[Gate-users] ICRP 110 AF Phantom

[Matthew Strugari]

Hi Khalid,

I cannot speak to your specific error, but did you make sure to update the dataDir directory variable in the ICRPtoSTL.py file? Also, I’m not sure if you are referring to Andrew’s README.txt file for organ names, i.e. ‘liver’, but with the ICRP 110 data that I downloaded here<https://www.icrp.org/publication.asp?id=icrp%20publication%20110>, the organ names are actually tagged with their medium number, i.e. ‘liver_30’. You can verify this by uncommenting the line “data.listOrgans()” in the ICRPtoSTL.py file.

The scripts appear to be written for python2 and I was unable to execute the scripts at all due to an import error for VTK. I converted all scripts to python3 with “2to3 -w <name>.py” and implemented the following changes:


  1.  In readICRP.py
-On line 88, I replaced “words = re.split(“ *”, line)” with “words = re.split(r’\W+’, line)” to correct a ValueError which was not properly splitting the contents of line; and


  1.  In dicomToSTL.py
-On line 71, the function expects a 3x1 vector for a kernel radius but Andrew’s implementation only passes a single integer. I admit, I do not know what this radius refers to or how it is applied, maybe someone can shed some light on this, but replacing “organMask=sitk.BinaryClosingByReconstruction(organMask,30)” with “organMask=sitk.BinaryClosingByReconstruction(organMask)” or “organMask=sitk.BinaryClosingByReconstruction(organMask,[30,30,30])”  mitigates the issue and I notice no apparent difference in the output.

I have attached the modified scripts which allows me to execute a conversion, for example, with “python ICRPtoSTL.py female teeth_1” which produces STL files that can be imported into GATE.

Cheers,
Matthew

From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of Khalid Hussain <khalidhussain1134 at gmail.com>
Date: Friday, April 30, 2021 at 14:36
To: Said Kaddouch <saidkaddouch at gmail.com>, gate-users <Gate-users at lists.opengatecollaboration.org>, Andrew Robinson <andrew.robinson at npl.co.uk>
Subject: Re: [Gate-users] ICRP 110 AF Phantom
CAUTION: The Sender of this email is not from within Dalhousie.
Can anyone advise me, how can I read ICRP110 AF phantom data to generate an image to use in GATE simulation?
I got this error while running Andrew code<https://github.com/a-p-robinson/STLPhantoms>.
[cid:image001.png at 01D73DF4.46A545F0]


Sincerely,
Khalid

Regards

KHALID HUSSAIN | PhD Scholar
Universiti Putra Malaysia (UPM), Malaysia
Email:hussain.khalid at student.upm.edu.my<mailto:hussain.khalid at student.upm.edu.my>
Cell: +60-11-6455-2354

On Fri, Apr 30, 2021 at 10:31 PM Khalid Hussain <khalidhussain1134 at gmail.com<mailto:khalidhussain1134 at gmail.com>> wrote:
Dear Said,
Thank you for your email.
I think this xmedcon is used once we have voxel image and in my case, I don't have voxel phantom, I only have data downloaded from icrp.org<https://www.icrp.org/publication.asp?id=ICRP%20Publication%20110> which is in the form of .dat files and needs to be read by the program such as python program advised by Andrew but it gives some parsing/namespace error, which I am requesting to Andrew or anyone else who has used this data before.

Can anyone advise me, how can I read ICRP110 AF phantom data to generate an image to use in GATE simulation?
[cid:image001.png at 01D73DF4.46A545F0]


Sincerely,
Khalid


On Fri, Apr 30, 2021 at 3:26 AM Said Kaddouch <saidkaddouch at gmail.com<mailto:saidkaddouch at gmail.com>> wrote:
Dear khalid
To read the voxelised phantom you can use xmedcon to read the phantom and translate it to intefile or analyse format. After you can use Matlab to read your phantom format analyse. You can find matlab analyse reader in the internet.
Hop this help.
Best regards.

On Mon, Apr 26, 2021, 3:27 PM Khalid Hussain <khalidhussain1134 at gmail.com<mailto:khalidhussain1134 at gmail.com>> wrote:
Dear Gate Users,

Is there anyone who has a python or matlab code to read the ICRP110 AF phantom?

I want to request you to please share the code to read this phantom. I am trying to translate the fortran code given in readme file but I did find the detail of some functions used in fortan code provided in readme file.

Thank you for your cooperation and support.

Regards

KHALID HUSSAIN | PhD Scholar
Universiti Putra Malaysia (UPM), Malaysia
Email:hussain.khalid at student.upm.edu.my<mailto:hussain.khalid at student.upm.edu.my>
Cell: +60-11-6455-2354
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