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Hi David and Julia,</div>
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Thank you both for your suggestions. I was able to succeed at opening Dicom and MHD images. I believe the problem with my Dicom dataset was due to the matlab dicomwrite function which requires 4 dimensional image data when exporting to a single file. I exported
my data to a series of slice_****.dcm files which appears to work as expected.</div>
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In the case of Dicom data, I cannot determine which Dicom parameter tag is required for setting the spacing along the axial direction to 0.14 mm. I have set SliceThickness and SliceLocation parameters to correspond to 0.14 mm but when I load my data into a
viewer such as VV, the image imports with spacing of (0.14, 0.14, 1). Fortunately, when exporting to MHD format, I can manually edit the header to (0.14, 0.14, 0.14). If I could set this properly in the Dicom header info then I would be able to avoid the conversion
to MHD.</div>
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Another problem that I am finding is in regards to the origin. I would expect the origin to correspond to the HalfSize of the loaded data such that the image volume is centered about the origin. When loaded, I find HalfSize= (35.84,35.84,71.96) while Origin=
(-35.91,-35.91,-72.03). This appears to correspond to an offset of two slices but I am not certain if this is a problem in my data or a feature that is set in GATE.</div>
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Again, any information is greatly appreciated.</div>
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Thank you!</div>
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Matthew</div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> David Sarrut <David.Sarrut@creatis.insa-lyon.fr><br>
<b>Sent:</b> November 4, 2019 4:30 AM<br>
<b>To:</b> Matthew Strugari <matthew.strugari@dal.ca><br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> Re: [Gate-users] DICOM parameters appear incorrect</font>
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<div dir="ltr">Hi Matthew,
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<div>this is weird ... could you please try to convert your Dicom file into a MHD and try again? To see if it comes from the Dicom reader or something else ... </div>
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<div>thanks, </div>
<div>David</div>
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<div dir="ltr" class="x_gmail_attr">On Tue, Oct 29, 2019 at 5:44 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca">matthew.strugari@dal.ca</a>> wrote:<br>
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<span>Hi all,</span></div>
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<span>I am attempting to implement a voxelized phantom and voxelized source for a study on Y90 radioembolization. To prepare my dicom data I had to stitch together 3 datasets which I suspect may be causing some issues. Regardless, when I import the dicom data
into GATE using the commands below, a number of the image parameters appear incorrect when compared to the metadata (see attached image). For example, the original image is 512x512x1028 while GATE states the matrix size as 71.68x71.68x1028 and resolution as
<span>512x512x1028</span>. Also, the voxel size is incorrect as it should be 0.14 mm isotropically which causes the loaded image to appear incorrect when I include the patient-HU2mat.txt file.</span></div>
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<span>From what I can tell, my input dicom file appears okay but I am not sure what modifications are required to successfully load the dicom data. Any suggestions would be greatly appreciated.<br>
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Thank you,<br>
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<p style="margin-top:0px; margin-bottom:0px"><span style="font-family:Calibri,Helvetica,sans-serif">Matthew</span></p>
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<p style="margin-top:0px; margin-bottom:0px"><span style="font-family:Calibri,Helvetica,sans-serif"><span># Voxelized phantom<br>
</span></span></p>
<div>/gate/world/daughters/name patient<br>
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<div>/gate/world/daughters/insert ImageNestedParametrisedVolume<br>
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<span>/gate/patient/geometry/setImage kidneyData/patient.dcm</span><br>
<p></p>
<p style="margin-top:0px; margin-bottom:0px"><span style="font-family:Calibri,Helvetica,sans-serif">#/gate/patient/geometry/setHUToMaterialFile kidneyData/patient-HU2mat.txt<br>
</span></p>
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<p style="margin-top:0px; margin-bottom:0px"><span style="font-size:10.5pt; color:black; font-family:Calibri,Helvetica,sans-serif">--</span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span>
<p style="margin-top:0px; margin-bottom:0px"><span style="font-size:10.5pt; color:black; font-family:Calibri,Helvetica,sans-serif">Matthew Strugari</span><span style="font-size:10.5pt; color:black"></span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span><span style="font-size:10.5pt; color:black" lang="EN-US"><span style="font-family:Calibri,Helvetica,sans-serif">Biomedical Translational Imaging Centre -
</span><span style="background-color:rgb(255,255,255); color:black; font-family:Calibri,Helvetica,sans-serif">BIOTIC</span><span style="font-family:Calibri,Helvetica,sans-serif">,</span><br>
<span style="font-family:Calibri,Helvetica,sans-serif">5890 University Ave, </span><br>
<span style="font-family:Calibri,Helvetica,sans-serif">Halifax, NS, B3K 6R8</span></span><br>
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-- <br>
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<div dir="ltr">David Sarrut, Phd<br>
Directeur de recherche CNRS<br>
CREATIS, UMR CNRS 5220, Inserm U1206
<div>Centre de lutte contre le cancer Léon Bérard<br>
28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
<a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
_________________________________</div>
<div> "2 + 2 = 5, for extremely large values of 2"<br>
_________________________________</div>
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