[Gate-users] Problems with voxelized_phantom_source file

Wed Nov 5 18:40:54 CET 2014

Thanks David.

Regards,
Ahmed

On Wed, Nov 5, 2014 at 12:22 PM, Ana Margarida Mota <ninimota87 at gmail.com>
wrote:

> Yes, thank you! I delete the ".md5" and it was OK!
>
> The other two questions are more complicated (I guess...)
>
> 2014-11-05 17:09 GMT+00:00 David Sarrut <David.Sarrut at creatis.insa-lyon.fr
> >:
>
>> 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*
>>>>
>>>>
>>>>
>>>> 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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