[Gate-users] Voxelized source

[Simon Stute]

Hi Ismet,

It appears that the voxelized source image reader, via ascii description is
bugged...
Number of voxels are not updated, so it always assumes that the total number
is 1.
That's why it just reads the first value inside your image description.

Try to use the interfile description, this one is working well !
It seems that nobody used the ascii reader since GATE was created, so the
associated classes were never updated...

Interfile is not so complicated, so don't panic ;-)

Cheers,
Simon

On Mon, Feb 21, 2011 at 11:23 AM, Ismet Isnaini <ismeth74 at yahoo.com> wrote:

>
> hi,
> Thanks for your reply.. it really help to some extent..
>
> 1. I have tried with different number of voxel point source, 10x10x1,
> 50x50x1, 100x100x1 with different size of voxel 0.6 mm, 1mm, 2mm, 5mm (for
> 10x10), but the all result is uniform projection.
>
> 2. Total activity print out in the output of GATE is, as I observed, the
> number of voxel times a number defined in the header of the ASCII voxelized
> source file. While, the total activity defined in each voxel of  the ASCII
> voxelized source file is actually higher. So, I dont really see any
> connection between that number defined in the header of the ASCII input
> file, and the real total activity contain in each voxel. But as we increase
> this number in ASCII file, acquisition takes longer time (other words,
> higher activity).
> The GATE documentation itself does not actually mentioned this total
> activity number being the header of the ASCII file, but as I run the
> experiment, after we defined the dimension of voxel and the size of voxel,
> we also need to define a number which signify the total activity.
>
> 3. Most of previous experiment is without visualizing the source. When I
> tried to visualizing the voxelized source, i could not find the source
> during visualization. I use the command (as in the manual book for
> analytical source)
>
>
> /gate/source/voxel/visualize 100 yellow 2
>
> but it always result in segmentation fault.. hence the program stop.
> Can we actually visualize a voxelized source? is there any special command
> for this ?
>
> Looking forward for your help...
>
> regards
>
>
>
> ------------------------------
> *From:* Simon Stute <gate.stute at gmail.com>
> *To:* Ismet Isnaini <ismeth74 at yahoo.com>
> *Cc:* GATE mailist <gate-users at lists.opengatecollaboration.org>
> *Sent:* Thu, February 17, 2011 6:56:55 PM
> *Subject:* Re: [Gate-users] Voxelized source
>
> Hi,
>
> Sorry, I understood the inverse from the previous mail. So you see a
> uniform projection, without point source. Did you try to set 3x3 pixels with
> higher activity (I mean like a larger point source) ?
> GATE print out the total activity concentration read into a voxelized
> source : was it the expected one, following what you set in your voxelized
> description ?
>
> And to clarify other questions : you can use an analytical phantom with a
> voxelized source, there is no problem. Also you can have voxels set to 0 in
> your voxelized activity map, there is no pb.
>
> Cheers,
> Simon
>
> On Thu, Feb 17, 2011 at 1:17 AM, Ismet Isnaini <ismeth74 at yahoo.com> wrote:
>
>>
>> Hi, Thanks for the reply..
>>
>> yes, I have tried different kind of ratio...
>> 1Kbq point source with background of 1Bq, but the result is the same.
>> ( I also read in the documentation, that the background shouldNOT be zero,
>> is
>> that right?)
>>
>> What I mean is I could not see the point source, not the background.
>> All the background seems to have high activity.. the image / sinogram is
>> just an
>> uniform square
>>
>>
>>
>> I am using an ASCII file for the input file, with a linear translator of
>> 1Bq per
>> voxel as the scale.
>>
>> Could you please explain the effect of total activity in the Voxelized
>> input
>> file in relation to the activity of individual voxel ???
>>
>> regards
>>
>>
>>
>>
>>
>>
>> ________________________________
>> From: Simon Stute <gate.stute at gmail.com>
>> To: Ismet Isnaini <ismeth74 at yahoo.com>
>> Cc: GATE mailist <gate-users at lists.opengatecollaboration.org>
>> Sent: Thu, February 17, 2011 1:56:46 AM
>> Subject: Re: [Gate-users] (no subject)
>>
>> Hi Ismet,
>>
>> You set a point/background ratio of 10000 ! it is probably the reason why
>> you do
>> not see the background in your projection.
>> Did you try to set a background activity of 1kBq, so that you get a ratio
>> of 10
>> ?
>>
>> Cheers,
>> Simon
>>
>>
>> On Wed, Feb 16, 2011 at 3:38 PM, Ismet Isnaini <ismeth74 at yahoo.com>
>> wrote:
>>
>> dear everyone...
>> >
>> >I have been running a simulation using a voxelized source (a simple point
>> source
>> >off the centre) 100x100 voxel of 1 slice.
>> >
>> >
>> >But, instead of using a voxelized phantom, I am using a a cylindrical
>> phantom
>> >and placed the voxelized source inside this phantom. Is this OK ?
>> >
>> >The result shows as if it does not recognized the low region of the
>> source (The
>> >hot area was around 10KBq, and the rest is 0 or 1 Bq, and simulation time
>> varies
>> >from 100-500 sec). The sinogram / image produced is a square of 100x100
>> voxel
>> of
>> >not uniform  activity..
>> >
>> >
>> >Can anybody suggest, what was wrong with it ?
>> >
>> >regards
>> >
>> >
>> >Ismet
>> >
>> >
>> >
>> >
>> >_______________________________________________
>> >Gate-users mailing list
>> >Gate-users at lists.opengatecollaboration.org
>> >http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>> >
>>
>>
>>
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>
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