[Gate-users] Error in reading NCAT phantom
Panagiotis Papadimitroulas
panpap_5 at hotmail.com
Tue May 24 21:08:09 CEST 2011
Dear Yanfei Mao,
I have two suggestions for you:
1) Try to write in your header file in the line
!name of data file := NCAT_act.i33 the whole path of your file, like this:
!name of data file := /home/username/NCAT_act.i33 ,or check where is your file. maybe in the data folder, so just write for your path the: data/NCAT_act.i33 (from where you run Gate)
2) My second suggestion if the above doesn't work, is just to copy the header file from the examples of GATE for voxelized phantoms... And just change there the written parameters with the parameters you have from your header file. Do not add more.. I put here an example for not searching... just copy this and change with your numbers (mostly the appropriate one, like pixel scaling, number of images, matrix size etc..)
Hope this will work.
Panagiotis.
!INTERFILE :=
!imaging modality := nucmed
!originating system := greetings
!version of keys := 3.3
date of keys := 1996:09:24
conversion program := (X)MedCon
program author := Erik Nolf
program version := 0.7.4
program date := 2002:02:18
;
!GENERAL DATA :=
!data offset in bytes := 0
!name of data file := /home/Desktop/Projects/Brain/brain_phantom.i33
patient name := hf
!patient ID := 271097
patient dob := 0000:00:00
patient sex := Unknown
!study ID := brain
exam type := pet study
data compression := none
data encode := none
;
!GENERAL IMAGE DATA :=
!type of data := Tomographic
!total number of images := 16
study date := 1997:11:28
study time := 00:00:00
imagedata byte order := LITTLEENDIAN
;
number of energy windows := 1
;
energy window [1] :=
energy window lower level [1] :=
energy window upper level [1] :=
flood corrected := N
decay corrected := N
;
!SPECT STUDY (general) :=
number of detector heads := 1
;
!number of images/energy window := 16
!process status := Reconstructed
!matrix size [1] := 32
!matrix size [2] := 32
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +8.800000e+00
scaling factor (mm/pixel) [2] := +8.800000e+00
!number of projections := 16
!extent of rotation :=
!time per projection (sec) := 0
study duration (sec) := 0
!maximum pixel count := +2.000000e+02
patient orientation := head_in
patient rotation := supine
;
!SPECT STUDY (reconstructed data) :=
method of reconstruction := Unknown
!number of slices := 16
number of reference frame := 0
slice orientation := Transverse
slice thickness (pixels) := +11.200000e+00
centre-centre slice separation (pixels) := +11.200000e+00
filter name := Unknown
filter parameters := Cutoff
method of attenuation correction := measured
scatter corrected := N
oblique reconstruction := N
!END OF INTERFILE :=
##########################################
### Panagiotis Papadimitroulas
### MSc Student, Department of Medical Physics
### University of Patras
### Greece
###
### email: panpap_5 at hotmail.com
### web page: http://www.teiath.gr/stef/tio/ni/
> Date: Tue, 24 May 2011 11:10:29 -0700
> From: yanfei_mao017 at yahoo.com
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Error in reading NCAT phantom
>
> Hi,
>
>
> I used 3D NCAT phantom for SPECT simulation. It always shows could not open header file NCAT_atn.i33. But my NCAT header file is NCAT_atn.h33, not NCAT_atn.i33. How can I solve this problem?
