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

[RAMESHwar]

Hello Der and Simon
Thanks a lot for your advice. It worked out.
Cheers
Ramesh

On Fri, Jun 24, 2011 at 12:07 AM, Simon Stute <gate.stute at gmail.com> wrote:

> 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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