aaewarren / pipa

Parcellated Inter-hemispheric PET Asymmetry (PIPA)

PIPA V1.0

Parcellated Inter-hemispheric PET Asymmetry (PIPA)

REQUIRED SOFTWARE

• Freesurfer (ideally version >6): https://freesurfer.net/fswiki/DownloadAndInstall
• FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
• ANTs: https://github.com/stnava/ANTs
• MRtrix3: https://mrtrix.readthedocs.io/en/latest/installation/package_install.html
• MATLAB: https://www.mathworks.com/products/get-matlab.html

USAGE

This Bash script performs Freesurfer recon-all, PET-to-T1 co-registration, and calculates asymmetry indices from PET data using HCPMMP1 cortical parcellation (+ Freesurfer subcortical parcellation).

USAGE: PIPA.sh -s [PATH TO SUBJECT FOLDER] -i [SUBJECT ID] -t [PATH TO T1 IMAGE] -p [PATH TO PET IMAGE] -f [OPTIONAL PATH TO FLAIR IMAGE]

[-h] = show this usage/help text

[-s] = full path to top-level subject folder where all output will be saved

[-i] = subject ID (arbitrary)

[-t] = path to T1 image (in .nii.gz format)

[-p = path to PET image (in .nii.gz format)

[-f] = optional path to FLAIR image (in .nii.gz format - if set, FLAIR will be incorporated into Freesurfer recon-all, attempting to improve pial surface recon)