[Gate-users] Interfile & Xmedcon question

Tahereh Niknejad tahereh.nik at gmail.com
Wed Mar 12 00:33:50 CET 2014


Dear Stephen,

If your XCAT phantom is generated in Linux then you should use Linux version of (x)medcon for creating interfile. And if the XCAT phantom is generated in windows then you should use windows version of (x)medcon. I had the same problem and that was the reason.

Regards,
Tahereh 


> On Mar 11, 2014, at 10:17 PM, gate-users-request at lists.opengatecollaboration.org wrote:
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> Today's Topics:
> 
>   1. Re: Interfile & Xmedcon question (Stephen Yip)
>   2. Potential bug with short time slice / low activity (Guillem Pratx)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 11 Mar 2014 22:50:28 +0100
> From: Stephen Yip <stephen.fyip1 at gmail.com>
> To: Kris Thielemans <kris.f.thielemans at gmail.com>
> Cc: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Interfile & Xmedcon question
> Message-ID:
>    <CADfqr+f5UO_c6nRSsC7NNn4Gp3gqHnSS-icCsDqrvmS-G9Rz5A at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> I did ask GATE to read the header file in the macro.
> 
> /gate/geometry/setMaterialDatabase
> /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db
> /gate/world/daughters/name phantom
> /gate/world/daughters/insert regularMatrix
> /gate/phantom/geometry/insertReader interfile
> /gate/phantom/interfileReader/insertTranslator range
> /gate/phantom/interfileReader/rangeTranslator/readTable
> /home/gate/example_PET/Gemini/test.dat
> 
> /gate/phantom/interfileReader/rangeTranslator/describe 1
> /gate/phantom/interfileReader/readFile
> /home/gate/example_PET/Gemini/m000-atn_1.h33
> /gate/phantom/placement/setTranslation 0. 0. 0. mm
> /gate/phantom/placement/setRotationAxis 1 0 0
> /gate/phantom/placement/setRotationAngle 0 deg
> /gate/phantom/attachVoxelPhantomSD
> 
> The errors just look very strange
> 
> ', assuming default BIGENDIAN'LITTLEENDIAN
> 
> 'nrecognised type name 'unsigned integer
> Header read from       '/home/gate/example_PET/Gemini/m000-atn_1.h33'
> 'Data file name         'm000-atn_1.i33
> Nb of planes:           120
> Nb of pixels per plane: 256 256
> Pixel size:             1.000e+00 1.000e+00
> Slice thickness:        2.000e+00
> Matrix size:            2.560e+02 2.560e+02
> Data type:
> Data byte order: BIGENDIAN
> 
> 
> '!ror: Could not open header file 'm000-atn_1.i33
> 
> -------- EEEE ------- G4Exception-START -------- EEEE -------
> *** G4Exception : GeomSolids0002
>      issued by : G4Box::G4Box()
> Dimensions too small for Solid: phantom_solid!
>     hX, hY, hZ = 0, 0, 0
> *** Fatal Exception *** core dump ***
> -------- EEEE -------- G4Exception-END --------- EEEE -------
> 
> 
> 
> 
> 
> On Tue, Mar 11, 2014 at 10:44 PM, Kris Thielemans <
> kris.f.thielemans at gmail.com> wrote:
> 
>> I suspect you need to pass the name of the header file to GATE, not the
>> binary file.
>> 
>> Kris
>>> -----Original Message-----
>>> From: gate-users-bounces at lists.opengatecollaboration.org
>> [mailto:gate-users-
>>> bounces at lists.opengatecollaboration.org] On Behalf Of Stephen Yip
>>> Sent: 11 March 2014 22:25
>>> To: Chaitanya Kolluru
>>> Cc: gate-users at lists.opengatecollaboration.org
>>> Subject: Re: [Gate-users] Interfile & Xmedcon question
>>> 
>>> Hi Chaitanya,
>>> 
>>> I did what you suggested. But I am getting the following error (where
>> m000-
>>> atn_1.i33 is my file name in unsigned integer 2 byte format). Do you know
>> what
>>> went wrong? Thanks!
>>> 
>>> '!ror: Could not open header file 'm000-atn_1.i33
>>> 
>>> -------- EEEE ------- G4Exception-START -------- EEEE -------
>>> *** G4Exception : GeomSolids0002
>>>      issued by : G4Box::G4Box()
>>> Dimensions too small for Solid: phantom_solid!
>>>     hX, hY, hZ = 0, 0, 0
>>> *** Fatal Exception *** core dump ***
>>> -------- EEEE -------- G4Exception-END --------- EEEE -------
>>> 
>>> 
>>> Here is my header file:
>>> 
>>> !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 := m000-atn_1.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 := 120
>>> 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 := 120
>>> !process status := Reconstructed
>>> !matrix size [1] := 256
>>> !matrix size [2] := 256
>>> !number format := unsigned integer
>>> !number of bytes per pixel := 2
>>> scaling factor (mm/pixel) [1] := +1.000000e+00
