<html dir="ltr"> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <style id="owaParaStyle" type="text/css">  P {margin-top:0;margin-bottom:0;}</style> </head> <body ocsi="0" fpstyle="1"> <div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Hermann, thanks for your answer. Being quite new to GATE I though struggle to change the input file format... I assume I'm suppose to change the insertReader through > /gate/myvoxelphantom/geometry/insertReader but what should I choose for a metafile input? I would though still like to find an answer to the Interfile problem, as from what I understand this is the only extension-type supported when using Voxelized Sources (which I will be doing). Is that right? Would you have any idea how to proceed in that case? Thanks again for all the help. Regards David <div style="font-family: Times New Roman; color: #000000; font-size: 16px"> <hr tabindex="-1"> <div style="direction: ltr;" id="divRpF396880">Från: Hermann Fuchs [hermann.fuchs@meduniwien.ac.at] Skickat: den 23 december 2014 18:17 Till: David Larsson; gate-users@lists.opengatecollaboration.org Ämne: Re: [Gate-users] Incorrect voxel values - Interfile import GATE </div> <div></div> <div>Hi David, have you tried the metafile (.mhd, .hdr) file format? It usually works better. Seasons greetings, Hermann <div class="gmail_quote">Am 23. Dezember 2014 17:59:13 MEZ, schrieb David Larsson <davlars@kth.se>: <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex"> <div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear GATE-users, <div style="font-family:Times New Roman; color:#000000; font-size:16px"> <div> <div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt"> I am trying to implement a voxelized phantom into my GATE-simulations for the first time, but seem to encounter problems in the Interfile-read of my script. Using a simple imageconverter ((x)medcon) I've created a test-interfile (.h33 + .i33) with a 10x10x10 matrix with voxel values ranging from 0 to 10. The conversion seems to work fine, and when I open to generated interfile-set in a random image viewer (ImageJ/MATLAB) I can see that the voxel values are preserved (ranging from 0 - 10). However, when I run my script I notice that the loader does not import the voxels as ranging from 0-10, instead I can see (through the error messages) that all voxels are given one value (in this specific case 9280). The original values and the corresponding input structure is therefore lost. I've tried to compare my generated code to the (working) example with the hof_brain but cannot seem to understand the problem. I've provided the essential parts of the mac-files and the interfile-header of my testfile below. Can anyone identify what the problem might be? ----------------------------main.mac---------------------------------------- # WORLD /gate/world/geometry/setXLength 400. cm /gate/world/geometry/setYLength 400. cm /gate/world/geometry/setZLength 400. cm # VOXEL PHANTOM /gate/world/daughters/name teststack /gate/world/daughters/insert fictitiousVoxelMap /gate/teststack/geometry/insertReader interfile /gate/teststack/interfileReader/insertTranslator range /gate/teststack/interfileReader/rangeTranslator/readTable attenuation_range.dat /gate/teststack/interfileReader/rangeTranslator/describe 1 /gate/teststack/interfileReader/readFile testintf.h33 /gate/teststack/placement/setTranslation 0. 0. 0. mm /gate/teststack/placement/setRotationAxis 1 0 0 /gate/teststack/placement/setRotationAngle 0 deg /gate/teststack/attachVoxelPhantomSD -------------------attenuation_range.dat-------------------------- 5 0 1 Air false 0.0 0.0 0.0 0.0 1 2 Water true 1.0 0.0 0.0 0.0 2 3 Water true 1.0 0.0 0.0 0.0 4 9280 Water true 1.0 0.0 0.0 0.2 9280 9280 Air true 1.0 0.0 0.0 0.2 #This changed for visualisation of incorrect values ------------------------- testintf.h33-------------------------- !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 := 0.13.0 program date := 2013:06:23 ; !GENERAL DATA := original institution := NucMed !data offset in bytes := 0 !name of data file := m000-testnew.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 := 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 := 10 study date := 0000:00:00 study time := 00:00:00 imagedata byte order := LITTLEENDIAN process label := ; 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 := 10 !process status := Reconstructed !matrix size [1] := 10 !matrix size [2] := 10 !number format := long float !number of bytes per pixel := 8 scaling factor (mm/pixel) [1] := +10.000000e+00 scaling factor (mm/pixel) [2] := +10.000000e+00 !number of projections := 10 !extent of rotation := !time per projection (sec) := 0 study duration (sec) := 0 !maximum pixel count := +1.000000e+01 patient orientation := Unknown patient rotation := Unknown ; !SPECT STUDY (reconstructed data) := method of reconstruction := Unknown !number of slices := 10 number of reference frame := 0 slice orientation := unknown slice thickness (pixels) := +10.000000e+00 centre-centre slice separation (pixels) := +1.000000e+00 filter name := Unknown filter parameters := Cutoff method of attenuation correction := measured scatter corrected := N oblique reconstruction := N !END OF INTERFILE := ---------------------------------------------------------------------------- Best regards, David </div> </div> </div> </div> <pre class="k9mail"><hr> Gate-users mailing list Gate-users@lists.opengatecollaboration.org <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></pre> </blockquote> </div> </div> </div> </div> </body> </html>