[Gate-users] DICOM parameters appear incorrect

Matthew Strugari matthew.strugari at dal.ca
Mon Nov 4 21:28:14 CET 2019

Hi again,

Please disregard the latter part of the email. The origin is set correctly after updating the ImagePositionPatient Dicom tag.


From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of Matthew Strugari <matthew.strugari at dal.ca>
Sent: November 4, 2019 2:39 PM
To: David.Sarrut at creatis.insa-lyon.fr <David.Sarrut at creatis.insa-lyon.fr>
Cc: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] DICOM parameters appear incorrect

Hi David and Julia,

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.

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.

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.

Again, any information is greatly appreciated.

Thank you!

From: David Sarrut <David.Sarrut at creatis.insa-lyon.fr>
Sent: November 4, 2019 4:30 AM
To: Matthew Strugari <matthew.strugari at dal.ca>
Cc: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] DICOM parameters appear incorrect

Hi Matthew,

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 ...


On Tue, Oct 29, 2019 at 5:44 PM Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>> wrote:
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,


# 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

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David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U1206
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
 "2 + 2 = 5,  for extremely large values of 2"
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