[Gate-users] Moby phantom interfile reading problem in GATE

[Simon Stute]

Hey,

On Linux, the dos2unix program does the job very well without any effort !

Cheers,
Simon

On Thu, Jun 23, 2011 at 11:35 PM, Der Sarkissian Henri, Haroutune <
Henri.Der-Sarkissian at eleves.ec-nantes.fr> wrote:

> Hello Rameshwar,
>
> your problem comes from the "end of line" character which is different on
> Linux, Mac and Windows. Basically, Linux uses the "\n" code as end of line,
> while Mac used \r and Windows \r\n.
>
> All you need is to use a program like TextWrangler on MacOS, and convert
> your header file end of line to \n, then it should work properly. On Linux,
> you can use the command sed.
>
> Cheers,
> Henri Der Sarkissian
>
>
> RAMESHwar <rjhaji at gmail.com> a écrit :
>
>
>  Hello All
>> I am trying to read Moby attenuation file as interfile. This I have
>> converted as unsigned integer using Matlab.I am able to open this image
>> into
>> AMIDE or ImageJ as interfile.
>> But when I am reading as voxelised phantom in GATE it is giving error as :
>>
>> PreInit> /gate/moby_mouse/**interfileReader/readFile moby_atn16bit.h33
>> /gate/moby_mouse/**interfileReader/readFile moby_atn16bit.h33
>> 'nrecognised type name 'unsigned integer
>> Header read from       'moby_atn16bit.h33'
>> 'Data file name
>> '/usr/local/gate/gate_v5.0.0/**gate_v5.0.0/moby_atn16bit.i33
>> Nb of planes:           250
>> 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:              UNSIGNED INTEGER
>>
>> '!ror: Could not open header file 'moby_atn16bit.i33
>>
>>
>> MY HEADER is as follows:
>> ==============================**=============
>> !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 := 0.10.7
>> program date := 2010:09:15
>> ;
>> !GENERAL DATA :=
>> original institution := NucMed
>> !data offset in bytes := 0
>> !name of data file := moby_atn16bit.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 := PT
>> 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 := 250
>> 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
>> ;
>> !SPECT STUDY (general) :=
>> number of detector heads := 1
>> ;
>> !number of images/energy window := 250
>> !process status := Reconstructed
>> !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
>> !number of projections := 250
>> !extent of rotation :=
>> !time per projection (sec) := 0
>> study duration (sec) := 0
>> !maximum pixel count := +4.000000e+000
>> patient orientation := head_in
>> patient rotation := supine
>> ;
>> !SPECT STUDY (reconstructed data) :=
>> method of reconstruction := Unknown
>> !number of slices := 250
>> number of reference frame := 0
>> slice orientation := Transverse
>> slice thickness (pixels) := +1.000000e+000
>> centre-centre slice separation (pixels) := +1.000000e+000
>> filter name := Unknown
>> filter parameters := Cutoff
>> method of attenuation correction := measured
>> scatter corrected := N
>> oblique reconstruction := N
>> !END OF INTERFILE :=
>> ==============================**=========================
>> my phantom mac is :
>>
>> /gate/world/daughters/name moby_mouse
>> /gate/world/daughters/insert regularMatrix
>> /gate/moby_mouse/geometry/**insertReader interfile
>> /gate/moby_mouse/**interfileReader/**insertTranslator range
>> /gate/moby_mouse/**interfileReader/**rangeTranslator/readTable range.dat
>> /gate/moby_mouse/**interfileReader/**rangeTranslator/describe 1
>> /gate/moby_mouse/**interfileReader/readFile moby_atn16bit.h33
>> /gate/moby_mouse/placement/**setTranslation  0. 0. 0. mm
>> /gate/moby_mouse/**attachVoxelPhantomSD
>>
>> Any comment will be highly appreciated.
>> Thanks and regards
>> Ramesh
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>>
>
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