<html dir="ltr"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> </head> <body style="background-color:rgb(255,255,255); line-height:initial" fpstyle="1" ocsi="0"> <div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"> <div> <div style="font-family:Tahoma; font-size:13px"><span lang="sv"> <div style="margin:0">Hi Albert,</div> <div style="margin:0"><br> </div> <div style="margin:0">I was suspecting that this might have been the problem. If you do have a working script to convert long float interfile data to "GATE-compatible" unsigned integer that you don't mind sharing, that would be very helpful. Hopefully this will resolve my issue.</div> <div style="margin:0"><br> </div> <div style="margin:0">Thanks again and Merry Christmas,</div> <div style="margin:0"><br> </div> <div style="margin:0">David</div> <div style="margin:0"><br> </div> <div style="margin:0"><br> </div> </span></div> </div> <div style="font-family: Times New Roman; color: #000000; font-size: 16px"> <hr tabindex="-1"> <div id="divRpF496170" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>Från:</b> Albert Hirtl [albert.hirtl@meduniwien.ac.at]<br> <b>Skickat:</b> den 23 december 2014 23:31<br> <b>Till:</b> David Larsson; gate-users@lists.opengatecollaboration.org<br> <b>Ämne:</b> AW: [Gate-users] Incorrect voxel values - Interfile import GATE<br> </font><br> </div> <div></div> <div> <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" 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=""><style id="owaParaStyle" type="text/css">  </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> </div> </div> </div> </body> </html>