<div dir="ltr">Hello!<div><br></div><div>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).</div>
<div><br></div><div>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).</div>
<div><br></div><div>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. </div><div><br></div><div>Thanks in advance for any suggestions!</div><div>
Cheers,</div><div>Ida</div><div><br></div><div><div>*********************************** part of simulation output.log **********************************</div><div><div>==== Source Voxel Reader Time Activity Translation Table ====</div>
<div>number of couples to be read : 8</div><div> 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</div>
<div>==== Source Voxel Reader Time Activity Curve Read From File /home/ida/Desktop/output/TACs_and_phantoms/brainWeb/TACs_FLT/water/C_GATE_Act.dat ====</div><div>number of couples to be read : 3600</div><div>At 0.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq</div>
<div>At 1.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq</div><div>At 2.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq</div><div>At 3.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq</div><div>
At 4.000e+00 seconds corresponds an Activity of 0.000e+00 Bcq</div><div>At 5.000e+00 seconds corresponds an Activity of 1.690e-01 Bcq</div><div>At 6.000e+00 seconds corresponds an Activity of 1.676e+00 Bcq</div><div>At 7.000e+00 seconds corresponds an Activity of 1.653e+00 Bcq</div>
<div>At 8.000e+00 seconds corresponds an Activity of 1.630e+00 Bcq</div><div>At 9.000e+00 seconds corresponds an Activity of 1.607e+00 Bcq</div></div><div>...</div><div><div>At 3.598e+03 seconds corresponds an Activity of 2.100e-01 Bcq</div>
<div>At 3.599e+03 seconds corresponds an Activity of 2.100e-01 Bcq</div><div> 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</div>
</div><div>...</div><div> The Object RTVPhantom is attached to the interfileReader Source Voxel Reader.<br></div><div> Header read from '/media/sf_g4work/Ida/output/TACs_and_phantoms/brainWeb/data/brain.h33'</div>
<div> Data file name '/media/sf_g4work/Ida/output/TACs_and_phantoms/brainWeb/data/brain_act_1.bin'</div><div> Nb of planes: 175</div><div> Nb of pixels per plane: 181 213</div><div> Pixel size: 1.000e+00 1.000e+00</div>
<div> Slice thickness: 1.000e+00</div><div> Matrix size: 1.810e+02 2.130e+02</div><div> Data type: UNSIGNED INTEGER</div><div><br></div><div> Voxel reader ----------> number of voxels : 0</div>
<div> total activity (Bq) : 0.000e+00</div><div> position (mm) : 0.000e+00 0.000e+00 0.000e+00</div><div> voxel size (mm) : 1.000e+00 1.000e+00 1.000e+00</div><div>GateVSourceVoxelReader::UpdateActivities(G4String, G4String) Time is 0.000e+00 cK = 1 p_cK = 0</div>
<div>0 x 0.000e+00 y 0.000e+00</div><div>1 x 1.000e+00 y 0.000e+00</div><div>2 x 2.000e+00 y 0.000e+00</div><div>3 x 3.000e+00 y 0.000e+00</div><div>4 x 4.000e+00 y 0.000e+00</div><div>5 x 5.000e+00 y 1.690e-01</div>
<div>6 x 6.000e+00 y 1.676e+00</div><div>7 x 7.000e+00 y 1.653e+00</div></div><div>...</div><div><div>403 x 4.030e+02 y 5.510e-01</div><div>404 x 4.040e+02 y 5.510e-01</div><div><br></div><div> *** Break *** segmentation violation</div>
<div>WARNING - Attempt to delete the physical volume store while geometry closed !</div><div>WARNING - Attempt to delete the logical volume store while geometry closed !</div><div>WARNING - Attempt to delete the solid store while geometry closed !</div>
</div><div>***************************************************************************************<br></div><div>********************************** voxelized source **********************************<br></div><div><div># Declaration of the fact that a voxellized source will be used.<br>
</div><div>/gate/source/addSource voxelSource voxel</div><div><br></div><div># Declaration that the voxellized source will be entered</div><div># using interfile data.</div><div>/gate/source/voxelSource/reader/insert interfile</div>
<div>/gate/RTVPhantom/AttachToSource voxelSource</div><div><br></div><div># TIME-ACTIVITY </div><div>/gate/source/voxelSource/interfileReader/translator/insert range</div><div>/gate/source/voxelSource/interfileReader/rangeTranslator/readTable rangeActivity.dat</div>
<div>/gate/source/voxelSource/interfileReader/SetTimeActivityTablesFrom materialTAC.dat</div><div>/gate/source/voxelSource/interfileReader/SetTimeSampling 1.0 s</div><div><br></div><div># The deafult position of the voxellized source is in the 1^{st}</div>
<div># quarter. So the voxellized source has to be shifted over half its</div><div># dimension in the negative direction on each axis</div><div>/gate/source/voxelSource/setPosition -90.5 -106.5 -87.5 mm</div><div><br></div>
