[Gate-users] How to import NCAT phantom to Gate (NCAT phantom with ECAT PET)(X-ray CT simulation manual)

Fri Feb 7 12:32:38 CET 2020

Dear Howard,

There is no GATE example combining NCAT 4D phantom with a CT scanner. 
Therefore, you should implement the NCAT 4D phantom into a CT scanner by yourself.
Once you build your own CT scanner in GATE, the NCAT 4D phantom could be implemented easily.

Let me answer your questions.

1. Is NCAT phantom included in GATE? In other words, do I need to download any data files in order to use it?
Answer: You can find the NCAT phantom files in the GATE example folders.(slide#4-5)

2. How is the respiratory motion implemented with the phantom?
Answer: The respiratory motion is implemented with the phantom (0.1 s/frame)
           If you open the slide#9, then you can see the motion of the NCAT phantom.

3. I know Duke Univ/Johns Hopkins Univ jointly developed 4D XCAT phantoms for Monte Carlo simulation. Does NCAT phantom have to do with them?
Answer: You can use NCAT phantom in GATE as your preference. 
            But you need a software licence to use XCAT phantoms.

Hopefully, my answers would be helpful for your questions.
Best regards,

Han Gyu Kang, Ph.D.

Imaging Physics Group, NIRS-QST, Japan.

-----Original Message-----
From: "Howard"<lomahu at gmail.com>
To: "강한규"<lovehangulp at naver.com>;
Cc: <gate-users at lists.opengatecollaboration.org>;
Sent: 2020-02-06 (목) 23:47:15 (GMT+09:00)
Subject: Re: [Gate-users] How to import NCAT phantom to Gate (NCAT phantom with ECAT PET)(X-ray CT simulation manual)

Dear Dr. Kang,

Thank you for your quick reply. The manual in your attachment is mainly for regular X-ray CT simulation without NCAT phantom implementation. What I am interested in is the application of NCAT phantom in CT simulation. Particularly I have the following questions:

1. Is NCAT phantom included in GATE? In other words, do I need to download any data files in order to use it?
2. How is the respiratory motion implemented with the phantom?
3. I know Duke Univ/Johns Hopkins Univ jointly developed 4D XCAT phantoms for Monte Carlo simulation. Does NCAT phantom have to do with them?

I would greatly appreciate it if you can help with these questions or point me to anybody who can help. 

Best regards,

Howard

On Thu, Feb 6, 2020 at 12:30 AM 강한규 <lovehangulp at naver.com> wrote: 

Dear Howard,

Attached is the manual of GATEv6.2 X-ray CT simulation with a non-voxelized phantom. 
I'm sorry that the manual is written in Korean. 
If you need an English version, please let me know.

You can also perform X-ray CT simulation with a voxelized phantom as below.
The GATE output (projection data) was reconstructed with OSCaR software.
In my opinion, the NCAT phantom could also be implemented easily by modifying the GATE macro files.(Please refer the my previous mail about NCAT phantom)

Hopefully, my answers would be helpful for your X-ray CT simulation with NCAT voxelized phantom.

If you have any question, please let me know.

Best regards,

Han Gyu Kang, Ph.D.

Imaging Physics Group, NIRS-QST, Japan.

-----Original Message-----
From: "Howard"<lomahu at gmail.com>
To: "강한규"<lovehangulp at naver.com>;
Cc: <gate-users at lists.opengatecollaboration.org>;
Sent: 2020-02-06 (목) 12:02:28 (GMT+09:00)
Subject: Re: [Gate-users] How to import NCAT phantom to Gate (NCAT phantom with ECAT PET)

Hi Dr. Kang,

I am trying to simulate respiratory motion with X-ray CT. It appears from the GATE documentation page that NCAT phantom can be used:

https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#real-time-motion-management-for-voxellized-source-and-phantom

However, the above page only shows for emission imaging, also from your posting. I wonder whether it is possible for CT simulation. Thank you very much for any help.

Best regards,

Howard

On Mon, Jan 13, 2020 at 9:48 PM 강한규 <lovehangulp at naver.com> wrote: 

Dear Jalil,

I have an experience in importing NCAT phantom into GATE before.

Attached is the manual how to use NCAT phantom with an ECAT PET system in GATEv6.2 (not vGATE).
(I'm sorry that the manual was written in Korean.) 

The NCAT phantoms (activity and attenuation bin files) are located on the "data" folder.(slide#8-9) 
The "rangeTranslator" was used for the mapping of the voxel value of the NCAT phantom to radioactivity (slide#10) and material type (slide#11). 

The voxelized NCAT phantom (atn.bin) was imported by using "regularMatrix" command.(slide#20)
The voxelized NCAT source (acti.bin) was imported by using "RTVPhantom" command.(slide#25-26)

Hopefully, the manual would be helpful for your research work. 

If you have any question, please let me know.

Best regards,

Han Gyu Kang, Ph.D.

Imaging Physics Group, NIRS-QST

-----Original Message-----
From: "Jalil Pirayesh"<pirayeshj at gmail.com>
To: <gate-users at lists.opengatecollaboration.org>;
Cc:
Sent: 2020-01-13 (월) 22:32:05 (GMT+09:00)
Subject: [Gate-users] How to import NCAT phantom to Gate

Dear vGate users,

Could someone please guide me on how to import the NCAT phantom files (XX_atn_av.bin and XX_act_av.bin) to the vGate phantom.mac without transferring to interfile and/or analyze format? in other words, how to prepare a phantom.mac with the files?
Regards
Jalil 

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