<div dir="ltr">I did ask GATE to read the header file in the macro. <div><br></div><div><div>/gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db</div><div>/gate/world/daughters/name phantom</div>
<div>/gate/world/daughters/insert regularMatrix</div><div>/gate/phantom/geometry/insertReader interfile</div><div>/gate/phantom/interfileReader/insertTranslator range</div><div>/gate/phantom/interfileReader/rangeTranslator/readTable /home/gate/example_PET/Gemini/test.dat</div>
<div><br></div><div>/gate/phantom/interfileReader/rangeTranslator/describe 1</div><div>/gate/phantom/interfileReader/readFile /home/gate/example_PET/Gemini/m000-atn_1.h33</div><div>/gate/phantom/placement/setTranslation 0. 0. 0. mm<span style="white-space:pre-wrap"> </span></div>
<div>/gate/phantom/placement/setRotationAxis 1 0 0</div><div>/gate/phantom/placement/setRotationAngle 0 deg</div><div>/gate/phantom/attachVoxelPhantomSD</div><div><br></div></div><div><span style="background-color:rgb(255,255,0)">The errors just look very strange </span></div>
<div><br></div><div><div><div>', assuming default BIGENDIAN'LITTLEENDIAN</div><div><br></div><div>'nrecognised type name 'unsigned integer</div><div> Header read from '/home/gate/example_PET/Gemini/m000-atn_1.h33'</div>
<div>'Data file name 'm000-atn_1.i33</div><div> Nb of planes: 120</div><div> Nb of pixels per plane: 256 256</div><div> Pixel size: 1.000e+00 1.000e+00</div><div> Slice thickness: 2.000e+00</div>
<div> Matrix size: 2.560e+02 2.560e+02</div><div> Data type: </div><div> Data byte order:<span style="white-space:pre-wrap"> </span> BIGENDIAN</div><div><br></div><div><br></div><div>'!ror: Could not open header file 'm000-atn_1.i33</div>
<div><br></div><div>-------- EEEE ------- G4Exception-START -------- EEEE -------</div><div>*** G4Exception : GeomSolids0002</div><div> issued by : G4Box::G4Box()</div><div>Dimensions too small for Solid: phantom_solid!</div>
<div> hX, hY, hZ = 0, 0, 0</div><div>*** Fatal Exception *** core dump ***</div><div>-------- EEEE -------- G4Exception-END --------- EEEE -------</div><div><br></div><div><br></div></div></div><div><br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Mar 11, 2014 at 10:44 PM, Kris Thielemans <span dir="ltr"><<a href="mailto:kris.f.thielemans@gmail.com" target="_blank">kris.f.thielemans@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
I suspect you need to pass the name of the header file to GATE, not the<br>
binary file.<br>
<span><font color="#888888"><br>
Kris<br>
</font></span><div><div>> -----Original Message-----<br>
> From: <a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a><br>
[mailto:<a href="mailto:gate-users-" target="_blank">gate-users-</a><br>
> <a href="mailto:bounces@lists.opengatecollaboration.org" target="_blank">bounces@lists.opengatecollaboration.org</a>] On Behalf Of Stephen Yip<br>
> Sent: 11 March 2014 22:25<br>
> To: Chaitanya Kolluru<br>
> Cc: <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
> Subject: Re: [Gate-users] Interfile & Xmedcon question<br>
><br>
> Hi Chaitanya,<br>
><br>
> I did what you suggested. But I am getting the following error (where<br>
m000-<br>
> atn_1.i33 is my file name in unsigned integer 2 byte format). Do you know<br>
what<br>
> went wrong? Thanks!<br>
><br>
> '!ror: Could not open header file 'm000-atn_1.i33<br>
><br>
> -------- EEEE ------- G4Exception-START -------- EEEE -------<br>
> *** G4Exception : GeomSolids0002<br>
> issued by : G4Box::G4Box()<br>
> Dimensions too small for Solid: phantom_solid!<br>
> hX, hY, hZ = 0, 0, 0<br>
> *** Fatal Exception *** core dump ***<br>
> -------- EEEE -------- G4Exception-END --------- EEEE -------<br>
><br>
><br>
> Here is my header file:<br>
><br>
> !INTERFILE :=<br>
> !imaging modality := nucmed<br>
> !originating system := greetings<br>
> !version of keys := 3.3<br>
> date of keys := 1996:09:24<br>
> conversion program := (X)MedCon<br>
> program author := Erik Nolf<br>
