/!\ This page is only to process PET-MR data acquired using BrainPET (Bay 6) scanner at the Athinoula A. Martinos Center for Biomedical Imaging.

Aether-Mirror Version

This version mirrors the attenuation map generation and reconstruction algorithms that were used on Aether. We recommend to use this version only for continuation studies.

PseudoCT mu-map generation

This function generates pseudoCT mu-map using SPM8 atlas-based method (David Izquierdo-Garcia et al.)

perl -i /<DIR>/<SUJID>/MR/MPRAGE -f 107000-000005-000001.dcm -c 0

perl -i /<DIR>/<SUJID>/MR_PET -f cp_iso_mprage.nii -c 0

Supporting Functions

Download and Organize MR and PET Data

This function to creates subject directory and its PET/MR/MR_PET sub-directories, download its MR and/or PET data, and unpack & organize MR data. You can download old and recently acquired data (see the note below for old data download). It also allows you to QC TOI/ScanID/ScanDate/PI through termainal output.

perl -d /<DIR> -s <SubjID> -id <ScanID> -mr 1 -pet 1

To download an old subject (acquired more than 4 years ago), please do the following:

  1. ssh to
  2. cd to where the code is located
  3. type: bash (and hit enter)
  4. re-run the script

The script automatically detects if the subject is old or recently acquired and an error message will pop up with instructions in case of an old subject.

Denoise MPRAGE

perl -i /<DIR>/<SUBJID>/MR_PET/cp_iso_mprage.nii -t 25 -s 0


perl -i /<DIR>/file.i

Development Version