BrainPET Reconstruction Algorithms

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

For questions/feedback, please contact Meena M. Makary (mmakary@mgh.harvard.edu) and Dr. Catana (ccatana@mgh.harvard.edu) OR preferably use this Teams Channel Positron

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 brainPET_pCT_AeMir.pl -h

For DICOM input:

-  ⇤ ← Revision 22 as of 2021-02-18 18:57:34 → 
  Size: 5160
  Editor: MeenaMakary
  Comment:
+   ← Revision 44 as of 2021-07-12 22:53:23 → ⇥
  Size: 6553
  Editor: MeenaMakary
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 18:
-= BrainPET =
+= BrainPET Reconstruction Algorithms =
 Line 21:
----- /!\ '''This page is only to process PET-MR data acquired using BrainPET (Bay 6) scanner at the Athinoula A. Martinos Center for Biomedical Imaging.''' ----
+---- /!\ '''This page is only to process PET-MR data acquired using BrainPET (Bay 6) scanner at the Athinoula A. Martinos Center for Biomedical Imaging.

For questions/feedback, please contact Meena M. Makary (mmakary@mgh.harvard.edu) and Dr. Catana (ccatana@mgh.harvard.edu) OR preferably use this Teams Channel [[https://teams.microsoft.com/l/channel/19%3ad54a14f65ec84583b9e1ca25ef9874f4%40thread.tacv2/Positron?groupId=8123966a-4997-4cb4-969a-e991a516c342&tenantId=720edb1f-5c4e-4043-8141-214a63a7ead5|Positron]]''' ----
-Line 32:
+Line 34:
-{{{
+{{{green
-Line 35:
+Line 37:
+{{{#!wiki red
def hello():
    print "Hello World!"
}}}
-Line 48:
+Line 53:
-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) before the 2nd pass of reconstruction. The resulting images can be viewed as either SUV, bqml, or nas images. Mu maps must be present.
+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) before the 2nd pass of reconstruction. The resulting images can be viewed as either SUV, bqml, or nas images. Mu maps must be present.
-Line 58:
+Line 63:
+== Dynamic Frame Reconstruction (TAC) ==

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. The resulting images can be viewed as either SUV, bqml, or nas images. Mu maps must be present.

(!) For full instructions type: ''' perl brainPET_recon_DF_AeMir.pl -h '''

{{{
perl brainPET_recon_DF_AeMir.pl -i /<full_path>/<subj_id>/PET -f Frame1.lst -d dynamic_frame_list.txt -e 5 -s '[1 0 1]' -t 0.8
}}}

This will reconstruct dynamic frame PET image according to frames length indicated in dynamic_frame_list.txt (which should be located inside PET folder) for [^11^C] list mode data (Frame1.lst).  It will output both SUV and SUV_BQML.
-Line 97:
+Line 115:
+UNDER CONSTRUCTION !!