[Gate-users] Voxelized source orientation

[Tom Buitenhuis]

Hi everyone,

I've been trying to implement a voxelized source and voxelized phantom in a
PET scanner, using GATE version 6.1 combined with GEANT version 4.9.2.p02.
This combination is not officially supported, but I've got it working and
producing reasonable output. According to the documentation (
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.1:Voxelized_Source_and_Phantom),
we can import a voxelized source using an InterFile 3.3 image, where
the
greyscale is converted to activity.The voxelized phantom can be imported
using an Analyze 7.5 image.

According to the documentation of these file formats, data is stored in
row-major order. For example, for the InterFile 3.3 format, the specs can
be found here: http://www.nucmed.si.mahidol.ac.th/nucmed1/pip/interfil1.html
Relevant section:
"I.5. IMAGE DATA

A. Image arrays are to be arranged with the first value (in the binary
data) corresponding to the pixel in the top left corner and with the value
corresponding to the pixel in the bottom right corner occurring last. Image
arrays in V3.3 remain 2-D. The order of the pixel data shall increment by
column from left to right, and then (for each such row) by row, from top to
bottom. This is also known as row major order."

more info on row-major order: http://en.wikipedia.org/wiki/Row-major_order

However, when I simulate a voxelized source, the activity seems to have the
y-axis inverted, i.e. it seems that GATE ignores this row-major part of the
InterFile specification. An example of this can be seen in the attached
image. On the left, there is a window where I display the InterFile source
in AMIDE, which correctly interprets the specs. The top, white, part of the
source has an activity of 10 Bq, where the bottom, green, part has an
activity of 500 Bq. On the right of the image, I display the root output of
the source-position of simulated coincidences, where we can see that the
top-part now has the higher activity, instead of the bottom part.

The same seems to hold for the Analyze 7.5 voxelized phantom. When we
center both the source and the phantom, this shouldn't be a problem in a
cylindrical symmetric PET-scanner, but when we translate one with respect
to the other, this could be problematic. The fix is ofcourse easy, i.e.
translate in the -y instead of the +y direction, but when this is
undocumented, incorrect simulations will be performed.

Does anyone else have any experience with this? Am I making a mistake, or
is this a bug in the implementation of the file specs in GATE?

Best regards,
Tom Buitenhuis
Kernfysisch Versneller Instituut
University of Groningen
The Netherlands
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/75f48de0/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: gateSourceOrientation.PNG
Type: image/png
Size: 82026 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/75f48de0/attachment-0001.png>