>>> scaling factor (mm/pixel) [2] := +1.000000e+00
>>> !number of projections := 120
>>> !extent of rotation :=
>>> !time per projection (sec) := 0
>>> study duration (sec) := 0
>>> !maximum pixel count := +1.704600e+04
>>> patient orientation := head_in
>>> patient rotation := supine
>>> ;
>>> !SPECT STUDY (reconstructed data) :=
>>> method of reconstruction := Unknown
>>> !number of slices := 120
>>> number of reference frame := 0
>>> slice orientation := Transverse
>>> slice thickness (pixels) := +2.00000e+00
>>> centre-centre slice separation (pixels) := +2.00000e+00
>>> filter name := Unknown
>>> filter parameters := Cutoff
>>> method of attenuation correction := measured
>>> scatter corrected := N
>>> oblique reconstruction := N
>>> !END OF INTERFILE :=
>>> 
>>> 
>>> 
>>> On Tue, Mar 11, 2014 at 8:50 PM, Chaitanya Kolluru
>>> <kolluru.chaitanya at gmail.com> wrote:
>>> 
>>> 
>>>      Hi Stephen,
>>> 
>>>      You could first compare your header file with the example header
>> file
>>> in Gate (it's in
>>> examples/example_Phantom_Source/Voxelized_phantom_source folder). It's
>>> called brain_phantom.h33
>>> 
>>>      There are four places in the header file where you give the number
>> of
>>> images value (140 in your case). They are:
>>>      Total number of images
>>>      number of images/energy window
>>>      number of projections
>>>      number of slices
>>> 
>>>      If it still doesn't work, try using this example header file
>> itself.
>> Make
>>> changes for a few fields like name of data file, scaling factor in x and
>> y, matrix
>>> size, slice thickness (this is actually in mm, not pixels as mentioned).
>>> 
>>>      Finally make sure your image file (i33) is in unsigned integer 2
>> byte
>>> format. Gate can read only that.
>>> 
>>>      Thanks,
>>>      Chaitanya.
>>> 
>>> 
>>>      On Tuesday, March 11, 2014, Stephen Yip <stephen.fyip1 at gmail.com>
>>> wrote:
>>> 
>>> 
>>>              Hello,
>>> 
>>>              For my binary XCAT phantom, I used Xmedcon to create a
>>> header (h33) and image (i33) files.
>>> 
>>>              medcon -f xcat.bin -c inf -i
>>> 
>>>              When it asked number of image? I typed 140 (number of
>> slices
>>> I have).
>>> 
>>>              Then for column and row, I entered 256, since my image is
>> 256
>>> by 256 by 140.
>>> 
>>>              However, when I tried to insert the phantom into a PET
>>> scanner, Gate always complains that one of the matrix dimensions is zero.
>>> 
>>>              I wonder if anybody knows what I did wrong.
>>> 
>>>              Thanks,
>>>              Stephen
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> ------------------------------
> 
> Message: 2
> Date: Tue, 11 Mar 2014 15:51:01 -0700
> From: Guillem Pratx <pratx at stanford.edu>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Potential bug with short time slice / low
>    activity
> Message-ID: <5CEFFAB7-1550-4CC9-B8B6-9CC92447135E at stanford.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear GATE users and developers,
> 
> I have noticed a strange behavior with PET simulations that use low counts and short time slices. In my set-up, I am simulating a point source inside the Inveon PET scanner. The activity of the point source is varied from 1 to 1000 Bq,the total run time is 100 sec, the the time slice is 0.2 s (so 500 slices).
> 
> For 1 Bq, one would expect ~ 7 counts on average but in fact I observed 23 (average over 250 realizations). For higher activity, the error is smaller but still statistically significant (see attached plot). The issue disappears around 1000 Bq or if the number of time slices is reduced to ~ 10 (instead of 500). Note that if the activity of the source is 0 Bq, then no counts are observed, so this is not a background issue.
> 
> So my question is is there an explanation for this behavior, or could this be a bug in how counts are generated within each time frame?
> 
> Thank you for your help in solving this issue.
> 
> Guillem Pratx, PhD
> _______________________________________________
> 
>   Assistant Professor            Office A247
>   Radiation Oncology            1050 Arastradero Rd
>   Stanford University             Palo Alto, CA 94304
>   http://pratxlab.stanford.edu           (650) 724-9829
> _______________________________________________
> 
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