>
>
> Here is my code:
> /gate/world/daughters/name NCAT
> /gate/world/daughters/insert regularMatrix
> /gate/NCAT/geometry/insertReader interfile
> /gate/NCAT/interfileReader/insertTranslator range
> /gate/NCAT/interfileReader/rangeTranslator/readTable range_atten_NCAT.dat
> /gate/NCAT/interfileReader/rangeTranslator/describe 1
> /gate/NCAT/interfileReader/readFile NCAT_atn.h33
> /gate/NCAT/placement/setTranslation 0. 0. 0. mm
> /gate/NCAT/placement/setRotationAxis 1 0 0
> /gate/NCAT/placement/setRotationAngle 0 deg
> /gate/NCAT/attachVoxelPhantomSD
>
> /gate/NCAT/addOutput doseOutput
> /gate/output/doseOutput/saveUncertainty true
> /gate/output/doseOutput/setFileName outputDose.bin
>
> # SOURCE
> /gate/source/addSource voxel_NCAT voxel
> /gate/source/voxel_NCAT/reader/insert interfile
> /gate/source/voxel_NCAT/interfileReader/translator/insert range
> /gate/source/voxel_NCAT/interfileReader/rangeTranslator/readTable activity_range_NCAT.dat
> /gate/source/voxel_NCAT/interfileReader/rangeTranslator/describe 1
> /gate/source/voxel_NCAT/interfileReader/readFile NCAT_act.h33
> /gate/source/voxel_NCAT/interfileReader/verbose 1
> /gate/source/voxel_NCAT/setType backtoback
> /gate/source/voxel_NCAT/gps/particle gamma
> /gate/source/voxel_NCAT/gps/energytype Mono
> /gate/source/voxel_NCAT/gps/monoenergy 511. keV
> /gate/source/voxel_NCAT/gps/angtype iso
> /gate/source/voxel_NCAT/gps/mintheta 0. deg
> /gate/source/voxel_NCAT/gps/maxtheta 90. deg
> /gate/source/voxel_NCAT/gps/minphi 0. deg
> /gate/source/voxel_NCAT/gps/maxphi 360. deg
> /gate/source/voxel_NCAT/gps/confine NULL
> /gate/source/voxel_NCAT/setPosition 0. 0. 0. mm
> /gate/source/voxel_NCAT/dump 1
>
>
> The error message:
>
> [G4] /tracking/storeTrajectory 1
> [G4] GateDetectorConstruction::insertARFSD entered
> [G4] created a ARF Sensivitive Detector
> [G4] created command /gate/systems/SPECThead/arf/setARFStage
> [G4] GetDirectoryName()+ setHeight = /gate/hole/geometry/setHeight
> [G4] Translation speed = 0 0 .05 cm/s
> [G4] Range Translator
> [G4] Range 0 : imageValue in [ 0.000e+00 , 0.000e+00 ] ---> material Air, visibility 0, coulour (0.000e+00,0.000e+00,0.000e+00,2.000e-01)
> [G4] Range 1 : imageValue in [ 1.350e+04 , 1.350e+04 ] ---> material Lung, visibility 1, coulour (0.000e+00,1.000e+00,1.000e+00,2.000e-01)
> [G4] Range 2 : imageValue in [ 4.701e+04 , 4.701e+04 ] ---> material Body, visibility 1, coulour (0.000e+00,1.000e+00,0.000e+00,2.000e-01)
> [G4] Range 3 : imageValue in [ 5.215e+04 , 5.215e+04 ] ---> material SpineBone, visibility 1, coulour (0.000e+00,0.000e+00,1.000e+00,2.000e-01)
> [G4] Range 4 : imageValue in [ 6.554e+04 , 6.554e+04 ] ---> material RibBone, visibility 1, coulour (1.000e+00,0.000e+00,0.000e+00,2.000e-01)
> 'G4] Unrecognised type name 'unsigned integer
> [G4] Header read from 'NCAT_atn.h33'
> 'G4] Data file name 'NCAT_atn.i33
> [G4] Nb of planes: 168
> [G4] Nb of pixels per plane: 168 168
> [G4] Pixel size: 3.125e+00 3.125e+00
> [G4] Slice thickness: 3.125e+00
> [G4] Matrix size: 5.250e+02 5.250e+02
> [G4] Data type:
> [G4]
> [G4-cerr]
> '! [G4-cerr] Error: Could not open header file 'NCAT_atn.i33