<div># The following lines characterize the size</div><div># no difference with an analytical source</div><div>/gate/source/voxelSource/setType backtoback</div><div>/gate/source/voxelSource/gps/particle gamma</div><div>/gate/source/voxelSource/setForcedUnstableFlag true</div>
<div>/gate/source/voxelSource/setForcedHalfLife 6586.2 s #Fluor-18</div><div>/gate/source/voxelSource/gps/energytype Mono</div><div>/gate/source/voxelSource/gps/monoenergy 0.511 MeV</div><div>/gate/source/voxelSource/gps/angtype iso</div>
<div>/gate/source/voxelSource/gps/mintheta 0. deg</div><div>/gate/source/voxelSource/gps/maxtheta 180. deg</div><div>/gate/source/voxelSource/gps/minphi 0. deg</div><div>/gate/source/voxelSource/gps/maxphi 360. deg</div>
<div>/gate/source/voxelSource/gps/confine NULL #voxelPhantom_P</div><div><br></div><div>/gate/source/voxelSource/dump 1</div><div>/gate/source/list<br></div></div><div>***************************************************************************************<br>
</div><div>********************************** materialTAC.dat **********************************<br></div><div><div>8</div><div>1<span class="" style="white-space:pre"> </span>1<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/water/C_GATE_Act.dat</div>
<div>2<span class="" style="white-space:pre"> </span>2<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/brain/C_GATE_Act.dat</div><div>3<span class="" style="white-space:pre"> </span>3<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/adipose/C_GATE_Act.dat</div>
<div>4<span class="" style="white-space:pre"> </span>4<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/muscle/C_GATE_Act.dat</div><div>5<span class="" style="white-space:pre"> </span>5<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/body/C_GATE_Act.dat</div>
<div>6<span class="" style="white-space:pre"> </span>6<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/skull/C_GATE_Act.dat</div><div>7<span class="" style="white-space:pre"> </span>7<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/blood/Cp_GATE_Act.dat</div>
<div>8<span class="" style="white-space:pre"> </span>8<span class="" style="white-space:pre"> </span>/...path.../brainWeb/TACs_FLT/tumor/C_GATE_Act.dat</div></div><div>*********************************************************************************************<br>
</div><div>********************************** water/C_GATE_Act.dat **********************************<br></div><div><div>3600</div><div>0.000<span class="" style="white-space:pre"> </span>0.000</div><div>1.000<span class="" style="white-space:pre"> </span>0.000</div>
<div>2.000<span class="" style="white-space:pre"> </span>0.000</div><div>3.000<span class="" style="white-space:pre"> </span>0.000</div><div>4.000<span class="" style="white-space:pre"> </span>0.000</div><div>5.000<span class="" style="white-space:pre"> </span>0.169</div>
<div>6.000<span class="" style="white-space:pre"> </span>1.676</div><div>7.000<span class="" style="white-space:pre"> </span>1.653</div><div>8.000<span class="" style="white-space:pre"> </span>1.630</div><div>9.000<span class="" style="white-space:pre"> </span>1.607</div>
</div><div>...</div><div><div>3598.000<span class="" style="white-space:pre"> </span>0.210</div><div>3599.000<span class="" style="white-space:pre"> </span>0.210</div></div><div><div>******************************************************************************************<br>
</div></div><div><div>********************************* brain.h33 *********************************************<br></div><div></div></div><div><div>!INTERFILE :=</div><div>name of data file := /...path.../brainWeb/data/brain.i33</div>
<div>!GENERAL DATA :=</div><div>!GENERAL IMAGE DATA :=</div><div>!type of data := PET</div><div>imagedata byte order := LITTLEENDIAN</div><div>!PET STUDY (General) :=</div><div>!PET data type := Image</div><div>process status := Reconstructed</div>
<div>!number format := UNSIGNED INTEGER</div><div>!number of bytes per pixel := 2</div><div>number of dimensions := 3</div><div>!matrix size [1] := 181</div><div>scaling factor (mm/pixel) [1] := 1</div><div>!matrix size [2] := 213</div>
<div>scaling factor (mm/pixel) [2] := 1</div><div>!number of slices := 175</div><div>slice orientation := Transverse</div><div>slice thickness (pixels) := 1</div><div>scaling factor (mm/pixel) [3] := 1</div><div>first pixel offset (mm) [1] := -90.5</div>
<div>first pixel offset (mm) [2] := -106.5</div><div>first pixel offset (mm) [3] := 0</div><div>number of time frames </div><div>image scaling factor[1] := 1</div><div>data offset in bytes[1] := 0</div><div>quantification units := 1</div>
<div>!END OF INTERFILE :=</div></div><div><div>***********************************************************************************************<br></div><div></div></div><div><br></div></div>