[Gate-users] Sinogram from Root file

[Kris Thielemans]

Hi Marc

Ana is currently visiting UCL, so we do know about STIR utilities :-)

We tried gatepet2stir, but it didn't seem to like the GATE 7.0 output (it complained about some Root fields not being recognised) and gave no output. Ana will have the error messages so hopefully she'll find the time to send those to this list, but she's quite pressed in time right now.

So, instead, what we tried is to use the ecat sinogram output via

/gate/output/sinogram/enable
/gate/output/sinogram/setFileName MySinogramFileName

That outputs the 3D sinogram as raw floats. There's then a STIR utility (that needed fixing for the data-type) to create the corresponding Interfile header. So Ana is currently running simulations with both Root and ecat sinogram output. That seems to work ok.

However, now we're wondering if we can use an existing Root file, read that into GATE, and use the above macro to get the corresponding sinogram output. Is that possible?  For instance, I see at

http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:How_to_run_Gate#How_to_launch_DigiGate

that DigiGate can read an existing root file by using "Gate -d  < somemacro.mac" (or is it "Gate --d"?). Would that work here as well? What would the appropriate contents of that macro then be (the same as the original one with the sinogram output enabled?). I can't seem to find any documentation on the -d option, but then I don't know Gate really.

Thanks

Kris Thielemans
Senior Lecturer at University College London,
Institute of Nuclear Medicine, UCL Hospital



 
From: gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf Of Marc Chamberland
Sent: 26 November 2014 18:25
To: Ana Margarida Mota
Cc: Gate Users
Subject: Re: [Gate-users] Sinogram from Root file

Hi Ana, 

Sorta. A couple of people have written tools over the years to convert the Root output to projection data readable by STIR (for image reconstruction) and STIR provides a utility to extract sinograms from the projection data.

This program generates projection data readable by STIR: http://sourceforge.net/projects/gatepet2stir/
You can get STIR from here: http://stir.sourceforge.net

The utility extract_segments from STIR allows you to extract the sinograms (in Interfile format, so you’ll to use Amide or a similar to program to display them). 

Cheers,
Marc



__________________________

Marc Chamberland, MSc
PhD candidate
Department of Physics
Carleton University
Ottawa (ON)

On Nov 26, 2014, at 12:35, Ana Margarida Mota <ninimota87 at gmail.com> wrote:

Dear Gate users,

I would like to know if there is any way to have a sinogram from the root file??

I know we can have directly the sinogram as output, but that's not the question. 
My simulation is still running and I it would be good to analyze the sinogram from data obtained so far.

Thanks in advance!!

Regards,
Ana Margarida
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