<html><head></head><body ocsi="0" fpstyle="1" data-blackberry-caret-color="#00a8df" style="background-color: rgb(255, 255, 255); line-height: initial;"><div style="font-size: initial; text-align: initial; width: 336px; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125);">Hi David,</div><div style="font-size: initial; text-align: initial; width: 336px; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125);"><br name="BB10" caretmarkerset="INVALID" class="markedForCaretMarkerRemoval"></div><div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, 'Slate Pro', sans-serif; font-size: initial; text-align: initial; line-height: initial;">Reading voxelized ‎sources can be nasty. One part of your problem is related to your interfile data which is long float. You need unsigned integer for Gate to do well. I usually do the conversion with a small python script, which I could share if you liked.</span></div><div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, 'Slate Pro', sans-serif; font-size: initial; text-align: initial; line-height: initial;"><br></span></div><div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, 'Slate Pro', sans-serif; font-size: initial; text-align: initial; line-height: initial;">I hope this helps.</span></div><div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, 'Slate Pro', sans-serif; font-size: initial; text-align: initial; line-height: initial;"><br></span></div><div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, 'Slate Pro', sans-serif; font-size: initial; text-align: initial; line-height: initial;">Cheers,</span></div><div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, 'Slate Pro', sans-serif; font-size: initial; text-align: initial; line-height: initial;">Albert</span></div> <div style="width: 100%; font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"><br style="display:initial"></div> <div style="font-size: initial; font-family: Calibri, 'Slate Pro', sans-serif; color: rgb(31, 73, 125); text-align: initial; background-color: rgb(255, 255, 255);"></div> <table width="100%" style="background-color:white;border-spacing:0px;"> <tbody><tr><td colspan="2" style="font-size: initial; text-align: initial; background-color: rgb(255, 255, 255);"> <div id="_persistentHeader" style="border-style: solid none none; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding: 3pt 0in 0in; font-family: Tahoma, 'BB Alpha Sans', 'Slate Pro'; font-size: 10pt;"> <div><b>Von: </b>David Larsson</div><div><b>Gesendet: </b>Dienstag, 23. Dezember 2014 18:01</div><div><b>An: </b>gate-users@lists.opengatecollaboration.org</div><div><b>Betreff: </b>[Gate-users] Incorrect voxel values - Interfile import GATE</div></div></td></tr></tbody></table><div style="border-style: solid none none; border-top-color: rgb(186, 188, 209); border-top-width: 1pt; font-size: initial; text-align: initial; background-color: rgb(255, 255, 255);"></div><br><div id="_originalContent" style=""> <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> <div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear GATE-users,<br> <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"><br> 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.<br> <br> 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).<br> <br> 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.<br> <br> 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?<br> <br> ----------------------------main.mac----------------------------------------<br> <br> # WORLD <br> /gate/world/geometry/setXLength 400. cm<br> /gate/world/geometry/setYLength 400. cm<br> /gate/world/geometry/setZLength 400. cm<br> <br> # VOXEL PHANTOM<br> <br> /gate/world/daughters/name teststack<br> /gate/world/daughters/insert fictitiousVoxelMap<br> /gate/teststack/geometry/insertReader interfile<br> /gate/teststack/interfileReader/insertTranslator range<br> /gate/teststack/interfileReader/rangeTranslator/readTable attenuation_range.dat <br> /gate/teststack/interfileReader/rangeTranslator/describe 1<br> /gate/teststack/interfileReader/readFile testintf.h33<br> /gate/teststack/placement/setTranslation 0. 0. 0. mm<br> /gate/teststack/placement/setRotationAxis 1 0 0<br> /gate/teststack/placement/setRotationAngle 0 deg<br> /gate/teststack/attachVoxelPhantomSD<br> <br> -------------------attenuation_range.dat--------------------------<br> <br> 5<br> 0 1 Air false 0.0 0.0 0.0 0.0<br> 1 2 Water true 1.0 0.0 0.0 0.0<br> 2 3 Water true 1.0 0.0 0.0 0.0<br> 4 9280 Water true 1.0 0.0 0.0 0.2<br> 9280 9280 Air true 1.0 0.0 0.0 0.2 #This changed for visualisation of incorrect values<br> <br> ------------------------- testintf.h33--------------------------<br> <br> !INTERFILE := <br> !imaging modality := nucmed <br> !originating system := (X)MedCon <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 := 0.13.0 <br> program date := 2013:06:23 <br> ; <br> !GENERAL DATA := <br> original institution := NucMed <br> !data offset in bytes := 0 <br> !name of data file := m000-testnew.i33 <br> patient name := Unknown <br> !patient ID := Unknown <br> patient dob := 0000:00:00 <br> patient sex := Unknown <br> !study ID := Unknown <br> exam type := Unknown <br> data compression := none <br> data encode := none <br> organ := Unknown <br> isotope := Unknown <br> dose := 0 <br> NUD/Patient Weight [kg] := 0.00 <br> NUD/imaging modality := NM <br> NUD/activity := 0 <br> NUD/activity start time := 00:00:00 <br> NUD/isotope half life [hours] := 0.000000 <br> ; <br> !GENERAL IMAGE DATA := <br> !type of data := Tomographic <br> !total number of images := 10 <br> study date := 0000:00:00 <br> study time := 00:00:00 <br> imagedata byte order := LITTLEENDIAN <br> process label := <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 := 10 <br> !process status := Reconstructed <br> !matrix size [1] := 10 <br> !matrix size [2] := 10 <br> !number format := long float <br> !number of bytes per pixel := 8 <br> scaling factor (mm/pixel) [1] := +10.000000e+00 <br> scaling factor (mm/pixel) [2] := +10.000000e+00 <br> !number of projections := 10 <br> !extent of rotation := <br> !time per projection (sec) := 0 <br> study duration (sec) := 0 <br> !maximum pixel count := +1.000000e+01 <br> patient orientation := Unknown <br> patient rotation := Unknown <br> ; <br> !SPECT STUDY (reconstructed data) := <br> method of reconstruction := Unknown <br> !number of slices := 10 <br> number of reference frame := 0 <br> slice orientation := unknown <br> slice thickness (pixels) := +10.000000e+00 <br> centre-centre slice separation (pixels) := +1.000000e+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> Best regards,<br> <br> David <br> </div> </div> </div> </div> <br></div></body></html>