PETprep: Partial Volume Correction module

This script uses PETPVC to apply partial volume correction to PET images. It additionally formats anatomical segmentation files to accomodate the PETPVC format.

The only requirement is to have Conda and Python (>=3.7.13) installed. In order to use this, clone the repo next to the folder of your BIDS-compatible data by running

git clone [email protected]:eric2302/petprep_pvc.git

Requirements

Make sure you have all the needed packages by running

conda env create -f environment.yml

using the environment file provided in this repostiory.

Use

In order to use this script, call on the terminal

python run_pvc.py --bids_dir BIDS_DIR --participant_label LABEL --pvc_method {GTM,LABBE,RL,VC,STC,MTC,IY,MG} --fwhm FWHM

to run the complete workflow. All the options inlcuded in this current version are:

--bids_dir BIDS_DIR   The directory with the input dataset formatted
                      according to the BIDS standard.
                      
--output_dir OUTPUT_DIR
                      The directory where the output files should be stored.
                      If you are running group level analysis this folder
                      should be prepopulated with the results of the
                      participant level analysis.
                      
--analysis_level {participant,group}
                      Level of the analysis that will be performed. Multiple
                      participant level analyses can be run independently
                      (in parallel) using the same output_dir.
                      
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                      The label(s) of the participant(s) that should be
                      analyzed. The label corresponds to
                      sub-<participant_label> from the BIDS spec (so it does
                      not include "sub-"). If this parameter is not provided
                      all subjects should be analyzed. Multiple participants
                      can be specified with a space separated list.
                      
--pvc_method {GTM,LABBE,RL,VC,STC,MTC,IY,MG}
                      Partial volume correction method.
                      
--fwhm FWHM           Full width at half maximum in mm for point spread
                      function.
                    
--skip_anat_prep      Whether or not to prepare anatomical data for PETPVC.