[Gate-users] Time-activity curves in voxelized source results in segmentation violation

Ida Häggström ida.haggstrom at radfys.umu.se
Mon Oct 14 13:59:51 CEST 2013 

Hello!

I've set up a voxelized phantom + source that I want to insert
time-activity curves into. I've done some small scale tests (1sec x 30
frames) with good results, i.e. the simulation runs as it should. Now I'm
trying to expand my simulation to 1sec x 3600  frames, but as the source
TACs are read I get a segmentation fault as in the output below. All that
differs between the small and large scale simulation is that the smaller
scale simulation uses only the 30 first frames of the larger one (TAC files
have only 30 entries).

I use "/gate/RTVPhantom/SetAttenuationMapAsActivityMap" for the phantom, so
I have 3600 data files for both phantom and source: "brain_act_1.bin" to
"brain_act_3600.bin". The phantom seems to be read properly and looks good
when I turn visualization on in GATE. The data files "brain_act_X.dat" do
not seem corrupt and can be opened properly in a visualization software
(Amide).

Below I pasted what I though would be the most relevant parts of my
simulation setup and output to keep the length down a bit.

Thanks in advance for any suggestions!
Cheers,
Ida

*********************************** part of simulation output.log
**********************************
==== Source Voxel Reader Time Activity Translation Table ====
number of couples to be read : 8
 activity range  [1.000e+00 - 1.000e+00] is associated  to Time Activity
Curve read from file
/home/ida/Desktop/output/TACs_and_phantoms/brainWeb/TACs_FLT/water/C_GATE_Act.dat
==== Source Voxel Reader Time Activity Curve Read From File
/home/ida/Desktop/output/TACs_and_phantoms/brainWeb/TACs_FLT/water/C_GATE_Act.dat
 ====
number of couples to be read : 3600
At 0.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq
At 1.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq
At 2.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq
At 3.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq
At 4.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq
At 5.000e+00 seconds corresponds an Activity of 1.690e-01 Bcq
At 6.000e+00 seconds corresponds an Activity of 1.676e+00 Bcq
At 7.000e+00 seconds corresponds an Activity of 1.653e+00 Bcq
At 8.000e+00 seconds corresponds an Activity of 1.630e+00 Bcq
At 9.000e+00 seconds corresponds an Activity of 1.607e+00 Bcq
...
At 3.598e+03 seconds corresponds an Activity of 2.100e-01 Bcq
At 3.599e+03 seconds corresponds an Activity of 2.100e-01 Bcq
 activity range  [2.000e+00 - 2.000e+00] is associated  to Time Activity
Curve read from file
/home/ida/Desktop/output/TACs_and_phantoms/brainWeb/TACs_FLT/brain/C_GATE_Act.dat
...
 The Object RTVPhantom is attached to the interfileReader Source Voxel
Reader.
 Header read from
'/media/sf_g4work/Ida/output/TACs_and_phantoms/brainWeb/data/brain.h33'
 Data file name
'/media/sf_g4work/Ida/output/TACs_and_phantoms/brainWeb/data/brain_act_1.bin'
 Nb of planes:           175
 Nb of pixels per plane: 181 213
 Pixel size:             1.000e+00 1.000e+00
 Slice thickness:        1.000e+00
 Matrix size:            1.810e+02 2.130e+02
 Data type:              UNSIGNED INTEGER

  Voxel reader ---------->   number of voxels       : 0
  total activity (Bq)    : 0.000e+00
  position  (mm)         : 0.000e+00 0.000e+00 0.000e+00
  voxel size  (mm)    : 1.000e+00 1.000e+00 1.000e+00
GateVSourceVoxelReader::UpdateActivities(G4String, G4String) Time is
0.000e+00  cK = 1   p_cK = 0
0 x 0.000e+00  y 0.000e+00
1 x 1.000e+00  y 0.000e+00
2 x 2.000e+00  y 0.000e+00
3 x 3.000e+00  y 0.000e+00
4 x 4.000e+00  y 0.000e+00
5 x 5.000e+00  y 1.690e-01
6 x 6.000e+00  y 1.676e+00
7 x 7.000e+00  y 1.653e+00
...
403 x 4.030e+02  y 5.510e-01
404 x 4.040e+02  y 5.510e-01