> program version := 0.7.4<br>
> program date := 2002:02:18<br>
> ;<br>
> !GENERAL DATA :=<br>
> !data offset in bytes := 0<br>
> !name of data file := m000-atn_1.i33<br>
> patient name := hf<br>
> !patient ID := 271097<br>
> patient dob := 0000:00:00<br>
> patient sex := Unknown<br>
> !study ID := brain<br>
> exam type := pet study<br>
> data compression := none<br>
> data encode := none<br>
> ;<br>
> !GENERAL IMAGE DATA :=<br>
> !type of data := Tomographic<br>
> !total number of images := 120<br>
> study date := 1997:11:28<br>
> study time := 00:00:00<br>
> imagedata byte order := LITTLEENDIAN<br>
> ;<br>
> number of energy windows := 1<br>
> ;<br>
> energy window [1] :=<br>
> energy window lower level [1] :=<br>
> energy window upper level [1] :=<br>
> flood corrected := N<br>
> decay corrected := N<br>
> ;<br>
> !SPECT STUDY (general) :=<br>
> number of detector heads := 1<br>
> ;<br>
> !number of images/energy window := 120<br>
> !process status := Reconstructed<br>
> !matrix size [1] := 256<br>
> !matrix size [2] := 256<br>
> !number format := unsigned integer<br>
> !number of bytes per pixel := 2<br>
> scaling factor (mm/pixel) [1] := +1.000000e+00<br>
> scaling factor (mm/pixel) [2] := +1.000000e+00<br>
> !number of projections := 120<br>
> !extent of rotation :=<br>
> !time per projection (sec) := 0<br>
> study duration (sec) := 0<br>
> !maximum pixel count := +1.704600e+04<br>
> patient orientation := head_in<br>
> patient rotation := supine<br>
> ;<br>
> !SPECT STUDY (reconstructed data) :=<br>
> method of reconstruction := Unknown<br>
> !number of slices := 120<br>
> number of reference frame := 0<br>
> slice orientation := Transverse<br>
> slice thickness (pixels) := +2.00000e+00<br>
> centre-centre slice separation (pixels) := +2.00000e+00<br>
> filter name := Unknown<br>
> filter parameters := Cutoff<br>
> method of attenuation correction := measured<br>
> scatter corrected := N<br>
> oblique reconstruction := N<br>
> !END OF INTERFILE :=<br>
><br>
><br>
><br>
> On Tue, Mar 11, 2014 at 8:50 PM, Chaitanya Kolluru<br>
> <<a href="mailto:kolluru.chaitanya@gmail.com" target="_blank">kolluru.chaitanya@gmail.com</a>> wrote:<br>
><br>
><br>
> Hi Stephen,<br>
><br>
> You could first compare your header file with the example header<br>
file<br>
> in Gate (it's in<br>
> examples/example_Phantom_Source/Voxelized_phantom_source folder). It's<br>
> called brain_phantom.h33<br>
><br>
> There are four places in the header file where you give the number<br>
of<br>
> images value (140 in your case). They are:<br>
> Total number of images<br>
> number of images/energy window<br>
> number of projections<br>
> number of slices<br>
><br>
> If it still doesn't work, try using this example header file itself.<br>
Make<br>
> changes for a few fields like name of data file, scaling factor in x and<br>
y, matrix<br>
> size, slice thickness (this is actually in mm, not pixels as mentioned).<br>
><br>
> Finally make sure your image file (i33) is in unsigned integer 2<br>
byte<br>
> format. Gate can read only that.<br>
><br>
> Thanks,<br>
> Chaitanya.<br>
><br>
><br>
> On Tuesday, March 11, 2014, Stephen Yip <<a href="mailto:stephen.fyip1@gmail.com" target="_blank">stephen.fyip1@gmail.com</a>><br>
> wrote:<br>
><br>
><br>
> Hello,<br>
><br>
> For my binary XCAT phantom, I used Xmedcon to create a<br>
> header (h33) and image (i33) files.<br>
><br>
> medcon -f xcat.bin -c inf -i<br>
><br>
> When it asked number of image? I typed 140 (number of slices<br>
> I have).<br>
><br>
> Then for column and row, I entered 256, since my image is<br>
256<br>
> by 256 by 140.<br>
><br>
> However, when I tried to insert the phantom into a PET<br>
> scanner, Gate always complains that one of the matrix dimensions is zero.<br>
><br>
> I wonder if anybody knows what I did wrong.<br>
><br>
> Thanks,<br>
> Stephen<br>
><br>
<br>
<br>
</div></div></blockquote></div><br></div></div>