[Gate-users] Tips&Tricks regarding Voxelized Sources

[David Sarrut]

Thanks for sharing !

I do not use interfile myself, but one information could be useful: in the
new 7.1 version (in the develop branch), voxelized source can now be
.mhd/raw images which could simplify some issues encountered with
interfile. This is a first version and particularly difficult to test, so I
would be happy if someone could report (hopefully) successful or
(unfortunately) unsuccessful use.

Note that the coordinate system with voxelized source is not consistent
with all other images coordinate systems: it is not centred in the image,
but in the corner. This may change in the future.

Sincerely,
David

On Fri, Mar 20, 2015 at 9:55 AM, J.J.M. Kouwenberg <
j.kouwenberg at erasmusmc.nl> wrote:

> Dear Gergely,
>
> This was done on the latest vGate, so Gate v7.0. It might still very well
> be that I made an error somewhere. These settings just made it work for me
> on both Gate 7.0 and Gate 6.2.
>
> With kind regards,
>
> Jasper J.M. Kouwenberg
> Medical Physics Graduate student
> Nuclear Medicine
>
> E-mail j.kouwenberg at erasmusmc.nl | Phone +316 2532 9809
>
> ________________________________________
> From: gate-users-bounces at lists.opengatecollaboration.org [
> gate-users-bounces at lists.opengatecollaboration.org] on behalf of Patay
> Gergely [patay.gergely at mediso.hu]
> Sent: 20 March 2015 09:49
> To: Gate User
> Subject: Re: [Gate-users] Tips&Tricks regarding Voxelized Sources
>
> Dear Jasper,
>
> concerning the Interfile-related issues: did you use v7.0, or code from the
> development git branch? Since the 7.0 release there were some enhancements
> in
> the Interfile reader code (e.g. correct filenames, endianness and
> byte/value),
> and I wonder whether it is still buggy or not.
>
> best regards,
>   Gergely
>
> --
> Gergely Patay
> physicist
> Mediso Medical Imaging Systems Ltd.
> Hungary
>
>
>
> On 2015-03-19 17:54, J.J.M. Kouwenberg wrote:
> > Dear all,
> >
> > After many hours of frustrated keyboard smashing, I managed to find a
> number of solutions to undocumented difficulties regarding voxelized
> sources by delving through the GATE source code.
> > In order to save some of you a lot of time, I made a small list with
> tips&tricks below. I'll consider contributing to the Wiki when I get
> positive responses to this mail.
> >
> > Voxelized sources in GATE:
> >   - It seems that voxelized sources only work when combined with
> voxelized phantoms. The names of the raw data files are determined adding
> respectively _atn_[frame number].bin and _act_[frame number].bin to the
> parameter '/gate/RTVPhantom/setBaseFileName [name]'. The datafile name is
> the header file does not influence this!
> >   - The Interfile format for GATE is somewhat peculiar. Instead of
> 'matrix size [3]' and 'scaling factor (mm/pixel) [3]' for the z-axis, it
> requires respectively 'number of slices' and 'slice thickness (pixels)',
> where the latter is still given mm.
> >   - While the Interfile offers an 'imagedata byte order' option, it does
> not seem to affect the actual readout. The default is BIGENDIAN with 16
> bits per value (2 bytes). One can alter this in
> GateSourceVoxelInterfileReader.cc. Note that the _RT_ functions are used
> instead of the regular functions!! To make sure your file is read
> correctly, check the raw data file with a binary reader (GHex e.g.) and
> compare it to the 'imageValue' values in GateSourceVoxelInterfileReader.cc.
> >   - When the voxel reader returns zero voxels (number of voxels: 0), it
> means that none of the voxel values where converted to an activity higher
> than zero becquerel. It does not mean that you data file is faulty, but
> more likely that there is an error in the translation.
> >   - The maximum number of subdivisions in your TimeActivity table is 400
> (at least on the vGate system). Higher values give a segment break error.
> >   - The 'SetTimeSampling' is not the same as the spacing in your
> TimeActivity table. The code interpolates the table using the
> SetTimeSampling interval and a B-Spline. This can be changed in
> GateVSourceVoxelReader.cc.
> >   - The code for the voxelized source is quite talkative. Many of the
> outputs are coded in the two mentioned source files and are unaffected by
> verbosity. It is highly recommended to comment out the activity curve
> filling output when using large tables.
> >   - When using STIR's generate_image to generate a source, the following
> Interfile settings are recommended:
> > "output file format type:= Interfile
> >    interfile Output File Format Parameters:=
> >      number format := unsigned integer
> >      number_of_bytes_per_pixel:=2
> >      scale_to_write_data:= 1
> >      byte order:=BIGENDIAN
> >    End Interfile Output File Format Parameters:="
> >
> > This is all for now.
> >
> > With kind regards,
> >
> > Jasper J.M. Kouwenberg
> > Medical Physics Graduate student
> > Nuclear Medicine
> >
> > E-mail j.kouwenberg at erasmusmc.nl | Phone +316 2532 9809
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > .
> >
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-- 
David Sarrut, Phd
Directeur 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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