[Gate-users] Ecat7 sinogram output. Cannot open it with a viewer

[Kris Thielemans]

Hi

If you use ECAT output and want to reconstruct with STIR, you should use
STIR utilities to see if everything is alright. Some suggestions:

- list_projdata_info should give accurate info. If not, you can use
ifheaders_for_ecat7 and edit the resulting Interfile text header
accordingly.
- display_projdata allows you to do a quick visual check (some problems
though on recent Ubuntu that the new window is sometimes empty)
- extract_segments writes one 3D volume per "segment", which you can then
load into Amide or so.


Kris Thielemans
Senior Research Fellow at King's College London
Honorary Lecturer at Imperial College London
Founder of Algorithms and Software Consulting Ltd




> -----Original Message-----
> From: gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-
> users-bounces at lists.opengatecollaboration.org] On Behalf Of COMTAT
> Claude
> Sent: 16 February 2012 16:42
> To: 'gate-users at lists.opengatecollaboration.org'
> Subject: Re: [Gate-users] Ecat7 sinogram output. Cannot open it with a
> viewer
> 
> Hi,
> 
> 
> 
> I'm not aware of a freely available software that would allow you to
display
> easily ecat7 sinograms. Most of the time, such software can display ecat7
> images, but not ecat7 sinograms.
> 
> 
> 
> You can try to visualize them as a flat format, using Vinci. The header
offset is
> 2048 bytes (main header --- 512, directory --- 512, and subheader ---
1024)
> and the data are stored as Big Endian. For the fist segment of HR+ data,
you
> have to specify (X : number of radial bins, Y : number of axial bins in
segment
> 0, Z : number of azimuthal bins) :
> 
> 
> 
> [cid:image002.jpg at 01CCECD2.0BFB7D20]
> 
> 
> 
> By default, an azimuthal mashing is applied to real HR+ ecat7 data (from
288
> to 144). If you use the "raw" sinogram output format, you keep your 288
> views.
> 
> 
> 
> In the raw sinogram output format, you have a series of 2D sinograms (2D
> means radial and angular), one per pair of rings in coincidence (1024 for
a 32
> rings system).
> 
> 
> 
> In the ecat7 output format, the data are organized differently and
> compressed (azimuthal and polar mashing).
> 
> 
> 
> Hope this helps,
> 
> 
> 
> Claude
> 
> 
> 
> -----Message d'origine-----
> De : gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-
> users-bounces at lists.opengatecollaboration.org] De la part de
> J.Jones at surrey.ac.uk
> Envoyé : jeudi 16 février 2012 17:13
> À :
> Objet : [Gate-users] FW: Ecat7 sinogram output. Cannot open it with a
> viewer
> 
> 
> 
> 
> 
>    Hi,
> 
> I am new to GATE and use Gate 6.1.98524.
> 
> I want to use the ecat7 module to produce ecat7 sinograms for processing
by
> STIR.
> 
> But first I would like to inspect the GATE / ecat7sinograms with a file
viewer.
> 
> 
> 
> I based my run on examples/examplePET/PET_Ecat_System.mac..
> 
> Gate produces a non-empty file yourSinogram.S but I can not view it.
> 
> With Amide 'unable to read file' is reported.
> 
> With ecatssum from Turku PET centre 'Missing Matrix/matrices' is reported.
> 
> With Vinci (Latest down loaded yesterday.) 'valid ecat7 file but wrong
plugin'.
> 
> 
> 
> Main Question: Does anybody know of a viewer that should work?
> 
> 
> 
> Whilst trying to read what is going on I noticed that 'Gate to Sinogram'
was
> reporting
> 
> 288 azimuthal bins but a few lines later GateSinoToEcat was reporting just
> 144.
> 
> Changing mashing from 2 to 1 increased the output file size but viewers
> would still
> 
> not open the yourSinogram.S file.  Does anybody think that might be
> significant?
> 
> 
> 
> Further reading led to one section of comment that indicated that 2D
> sinograms were
> 
> being built but another suggested 4D sinograms. Does anybody know which
> is correct?
> 
> 
> 
> Thanks
> 
> John
> 
> 
> 
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