> [G4] GateSourceVoxellizedMessenger::SetNewValue
> [G4] Range Translator
> [G4] Range 0 : imageValue in [ 0.000e+00 , 0.000e+00 ] ---> activity (Bq) 0.000e+00
> [G4] Range 1 : imageValue in [ 1.748e+03 , 1.748e+03 ] ---> activity (Bq) 2.000e+00
> [G4] Range 2 : imageValue in [ 3.495e+03 , 3.495e+03 ] ---> activity (Bq) 4.000e+00
> [G4] Range 3 : imageValue in [ 1.311e+04 , 1.311e+04 ] ---> activity (Bq) 1.500e+01
> [G4] Range 4 : imageValue in [ 5.243e+04 , 5.243e+04 ] ---> activity (Bq) 6.000e+01
> [G4] Range 5 : imageValue in [ 6.554e+04 , 6.554e+04 ] ---> activity (Bq) 7.500e+01
> [G4] GateSourceVoxelImageReader::ReadFile : fileName: NCAT_act.h33
> 'G4] Unrecognised type name 'unsigned integer
> [G4] Header read from 'NCAT_act.h33'
> 'G4] Data file name 'NCAT_act.i33
> [G4] Nb of planes: 168
> [G4] Nb of pixels per plane: 168 168
> [G4] Pixel size: 3.125e+00 3.125e+00
> [G4] Slice thickness: 3.125e+00
> [G4] Matrix size: 5.250e+02 5.250e+02
> [G4] Data type:
> [G4]
> [G4-cerr]
> '! [G4-cerr] Error: Could not open header file 'NCAT_act.i33
> [G4] **** Error: Volume does not exist ****
> [G4] Ignoring confine condition
> [G4] GateSourceVoxellizedMessenger::SetNewValue
> [G4] Source ---------------> voxel_NCAT
> [G4] ID : 0
> [G4] type : backtoback
> [G4] startTime (s) : 0.000e+00
> [G4] time (s) : 0.000e+00
> [G4] forcedUnstable : 0
> [G4] verboseLevel : 0
> [G4] -----------------------
> [G4] Voxel reader ----------> number of voxels : 0
> [G4] total activity (Bq) : 0.000e+00
> [G4] position (mm) : 0.000e+00 0.000e+00 0.000e+00
> [G4] voxel size (mm) : 1.000e+00 1.000e+00 1.000e+00
> [G4] Source --------------> voxel_NCAT
> [G4] ID : 0
> [G4] type : backtoback
> [G4] activity (Bq) : 0.000e+00
> [G4] startTime (s) : 0.000e+00
> [G4] time (s) : 0.000e+00
> [G4] forcedUnstable : 0
> [G4] forcedHalfLife (s) : -6.931e-01
> [G4] verboseLevel : 0
> [G4] relative to vol : World
> [G4] ----------------------
> [G4]
> [G4] GPS info ---------------->
> [G4] particle : gamma
> [G4] SourcePosType : Point
> [G4] Shape : NULL
> [G4] halfx,halfy,halfz (mm) : 0.000e+00 0.000e+00 0.000e+00
> [G4] Radius (mm) : 0.000e+00
> [G4] CentreCoords (mm) : 0.000e+00 0.000e+00 0.000e+00
> [G4] EnergyDisType : Mono
> [G4] AngleDisType : iso
> [G4] MinTheta, MaxTheta (deg) : 0.000e+00 9.000e+01
> [G4] MinPhi, MaxPhi (deg) : 0.000e+00 3.600e+02
> [G4] --------------------------
> [G4]
> [G4]
> [G4] GATE object: 'systems/SPECThead'
> [G4] Components:
> [G4]
> [G4] GATE object: 'systems/SPECThead/base'
> [G4] Attached to volume: SPECThead
> [G4] Nb of children: 1
>
> [G4] GATE object: 'systems/SPECThead/crystal'
> [G4] Attached to volume: crystal
> [G4] Nb of children: 1
>
> [G4] GATE object: 'systems/SPECThead/pixel'
> [G4] Attached to volume: ---
>
>
> List of Enabled processes:
>
>
> === Process: RayleighScattering ===
> Particle: gamma
> * Model(s):
> - PenelopeModel
>
> === Process: PhotoElectric ===
> Particle: gamma
> * Model(s):
> - StandardModel
>
> === Process: MultipleScattering ===
> Particle: e-
>
> === Process: ElectronIonisation ===
> Particle: e+
> * Model(s):
> - <!> *** Warning *** <!> No model selected!
