[Gate-users] Problems with voxelized_phantom_source file

[David Sarrut]

Hello,

md5 is only the signature of the data (see en.wikipedia.org/wiki/MD5) used
to retrieve the data from the website (see my previous reply). Just ignore
the link.

If you want to change the phantom, put the file in a folder and modify the
Gate macro.

For the other error related to interfile file format, I dont know I do not
use this format.

David

On Wed, Nov 5, 2014 at 5:54 PM, Ahmed Elmekawy <ahmedfelmekawy at gmail.com>
wrote:

> Hi Ana,
>
> I believe the brain_phantom.md5 is soft link but also I don't understand
> ẃhy the user put it in soft link if you need to understant more just go to
> brain_phantom.i33 and then write $ ls -ltr brain_phantom.i33 so you will
> find the soft link.
>
> I think the problem not coming from your phantom but  you have to attach
> this soft link to your phantom specially the .i33 file.
>
> any way I have the same problem right now.
>
>
> Regards
> Ahmed
>
> On Wed, Nov 5, 2014 at 5:31 PM, Ana Margarida Mota <ninimota87 at gmail.com>
> wrote:
>
>> Dear Gate users,
>>
>> I am having some problems with GATE7. I am new at Gate so I apologize if
>> the questions I ask here are basic. I have mainly 3 questions:
>>
>> (1) In examples/example_PHANTOM_SOURCE/Voxelized_Phantom_Source/ why the
>> data file brain_phantom.i33 is brain_phantom.md5?What is the meaning of md5?
>>
>> (2) In the same folder, when I try to run mainMacro.mac, it starts
>> normally but than suddenly stops and I receive the message
>> "*GateVImageVolume.cc (l.570):  I find R=25907 in the image, while range
>> stop at 15*"
>> What's wrong?
>>
>> (3) I try to run the same file but with my voxelized source and I receive
>> the following error:
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>> *GateSourceVoxelImageReader::ReadFile : fileName: ', assuming default
>> BIGENDIAN'LITTLEENDIAN'nrecognised type name 'unsigned integer', assuming
>> default BIGENDIAN'BIGENDIAN'nrecognised type name 'unsigned integer Header
>> read from       'PET_PVC-MTC.h33' Data file name
>> 'PET_PVC-MTC.i33' Nb of planes:           176 Nb of pixels per plane: 448
>> 512 Pixel size:             5.273e-01 5.273e-01 Slice thickness:
>> 2.086e+00 Matrix size:            2.363e+02 2.700e+02 Data
>> type:               Data byte order:     BIGENDIAN **** Error: Volume does
>> not exist ****  Ignoring confine condition*
>>
>>
>> and after some lines:
>>
>>
>> **** Break *** segmentation violation*
>>
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>> My interfile is:
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>> *!INTERFILE := !imaging modality :=nucmed !originating system :=ImageJ
>> !version of keys :=3.3 !date of keys :=1992:01:01 !conversion program
>> :=ImageJ !program author :=J. Anthony Parker, MD PhD (J.A.Parker at IEEE.org)
>> !program version :=15January2002 !program date :=2002:01:15 ; !GENERAL DATA
>> := original institution := NucMed !data offset in bytes := 0 !name of data
>> file := PET_PVC-MTC.img 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 := 176 study date :=
>> 0000:00:00 study time := 00:00:00 imagedata byte order := LITTLEENDIAN
>> process label :=  ; quantification units := +1.000000e+000 NUD/rescale
>> slope := +1.000000e+000 NUD/rescale intercept := +0.000000e+000 ; 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 := 176 !process status := Reconstructed !matrix size
>> [1] := 512 !matrix size [2] := 448 !number format := unsigned integer
>> !number of bytes per pixel := 2 scaling factor (mm/pixel) [1] :=
>> +5.273440e-001 scaling factor (mm/pixel) [2] := +5.273440e-001 !number of
>> projections := 176 !extent of rotation :=  !time per projection (sec) := 0
>> study duration (sec) := 0 !maximum pixel count := +2.550000e+002 patient
>> orientation := Unknown patient rotation := Unknown ; !SPECT STUDY
>> (reconstructed data) := method of reconstruction := Unknown !number of
>> slices := 176 number of reference frame := 0 slice orientation := unknown
>> slice thickness (pixels) := +2.085925e+000 centre-centre slice separation
>> (pixels) := +2.085925e+000 filter name := Unknown filter parameters :=
>> Cutoff method of attenuation correction := measured scatter corrected := N
>> oblique reconstruction := N !END OF INTERFILE :=*
>>
>> Can anyone help me please??
>>
>> Thank you!!
>>
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>
>
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-- 
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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