BrainPET

HI

$/!\$ 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 for the purpose of continuation studies.

PseudoCT mu-map generation

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

For DICOM input:

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

For NIFTI input

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

IMP1: The r-l flip is applied only to .dcm input but not to .nii input (see Imp2)
IMP2: If you input a nifti file, it should be named as cp_iso_mprage.nii and it should be r-l flipped (i.e., it is the output of a previously ran pesudo CT).

Supporting Functions

Denoise MPRAGE

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

ifile2nifti

perl brainPET_ifile2nifti.pl -i /<DIR>/file.i