 *** Break *** segmentation violation
WARNING - Attempt to delete the physical volume store while geometry closed
!
WARNING - Attempt to delete the logical volume store while geometry closed !
WARNING - Attempt to delete the solid store while geometry closed !
***************************************************************************************
********************************** voxelized source
**********************************
# Declaration of the fact that a voxellized source will be used.
/gate/source/addSource voxelSource voxel

# Declaration that the voxellized source will be entered
# using interfile data.
/gate/source/voxelSource/reader/insert interfile
/gate/RTVPhantom/AttachToSource voxelSource

# TIME-ACTIVITY
/gate/source/voxelSource/interfileReader/translator/insert range
/gate/source/voxelSource/interfileReader/rangeTranslator/readTable
rangeActivity.dat
/gate/source/voxelSource/interfileReader/SetTimeActivityTablesFrom
materialTAC.dat
/gate/source/voxelSource/interfileReader/SetTimeSampling 1.0 s

# The deafult position of the voxellized source is in the 1^{st}
# quarter. So the voxellized source has to be shifted over half its
# dimension in the negative direction on each axis
/gate/source/voxelSource/setPosition -90.5 -106.5 -87.5 mm

# The following lines characterize the size
# no difference with an analytical source
/gate/source/voxelSource/setType backtoback
/gate/source/voxelSource/gps/particle gamma
/gate/source/voxelSource/setForcedUnstableFlag true
/gate/source/voxelSource/setForcedHalfLife 6586.2 s #Fluor-18
/gate/source/voxelSource/gps/energytype Mono
/gate/source/voxelSource/gps/monoenergy 0.511 MeV
/gate/source/voxelSource/gps/angtype iso
/gate/source/voxelSource/gps/mintheta 0. deg
/gate/source/voxelSource/gps/maxtheta 180. deg
/gate/source/voxelSource/gps/minphi     0. deg
/gate/source/voxelSource/gps/maxphi   360. deg
/gate/source/voxelSource/gps/confine NULL #voxelPhantom_P

/gate/source/voxelSource/dump 1
/gate/source/list
***************************************************************************************
********************************** materialTAC.dat
**********************************
8
1 1 /...path.../brainWeb/TACs_FLT/water/C_GATE_Act.dat
2 2 /...path.../brainWeb/TACs_FLT/brain/C_GATE_Act.dat
3 3 /...path.../brainWeb/TACs_FLT/adipose/C_GATE_Act.dat
4 4 /...path.../brainWeb/TACs_FLT/muscle/C_GATE_Act.dat
5 5 /...path.../brainWeb/TACs_FLT/body/C_GATE_Act.dat
6 6 /...path.../brainWeb/TACs_FLT/skull/C_GATE_Act.dat
7 7 /...path.../brainWeb/TACs_FLT/blood/Cp_GATE_Act.dat
8 8 /...path.../brainWeb/TACs_FLT/tumor/C_GATE_Act.dat
*********************************************************************************************
********************************** water/C_GATE_Act.dat
**********************************
3600
0.000 0.000
1.000 0.000
2.000 0.000
3.000 0.000
4.000 0.000
5.000 0.169
6.000 1.676
7.000 1.653
8.000 1.630
9.000 1.607
...
3598.000 0.210
3599.000 0.210
******************************************************************************************
********************************* brain.h33
*********************************************
!INTERFILE  :=
name of data file := /...path.../brainWeb/data/brain.i33
!GENERAL DATA :=
!GENERAL IMAGE DATA :=
!type of data := PET
imagedata byte order := LITTLEENDIAN
!PET STUDY (General) :=
!PET data type := Image
process status := Reconstructed
!number format := UNSIGNED INTEGER
!number of bytes per pixel := 2
number of dimensions := 3
!matrix size [1] := 181
scaling factor (mm/pixel) [1] := 1
!matrix size [2] := 213
scaling factor (mm/pixel) [2] := 1
!number of slices := 175
slice orientation := Transverse
slice thickness (pixels) := 1
scaling factor (mm/pixel) [3] := 1
first pixel offset (mm) [1] := -90.5
first pixel offset (mm) [2] := -106.5
first pixel offset (mm) [3] := 0
number of time frames
image scaling factor[1] := 1
data offset in bytes[1] := 0
quantification units := 1
!END OF INTERFILE :=
***********************************************************************************************
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