> Particle: e-
> * Model(s):
> - StandardModel
>
> === Process: Compton ===
> Particle: gamma
> * Model(s):
> - PenelopeModel
>
> === Process: Bremsstrahlung ===
> Particle: e+
> * Model(s):
> - <!> *** Warning *** <!> No model selected!
> Particle: e-
> * Model(s):
> - StandardModel
>
>
>
>
> List of initialized processes:
>
>
>
> [Core-0] Initialization of geometry
> [G4-cerr] ERROR - G4Box()::G4Box(): NCAT_solid
> [G4-cerr] Dimensions too small ! - 0, 0, 0
> [G4-cerr]
> [G4-cerr] *** G4Exception : InvalidSetup
> [G4-cerr] issued by : G4Box::G4Box()
> [G4-cerr] Invalid dimensions. Too small.
> [G4-cerr] *** Fatal Exception *** core dump ***
> [G4-cerr]
> [G4-cerr] *** G4Exception: Aborting execution ***
>
> My NCAT_act.h33:
>
> !INTERFILE :=
> !imaging modality := nucmed
> !originating system := (X)MedCon
> !version of keys := 3.3
> date of keys := 1996:09:24
> conversion program := (X)MedCon
> program author := Erik Nolf
> program version := 0.10.7
> program date := 2010:09:15
> ;
> !GENERAL DATA :=
> original institution := NucMed
> !data offset in bytes := 0
> !name of data file := NCAT_act.i33
> patient name := Unknown
> !patient ID := Unknown
> patient dob := 0000:00:00
> patient sex := Unknown
> !study ID := Unknown
> exam type := Unknown
> data compression := none
> data encode := none
> organ := Unknown
> isotope := Unknown
> dose := 0
> NUD/Patient Weight [kg] := 0.00
> NUD/imaging modality := NM
> NUD/activity := 0
> NUD/activity start time := 00:00:00
> NUD/isotope half life [hours] :=
> 0.000000
> ;
> !GENERAL IMAGE DATA :=
> !type of data := Tomographic
> !total number of images := 168
> study date := 0000:00:00
> study time := 00:00:00
> imagedata byte order := LITTLEENDIAN
> process label := Unknown
> ;
> number of energy windows := 1
> ;
> energy window [1] :=
> energy window lower level [1] :=
> energy window upper level [1] :=
> flood corrected := N
> decay corrected := N
> ;
> !SPECT STUDY (general) :=
> number of detector heads := 1
> ;
> !number of images/energy window := 168
> !process status := Reconstructed
> !matrix size [1] := 168
> !matrix size [2] := 168
> !number format := unsigned integer
> !number of bytes per pixel := 2
> scaling factor (mm/pixel) [1] :=
> +3.125000e+00
> scaling factor (mm/pixel) [2] :=
> +3.125000e+00
> !number of projections := 168
> !extent of rotation :=
> !time per projection (sec) := 0
> study duration (sec) := 0
> !maximum pixel count := +6.553500e+04
> patient orientation := head_in
> patient rotation := supine
> ;
> !SPECT STUDY (reconstructed data) :=
> method of reconstruction := Unknown
> !number of slices := 168
> number of reference frame := 0
> slice orientation := Transverse
> slice thickness (pixels) :=
> +3.125000e+00
> centre-centre slice separation (pixels)
> := +3.125000e+00
> filter name := Unknown
> filter parameters := Cutoff
> method of attenuation correction :=
> measured
> scatter corrected := N
> oblique reconstruction := N
> !END OF INTERFILE :=
> Thank you!
> Yanfei Mao
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