Positron Emission Tomography (PET) is a state-of-the-art neuroimaging tool for quantification of the in vivo spatial distribution of specific molecules in the brain. It is affected by various kinds of patient movement during a scan. The PETprep_HMC application allows for correction of the PET results in the presence of head motions.

References:

• Martin Nørgaard, Melanie Ganz, Claus Svarer, Vibe G. Frokjaer, Douglas N. Greve, Stephen C. Strother, Gitte M. Knudsen
  Optimization of preprocessing strategies in Positron Emission Tomography (PET) neuroimaging: A [11C]DASB PET study NeuroImage , 199 (2019) 466–479.

• PETprep_HMC Github page

• Module Name: RFdissusion (see the modules page for more information)
• Unusual environment variables set
  • PETPREP_HMC_HOME  installation directory
  • PETPREP_HMC_BIN       executable directory
  • PETPREP_HMC_SRC       source code directory
  • PETPREP_HMC_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3335 ~]$ module load petprep_hmc 
[+] Loading singularity  3.10.5  on cn4174
[+] Loading freesurfer  7.3.2  on cn4174
[+] Loading freetype 2.12.1 on cn4174
[+] Loading FSL 6.0.4  ...
[+] Loading petprep_hmc  0.06
[user@cn3335 ~]$
[user@cn3335 ~]$ run.py -h
usage: run.py [-h] --bids_dir BIDS_DIR [--output_dir OUTPUT_DIR]
              [--analysis_level {participant,group}]
              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
              [--mc_start_time MC_START_TIME] [--mc_fwhm MC_FWHM] [--mc_thresh MC_THRESH]
              [--n_procs N_PROCS] [--no_resample] [--skip_bids_validator] [-v]

BIDS App for PETPrep head motion correction workflow

optional arguments:
  -h, --help            show this help message and exit
  --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 theparticipant 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- 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.
  --mc_start_time MC_START_TIME
                        Start time for when to perform motion correction (subsequent frame will be
                        chosen) in seconds
  --mc_fwhm MC_FWHM     FWHM for smoothing of frames prior to estimating motion
  --mc_thresh MC_THRESH
                        Threshold below the following percentage (0-100) of framewise ROBUST RANGE
                        prior to estimating motion correction
  --n_procs N_PROCS     Number of processors to use when running the workflow
  --no_resample         Whether or not to resample the motion corrected PET data to lowest x/y/z
                        dim in original data
  --skip_bids_validator
                        Whether or not to perform BIDS dataset validation
  -v, --version         show program's version number and exit
[user@cn3335 ~]$ 

[user@cn3335 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$