[Gate-users] Problems with voxelized_phantom_source file

Wed Nov 5 18:22:06 CET 2014

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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