[Gate-users] CT import for voxelized phantom

[Nada Fakhoury]

Dear Sylvain,

I did try creating the mhd file with vv and now it runs smoothly!
Thanks for the tip!!

Best regards,
Nada

Quoting REUZE SYLVAIN <SYLVAIN.REUZE at gustaveroussy.fr>:

> 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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> Gate-users at lists.opengatecollaboration.org
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-- 
Nada Fakhoury
MSc "Medical Physics" Student