[Gate-users] Gate on a cluster

Mon Mar 2 09:43:53 CET 2020

Hi Mohammed,

Last week I installed GATE on a shared cluster that uses the Slurm queueing system. I am not using the GATE tools to set up my runs, but I am instead starting many jobs across the cluster, each with unique random seeds, and combining their results at the end. I am happy for you to contact me if this sounds relevant to you, and happy for anyone on the list to correct me if there is something fundamentally wrong with this method!

Sam

-----Original Message-----
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> On Behalf Of gate-users-request at lists.opengatecollaboration.org
Sent: 02 March 2020 04:01
To: gate-users at lists.opengatecollaboration.org
Subject: Gate-users Digest, Vol 166, Issue 3

Send Gate-users mailing list submissions to
	gate-users at lists.opengatecollaboration.org

To subscribe or unsubscribe via the World Wide Web, visit
	http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
or, via email, send a message with subject or body 'help' to
	gate-users-request at lists.opengatecollaboration.org

You can reach the person managing the list at
	gate-users-owner at lists.opengatecollaboration.org

When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..."

Today's Topics:

   1. Gate on a cluster (Mohammed REZZOUG)
   2. Re: Gate on a cluster (Nils Krah)
   3. RE :  How to access Dicom Images of small Animals (RAT, Cat,
      Frog) (Mahdjoub Hamdi)

----------------------------------------------------------------------

Message: 1
Date: Sun, 1 Mar 2020 14:54:53 +0100
From: Mohammed REZZOUG <nmedrezz at gmail.com>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] Gate on a cluster
Message-ID:
	<CAOGFTHCCQjEg0f1rQ7BXuAgwg9hNUts++93gP4C7AuQt7KgiJw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

 Hi

I need to use Gate on a cluster but I don't know where to start.
I use vGate 8.2

MDrg
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200301/588997da/attachment-0001.html>

------------------------------

Message: 2
Date: Sun, 1 Mar 2020 16:10:01 +0100
From: Nils Krah <nils.krah at creatis.insa-lyon.fr>
To: Mohammed REZZOUG <nmedrezz at gmail.com>
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Gate on a cluster
Message-ID:
	<8528626D-989C-4784-B387-A55A275AE4D2 at creatis.insa-lyon.fr>
Content-Type: text/plain;	charset=utf-8

Have you checked the docs? 
https://opengate.readthedocs.io/en/latest/how_to_use_gate_on_a_cluster.html

Depends also in the infrastructure of the cluster you are using. What job submission system you have (like qsub).

Virtually impossible to give you a generic “do this” answer without more details. 

Nils

> On 1 Mar 2020, at 14:54, Mohammed REZZOUG <nmedrezz at gmail.com> wrote:
> 
> Hi
> 
> I need to use Gate on a cluster but I don't know where to start.
> I use vGate 8.2
> 
> MDrg
> 
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

------------------------------

Message: 3
Date: Mon, 2 Mar 2020 04:25:32 +0000
From: Mahdjoub Hamdi <mahdjoub.hamdi at hotmail.fr>
To: Atiq Ur Rahman <atiqchep at gmail.com>,
	"gate-users at lists.opengatecollaboration.org"
	<gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] RE :  How to access Dicom Images of small
	Animals (RAT, Cat, Frog)
Message-ID:
	<VE1PR09MB2992DF6759945935A2C3A502EFE70 at VE1PR09MB2992.eurprd09.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

Hi Atik,

As a quick answer, you need to convert the mouse image provided as an analyze format (*.hdr, *.img) to interfile format (*.h33, *.i33), I usually Xmedcon (available here https://xmedcon.sourceforge.io/ ).

In case you want to manipulate the images before you convert them to interfile using MATLAB or IDL, please be aware of the Endianness, if I remember well Linux uses a Big-endian bit order (you can try Little-endian).

I’m familiar with Xrays, but I think it shouldn’t be an issue, we can just modify the Xrays with the protons beam.

Please give it a try and let's see.

Thanks,

Mahdjoub

De : Atiq Ur Rahman<mailto:atiqchep at gmail.com> Envoyé le :Sunday, March 1, 2020 10:04 PM À : Mahdjoub Hamdi<mailto:mahdjoub.hamdi at hotmail.fr>
Objet :Re: [Gate-users] How to access Dicom Images of small Animals (RAT, Cat, Frog)

Hi Mahdjoub,
Thank you a lot for your detailed answer. I actually now able to do that with .hdr and .image file. As on the website you mentioned, the ct information is given in .hdr and .img format. Can you tell how we can convert a .hdr and .img  into the .h33 and .i33 format?
Actually, what I am doing is using a Proton beam to generate the positron emitter distribution using mouse phantom in one simulation and then reading it in the other PET simulation. My aim is to see the image of the Proton beam. I have physics background with a beginner level experience in Gate and image reconstruction.
Regards
Atiq

On Sat, Feb 29, 2020 at 3:12 AM Mahdjoub Hamdi <mahdjoub.hamdi at hotmail.fr<mailto:mahdjoub.hamdi at hotmail.fr>> wrote:

Hi Atik,

Sorry for the delay!

