[Gate-users] RE : CT import for voxelized phantom

[REUZE SYLVAIN]

Dear Nada,

I had the same problem a few months ago.
There is an issue with the mhd file provided in Gate example, and mhd produced by ImageJ cannot be used in Gate simulations. You should convert your dicom images into mhd using VV software. Let me know if it works.

I also expanded the range of HU in my Gate sources, and some other things for radiotherapy simulations (with input phase spaces as sources). I had to send my own source files to Gatelab in order to test a new application, so I don't know if the original version accepts my CT images.

I will send all my corrections (CT and phase space) for a new release of Gate in a few weeks.

Best regards,

--
Sylvain Reuzé
PhD student in oncology / medical physics
INSERM U1030 "Molecular Radiotherapy"
GUSTAVE ROUSSY
Radiotherapy Department
Tel: (+0033) 1 42 11 54 06
www.gustaveroussy.fr

________________________________________
De : gate-users-bounces at lists.opengatecollaboration.org [gate-users-bounces at lists.opengatecollaboration.org] de la part de Nada Fakhoury [nfachour at physics.auth.gr]
Date d'envoi : dimanche 13 septembre 2015 13:10
À : gate-users at lists.opengatecollaboration.org
Objet : [Gate-users] CT import for voxelized phantom

Dear all,

I have been struggling with an issue for quite some time now and I
cannot seem to find a solution for it.
The issue is when trying to create a voxelized phantom from a
patient's CT, I get an error for out of range Hounsfield Units from my
CT file:

|
|
|GateVImageVolume.cc (l.365):  I find H=8448 in the image, while
Hounsfield range stop at 3000
|
|

I have tried to "override" this problem by simply expanding the range
and then of course my simulation runs.
However, even though it works on my build, on my laptop, when I try to
run it on the GateLab cluster, I get another error, this time in the
HounsfieldMaterialTable.cc:

|
|
|GateHounsfieldMaterialTable.cc (l.127): Current H1=-1050 is different
from previous H2=-32768. Abort.
|
|

Now, the problem is that the only time I actually managed to run my
simulation with a CT-based phantom was when I used the .mhd file
provided in the Gate radiotherapy examples, instead of the .hdr ones
generated by the CTs I have.

At first I thought I probably should change the HU range, but in my
Dicom files the HU conversion is the default one..

Note that this problem arose in every version of Gate I installed,
whether it was 6.2, 7.0 or 7.1.. I've tried to use every solution I
could find on the user's list archive..

May it be that something goes wrong when I convert it from dicom to
.hdr? (I use ImageJ for this)

I tried converting it to .mhd but then I get again the same problem..

|
|
|GateVImageVolume.cc (l.365):  I find H=63488 in the image, while
Hounsfield range stop at 3000.
|
|

I also tried importing CTs from different modalities, but I still have
no luck..

If anyone has any thoughts, I'd really appreciate the help.


Thank you in advance for any feedback.

Nada
--
Nada Fakhoury
MSc "Medical Physics" Student

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