[Gate-users] DICOM parameters appear incorrect

[Brosch, Julia]

Hi Matthew,

I am not at all an expert for dicom files as I am mainly working with "interfile" file format. But I had similar problems, when I tried to use voxelized geometry and source with Gate in interfile format. I guess in both cases, there are some small differences in either my interfile header or in some of your dicom tags compared to what Gate wants as an input.
For now, I simply use the mhd format instead and had no problems anymore. There are many ways (and softwares) to convert file formats. You could for example use amide (http://amide.sourceforge.net/index.html), which is free, to convert your dicom file into a raw image and then simply create the mhd header textfile with your image parameters.
The NAME.mhd requires these lines:

NDims = 3
DimSize = 512 512 1028
ElementSpacing = 0.14 0.14 0.14
ElementNumberOfChannels = 1
ElementByteOrderMSB = False
ElementType = MET_FLOAT
ElementDataFile = NAMEofIMAGE.raw

I hope this workaround works for you too!

Best,
Julia

Von: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> Im Auftrag von Matthew Strugari
Gesendet: Dienstag, 29. Oktober 2019 17:45
An: gate-users at lists.opengatecollaboration.org
Betreff: [Gate-users] DICOM parameters appear incorrect

Hi all,

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 512x512x1028. 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.

>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.

Thank you,

Matthew





# Voxelized phantom
/gate/world/daughters/name                                 patient
/gate/world/daughters/insert                                 ImageNestedParametrisedVolume
/gate/patient/geometry/setImage                         kidneyData/patient.dcm

#/gate/patient/geometry/setHUToMaterialFile      kidneyData/patient-HU2mat.txt





--

Matthew Strugari
Biomedical Translational Imaging Centre - BIOTIC,
5890 University Ave,
Halifax, NS, B3K 6R8
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20191029/0e688770/attachment.html>