based processing Apr 15, 2015
manroi_sample.param Added example parameter files for manual roi and template roi based p… Feb 5, 2014
pet.param sample output Jan 9, 2014
templateroi.param Added example parameter files for manual roi and template roi based p… Feb 5, 2014

README.md

PUP

PET Unified Pipeline

PUP is a package for processing PET images. It is developed by Yi Su, PhD (ysu001@gmail.com)

The package includes the following subfolders of different components:

4dfp

A package developed by Dr. Abraham Z. Snyder (azsnyder@wustl.edu) at Washington University School of Medicine in St. Louis for image analysis and quantification.

src

source code for PUP that needs compilation.

scripts

PUP scripts

AVtemplate

Florbetapir templates for PET templates-based processing (not required for standard PUP processing).

IDAIF

Experimental code for image-derived arterial input function extraction (not required for standard PUP processing).

matlabcode

Matlab code that are used by some of the scripts (not required for standard PUP processing).

INSTALLATION

  1. Following the included instructions for the 4dfp package for its installation. This should be done first, and the package is required by PUP. If the user already has 4dfp installed compare the included tools and make sure the existing installation is not missing any components.

  2. Compile source code in the src folder using the included makefile using the release target. It will put the binaries at the same location as the 4dfp $RELEASE folder.

  3. Copy the content of the scripts folder to desired location or add its location to your path.


This README is prepared by Yi Su, PhD (ysu001@gmail.com) on 2018/10/16