[Gate-users] GATE V6.2 - Possible Bugs, including Radiotherapy Physics

[David Sarrut]

Hello Matt,

thanks for the report. The analyze reader included in Gate should be able
to read big/little endian (see file ganereal/src/GateAnalyzeHeader.cc).
However, I personally have not tested this.

Anyway, we have had (other) problems with the analyze image file format and
now advocate the use of mhd/raw (sometimes called
metaimage<http://www.itk.org/Wiki/ITK/File_Formats>)
file format instead. It has some similarity, but the header .mhd is in text
 (so useful to read/change). The .img and .raw are exactly the same data.
mhd file format allows to store origin coordinate of the images (for
example overlay of image+dose, see for example with
vv<http://vv.creatis.insa-lyon.fr>
)

Hope it helps.
David
PS: please post on the gate-users mailing list


On Thu, Feb 21, 2013 at 2:40 PM, Matt <mdbelley at gmail.com> wrote:

> Dear Dr. Sarrut,
>
> I may have encountered another bug with the radiotherapy applications in
> GATE.  The problem is encountered when using the ANALYZE image format for
> use with the Dose Actor.  I have found a temporary work-around.  I am not
> sure if the problem is with GATE itself, it may be with the way I am
> creating the ANALYZE image in ImageJ and AMIDE.
>
> I start with a raw (big-endian) ".bin" output file of a voxelized phantom
> phantom with pixel values of 0,1,2,3.
>
>    - I open this raw file (big-endian byte order) in either AMIDE or
>    ImageJ.
>    - I "Save As ANALYZE" to get two files -- a ".hdr" and a ".img" file.
>    - If I simply use these files as input to GATE, the byte order
>    (endianess) is usually wrong.  Instead of values 0,1,2,3, Gate interprets
>    the phantom values as 0, 256, 512....
>
>
>    - Here is what I have been doing as a work-around
>       - In ImageJ, I open the ANALYZE ".img" raw file with
>       "little-endian" byte order so that the values that are displayed are wrong
>       (0,256,512).
>       - I then re-save the file as ".img" to change the byte order.  Now,
>       Gate uses the correct values in the simulation of 0,1,2,3...
>
>
> I would appreciate if you are able to tell me if this is a problem with
> Gate or if it is a problem with the way I am generating the ANALYZE images.
>  It seems like Gate is not able to use the ".HDR" file to determine byte
> order.
>
> Best Regards,
> Matt
>
> On Wed, Nov 21, 2012 at 6:52 AM, David Sarrut <
> David.Sarrut at creatis.insa-lyon.fr> wrote:
>
>> Hello Matt,
>>
>> a short update regarding the potential problem with Penelope model : it
>> seems to appear when a material contains a element fraction equal to zero.
>> A bug in G4 leads to infinite loop. A workaround could be to remove those
>> line (with fraction=0) in the GateMaterialDatabase.
>>
>> hope it helps,
>> David
>>
>>
>>
> --
> Matthew Belley
>
> Doctoral Student
> Medical Physics Graduate Program, Duke University
> Duke Radiation Dosimetry Laboratory, Duke University Medical Center
>  Durham, North Carolina 27705
>



-- 
David Sarrut, Phd
Chargé de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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