/!\ 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. Scripts are located inside: /autofs/cluster/petcore/PET_computer_backup/brainPET_code/Aether-Mirror. You will have to cd to this folder before running any of the functions below.

PseudoCT mu-map generation

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

(!) For full instructions type: perl -h

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

where 107000-000005-000001.dcm is the file name of the first dcm file.

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

Single Frame Dual Pass

This function generates single frame PET image files from list mode data. It assumes a particular folder structure for it to work: Parent Folder: MR, MR_PET (> mu_maps > mu_map), PET > (list mode data). From the list mode data, TAC will generate images with a user defined duration for a number of selectable isotopes. It first reconstructs PET frames using the native position of mu-map (1st pass) and later registers the mu-map to the position of late PET window (e.g. 60-90 for PBR28) in the 2nd pass of reconstruction. The resulting images can be viewed as either SUV, bqml, or nas images. Mu maps must be present.

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

This function performs thresholding-based denoising for the MPRAGE image to clean it for better pseudo-CT results. Use it only if the mprage is noisy. It works only with nifti (.nii) file as input. It takes a denoising threshold (intensity) to remove noise in the image, and a Gauss smoothing factor (mm) to facilitate denoising.

(!) For full instructions type: perl -h

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

Outputs: cp_iso_mprage_denoised_thres<>_smooth<>mm.nii and scp_iso_mprage.nii (this is the smoothed version of the input image, it should be identical to the input if the smoothing was set to 0). The output is saved in the same folder as the input.


This function converts brainPET ifile to nifit format.

(!) For full instructions type: perl -h

perl -i /<DIR>/file.i

Development Version