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 only for 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

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 brainPET_mrpet_dwnld_unpack.pl -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:

ssh to pinto.nmr.mgh.harvard.edu
cd to where the code is located
type: bash (and hit enter)
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 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

-  ⇤ ← Revision 1 as of 2019-06-20 14:18:26 → 
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  Editor: MeenaMakary
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'''Index'''
<<TableOfContents(2)>>

= 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 only for 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 =

== 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 brainPET_mrpet_dwnld_unpack.pl -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 pinto.nmr.mgh.harvard.edu
 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 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
}}}

= Development Version =