[Gate-users] Sinogram from Root file

Fri Nov 28 15:07:03 CET 2014

Hi,

Ah, my apologies. I believe GatePet2Stir and the c code only works on cylindricalPET systems in Gate, then. Those systems are made up of components rsector, module, submodule, and crystal in Gate, whereas the ecat system only has components block and crystal.

At this point, modifying the c code probably is your best option.

Marc

On Nov 28, 2014, at 07:49, Kris Thielemans <kris.f.thielemans at gmail.com<mailto:kris.f.thielemans at gmail.com>> wrote:

Hi

This file gives us the same problems as GatePet2Stir. A closer look shows that this c file is looking for module and submodule info in the root file, while in our root file there is only block info. Indeed, in the Gate 7.0 ecat macro, there is no info on modules at all.

I think I can modify the C code accordingly but if anyone can provide pointers, or tell us why this happened, this would be great.

Kris

-----Original Message-----
From: Marc Chamberland [mailto:MarcChamberland at cmail.carleton.ca]
Sent: 27 November 2014 12:42
To: Kris Thielemans
Cc: Ana Margarida Mota; Gate Users
Subject: Re: [Gate-users] Sinogram from Root file

Hi Kris, hi Ana,

I’ve never used the DigiGate option, but it might work. However, it only
works if you have saved the Hits (and not just the coincidences or the singles)
in your Root output. You would then just use the -d (or --d? I'll check and
correct the Gate wiki, if needed) option, with the same macro you used
before (but adding the sinogram output).

Again, I'm not sure if that would work, but it's worth a try.

Another possibility is to use Ross Schmidtlein and Sadek Nehmeh's code for
generating projection data from Root output:
http://www.opengatecollaboration.org/sites/opengatecollaboration.org/file
s/Bin_GATE_v1.0.c

That's the code I've used before (and my personal preferred way of going
from Gate to STIR). You just need to put in the correct values for your
scanner.

Cheers,
Marc

__________________________

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

On Nov 26, 2014, at 17:37, Kris Thielemans <kris.f.thielemans at gmail.com>
wrote:

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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