I didn't look into this couple of years ago! But here is a working example for the mouse atlas voxelized phantom.

1- Back then GATE didn't read DICOM files so I had to use Interfile format (see attached *.h33 and *.i33).

2- Since using the whole mouse phantom is computationally intensive (even with a cluster computing), I kept the chest and truncated the rest of the mouse body.

Here are responses to your questions:

How to define this file in GATEfor the given atlas data?

I've attached a file 'Voxel_mouse.mac' where you can see how I have defined the atlas data in GATE.

 All the elements are also defined in text files.

If you're not using a whole-body mouse as a voxelized phantom, you don't have to define all organ labels in the text file, you can specify just the ones that exist in the region you're studying (like brain structures for example).

My problem is, that I do not know the interval defined in the attenuation range file.

In the case of the atlas, you just add the tissue composition of each organ in the GATE material database, and then you specify these materials in the attenuation range file. I have attached an attenuation range file, for the same attached voxelized mouse phantom, take a look on it.

in the attached attenuation range file, you will find these names: SoftTissue, Heart, Water, Pancreas and here is how I have defined the Heart into the GATE material database:

Heart: d=1.05 g/cm3 ; n=11

    +el: name=Hydrogen ; f=0.104

    +el: name=Carbon ; f=0.139

    +el: name=Nitrogen ; f=0.029

    +el: name=Oxygen ; f=0.718

    +el: name=Sodium ; f=0.001

    +el: name=Phosphor ; f=0.002

    +el: name=Sulfur ; f=0.002

    +el: name=Chlorine ; f=0.002

    +el: name=Potassium ; f=0.003

    +el: name=Calcium ; f=0.0

    +el: name=Scandium ; f=0.0

I hope it helps,
Mahdjoub

De : Atiq Ur Rahman <atiqchep at gmail.com<mailto:atiqchep at gmail.com>>
Envoyé : samedi 22 février 2020 10:46
À : Mahdjoub Hamdi <mahdjoub.hamdi at hotmail.fr<mailto:mahdjoub.hamdi at hotmail.fr>>
Objet : Re: [Gate-users] How to access Dicom Images of small Animals (RAT, Cat, Frog)

Dear Mahdjoub Hamdi,
In the Atlas data file, we have three the files. In usual .dcm phantoms we use to provide an attenuation_range.txt file which is shown below. How to define this file in the gate for the given atlas data?  All the elements are also defined in a text files. My problem is , that I do not know the interval define in the attenuation range file.
[cid:image002.png at 01D5F015.AD416060]

old and New and code....
[cid:image004.png at 01D5F018.50C9C720]
Attenuation range file..
[cid:image005.png at 01D5F015.AD416060]
How I can writ new Material conversion file. The given atlas data file, materials are described but the interval or ranges are not known.
Regards
Atiq

On Sat, Feb 22, 2020 at 12:04 AM Mahdjoub Hamdi <mahdjoub.hamdi at hotmail.fr<mailto:mahdjoub.hamdi at hotmail.fr>> wrote:
Hi Atik,

Take a look here: https://neuroimage.usc.edu/neuro/Digimouse.
This is the Digimouse project, where you can find coregistered  PET/CT and cryosection mouse image plus the Atlas.
You don't have to use them as Dicom format, you can use them as an interfile format where the binary file is short integer.
I used to work with these images for small animal radiation therapy, let me know if you face any issues.

Thanks,
Mahdjoub

De : Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> de la part de Atiq Ur Rahman <atiqchep at gmail.com<mailto:atiqchep at gmail.com>>
Envoyé : vendredi 21 février 2020 06:26
À : 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>>
Objet : [Gate-users] How to access Dicom Images of small Animals (RAT, Cat, Frog)

Dear Users,
I have simulated a PET with small geometric efficiency. I want to try some animal CT dicom Images as Phantom.  Can you please point me some free online repository, database or someone share if he have for study and research purposes. I have surfed but somehow not able to find any free resource.
Regards
Atiq

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200302/b24780cf/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 5A0F2B693F624BA88F82FBA7D2698061.png
Type: image/png
Size: 6199 bytes
Desc: 5A0F2B693F624BA88F82FBA7D2698061.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200302/b24780cf/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: B0E4348CBC9E44FAA351837B60FDF334.png
Type: image/png
Size: 7943 bytes
Desc: B0E4348CBC9E44FAA351837B60FDF334.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200302/b24780cf/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 36D68299E58F43568B96BF457B19570C.png
Type: image/png
Size: 160 bytes
Desc: 36D68299E58F43568B96BF457B19570C.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200302/b24780cf/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 4C0B9EA7B80D435E8E405699308CAA2E.png
Type: image/png
Size: 186481 bytes
Desc: 4C0B9EA7B80D435E8E405699308CAA2E.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200302/b24780cf/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: B89532F1741D432AA40EF050B58B8CE5.png
Type: image/png
Size: 160 bytes
Desc: B89532F1741D432AA40EF050B58B8CE5.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200302/b24780cf/attachment-0004.png>

------------------------------

Subject: Digest Footer

_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

------------------------------

End of Gate-users Digest, Vol 166, Issue 3
******************************************