[Gate-users] error with voxelized phantom: unrecognised type name'unsigned integer

[Ravindranath, Bosky]

Hi,
I see the exact same error with the Hoffmann phantom provided with Gate as well.
Bosky






-----Original Message-----
From: Park MinJae [mailto:MJ at ToTi.us]
Sent: Wed 3/26/2008 9:12 PM
To: Ravindranath, Bosky; gate-users at lists.healthgrid.org
Subject: RE: [Gate-users] error with voxelized phantom: unrecognised type name'unsigned integer
 
Dear Ravindranath,

I do not remember what the problem was...

but there was a problem with converting into interfile by xmedcon...

Converted file by xmedcon did not work on Gate interfile reader...

Therefore, I changed parameters of well-working interfile header...

Good Luck,
MJ

//=================================================
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//  SNU BME Ph.D. Candidate
//
//  DialTo:+82-17-711-7809
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-----Original Message-----
From: gate-users-bounces at lists.healthgrid.org
[mailto:gate-users-bounces at lists.healthgrid.org] On Behalf Of Ravindranath,
Bosky
Sent: Thursday, March 27, 2008 5:12 AM
To: gate-users at lists.healthgrid.org
Subject: [Gate-users] error with voxelized phantom: unrecognised type
name'unsigned integer

Hello List,

 

I am getting some errors while using the interfile input file as a voxelised
phantom. Initially I created a ncat phantom (4 byte float, raw binary),
converted that to unsigned integer 16 in matlab and then converted that to
the interfile format in xmedcon. This file was used as a voxelized phantom
as shown below:

 

###############################################

 

/gate/world/daughters/name test

/gate/world/daughters/insert parameterizedBoxMatrix

/gate/test/geometry/insertReader interfile

/gate/test/interfileReader/insertTranslator range

/gate/test/interfileReader/rangeTranslator/readTable range.dat

/gate/test/interfileReader/rangeTranslator/describe 1

/gate/test/interfileReader/readFile test1_uint16_1_slice.h33 

/gate/test/placement/setTranslation  0. 0. 0. mm

/gate/test/placement/setRotationAxis 0 0 0  

/gate/test/placement/setRotationAngle 0 deg

/gate/test/attachVoxelPhantomSD

 

###############################################

 

I added the above component in the PET_Ecat_System macro found in the
"examples" folder in Gate just to make sure that there are no issues with
other sections of my code.

 

Upon execution, I get the following error:

 

'nrecognised type name 'unsigned integer

 Header read from       'test1_uint16_1_slice.h33'

'Data file name         'test1_uint16_1_slice.i33

 Nb of planes:           1

 Nb of pixels per plane: 128 128

 Pixel size:             1.000e+00 1.000e+00

 Slice thickness:        1.000e+00

 Matrix size:            1.280e+02 1.280e+02

 Data type:              

 

 

'!ror: Could not open header file 'test1_uint16_1_slice.i33

ERROR - G4Box()::G4Box(): test_S

        Dimensions too small ! - 0, 0, 0

 

*** G4Exception : InvalidSetup

      issued by : G4Box::G4Box()

Invalid dimensions. Too small.

*** Fatal Exception *** core dump ***

 

*** G4Exception: Aborting execution ***

Abort (core dumped)

 

 

 

 

 

I see the  same error when I use the Hoffmann phantom provided with gate as
well. 

I have seen a couple of posts with exactly the same problem, and I'm
wondering if they could get around this error (its unclear from the thread).

 

I'm quite sure that my data is in the correct format - uint16  since my file
size matches with :->total number of voxels * 2 bytes

 

Any suggestions appreciated.

 

Thanks.

Bosky

 

 

 

Below is the header of my ncat phantom file:

 

 

!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 := 0.10.3
program date := 2008:03:01
;
!GENERAL DATA :=
original institution := UZGENT
!data offset in bytes := 0
!name of data file := test1_uint16_1_slice.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 := Static
!total number of images := 1
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
;
!STATIC STUDY (General) :=
number of images/energy window := 1
;
!Static Study (each frame) :=
!image number := 1
!matrix size [1] := 128
!matrix size [2] := 128
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +1.000000e+000
scaling factor (mm/pixel) [2] := +1.000000e+000
image duration (sec) := 0.000000e+000
image start time := 00:00:00
label := Unknown
!maximum pixel count := +2.000000e+001
!minimum pixel count := +0.000000e+000
!number of slices := 1
slice thickness (pixels) := +1.000000e+00
centre-centre slice separation (pixels) := +1.000000e+00
!END OF INTERFILE :=
^Z

 

 

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