[Gate-users] Question about the Thermal Actor and ITK

Tue Apr 21 20:10:09 CEST 2020

Dear Simon
After installing git-lfs  I deleted GateContribute in the folder of gate-8.2 then I copied the URL of this page:

https://github.com/OpenGATE/GateContrib
Then In the terminal using the command
git clone https://github.com/openGate/GateContrib
I located the clone. Then Inside the folder of GateContrib/ imaging/Thermal
I run the Thermal.mac
But I took error, Should I compile the Gate again or do anything else.
The folder of Thermal in the Imaging folder has these files "

[cid:6a737841-dbf5-4649-9a23-b01816e11b5e][cid:3241bd22-0ba6-44d4-9dd3-ffb5c4fadca3]
[cid:9c0b23fe-4df6-4000-aacc-fb9984c83f18]

In the folder of Thermal and for the Thermal mac there is no Readme text but in the folder of Contrib, there is.

I would be thankful if you provide me with your giudance.
Best

Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

________________________________
From: Simon Rit <simon.rit at creatis.insa-lyon.fr>
Sent: Tuesday, April 21, 2020 4:19 PM
To: Somayeh Asadi <somayeh.asadi at polimi.it>
Cc: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Question about the Thermal Actor and ITK

This is just a warning, and a quick google search indicates that you can probably ignore it, see, e.g., here<https://stackoverflow.com/questions/48392440/git-lfs-clone-vs-git-clone>. Did it solve your issue?

On Tue, Apr 21, 2020 at 4:11 PM Somayeh Asadi <somayeh.asadi at polimi.it<mailto:somayeh.asadi at polimi.it>> wrote:
Dear Simon
I really appreciate your help and your time. I tried to do what you said. Following the instructor in this link"

readme.md<https://github.com/OpenGATE/GateContrib/blob/master/readme.md>
I have started to download the git, in the terminal I took this message is it matter or not?
Warning"
git lfs clone' is deprecated and will not be updated with new flags from 'git clone'

Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

________________________________
From: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Sent: Tuesday, April 21, 2020 3:51 PM
To: Somayeh Asadi <somayeh.asadi at polimi.it<mailto:somayeh.asadi at polimi.it>>
Cc: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: Re: [Gate-users] Question about the Thermal Actor and ITK

I provided the link to readme.md<https://github.com/OpenGATE/GateContrib/blob/master/readme.md>! It's the first page on the github repository and it's always a good idea to read it first (hence the name). So delete your GateContrib, install git-lfs and clone the repository.

On Tue, Apr 21, 2020 at 3:45 PM Somayeh Asadi <somayeh.asadi at polimi.it<mailto:somayeh.asadi at polimi.it>> wrote:
Dear Simon
Thank you very much for your prompt response and a very good idea.
When I installed the Gate in the GateContrib-master folder there were different examples for dosimetry, imaging...., It was a ready written program and there was no Readme.txt file inside.
I think you right but I don't know where I find this file from and install in the related path for Thermal.
Could you please guide me in this regard.
I would be so grateful if you provide me with your guidance.

Best

GateContrib-master

Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

________________________________
From: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Sent: Tuesday, April 21, 2020 3:32 PM
To: Somayeh Asadi <somayeh.asadi at polimi.it<mailto:somayeh.asadi at polimi.it>>
Cc: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: Re: [Gate-users] Question about the Thermal Actor and ITK

Hi,
Have you installed git-lfs first (see readme.md<https://github.com/OpenGATE/GateContrib/blob/master/readme.md>)? Because it looks like it cannot read the file and if output/Mobydose-AbsorptionMap.mhd is there, maybe output/Mobydose-AbsorptionMap.raw isn't because you have not installed git-lfs.
Simon

On Tue, Apr 21, 2020 at 3:25 PM Somayeh Asadi <somayeh.asadi at polimi.it<mailto:somayeh.asadi at polimi.it>> wrote:
Dear Gate User
For the ready program related to thermal therapy with the name of thermaltherapy.mac in the folder of Imaging/Thermal in the subfolder of GateContrib-master, there is an error that seems to be related to ITK.
the error is:
terminate called after throwing an instance of 'itk::ImageFileReaderException'
  what():  /home/BuildFiles/ITK/InsightToolkit-5.0.0-Source/Modules/IO/ImageBase/include/itkImageFileReader.hxx:136:
 Could not create IO object for reading file output/Mobydose-AbsorptionMap.mhd
  Tried to create one of the following:
    GDCMImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.
Aborted (core dumped)

I have downloaded and tried the ITK both the versions of 5.0.1 and 14.2, but after compiling the Gate with them I get the error.
For downloading the ITK, I use this link:
https://itk.org/download/
I have recently check it with the ITK version 4.13.2 but I couldn't download all the related files.
Has any person had the same problem and experience with the thermal actor?
Has any person used the ITK version 5 and work with the thermal actor in which he/she didn't get any error?

Thank you very much for your time and any suggestion.

Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

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