[Castor-users] SPECT reading Interfile

[Didier Benoit]

With a time value set to 0, the SPECT reconstruction should work.

In your second question, what do you exactly mean by "SYSTEM location" ? 
I'm not sure to understand. Is it your scanner system location defined 
by "CASTOR_CONFIG" during the compilation ? If it's the case you can't 
add a path in the Cdf file for the tag " Scanner name". If you want to 
create a custom scanner file you have to save it in the "CASTOR_CONFIG" 
directory.

Kind Regards,
Didier



On 04/18/2017 03:26 PM, Michael Ljungberg wrote:
>
> Dear Didier
>
> Thank you for your explanation. I think it will not be a major problem 
> to implement. For SPECT reconstructions, does the Time value be 
> clearly defined?
>
> Another related question regards the files for the system. I wonder if 
> it would be possible to allow castor-recon program to first look in 
> the local folder for a geometry file before looking in the standard 
> SYSTEM location? If I implement direct writing to the caster format in 
> the simind program, I can foresee that the SYSTEM folder can be 
> quickly filled with files.  Alternatively, is it possible to add a 
> path to the system name in the cdh file?
>
> Hälsningar / Best regards
>
> Michael
>
> *From: *Castor-users <castor-users-bounces at lists.castor-project.org> 
> on behalf of Didier Benoit <didier.benoit at inserm.fr>
> *Date: *Tuesday, 18 April 2017 at 14:52
> *To: *"castor-users at lists.castor-project.org" 
> <castor-users at lists.castor-project.org>
> *Subject: *Re: [Castor-users] SPECT reading Interfile
>
> Dear Michael,
>
> Thanks for your interest. Interfile format is only used as 
> input/output format for image (not projection data). As you have seen, 
> input data for SPECT (and also for PET) is composed of 2 files: a 
> header file (*.Cdh) and a binary file (*.Cdf) storing the data from a 
> machine or a Monte Carlo simulation. Here is some information about 
> this Cdf file. This file is not a pure histogram (a successive number 
> of counts by bin). The Data should (must) be arrange as described in 
> the “CASToR general documentation” page 30.
>
> For instance, in the case of a 64x64 float matrix for 64 angles (and I 
> consider you don't have both normalization and scatter informations), 
> your Cdf file should contain 262 144 events (64x64x64) with the 
> following format:
>
> EVENT 0:
> time: 0 (uint32_t)
> data: 32 (float/double) it's your data for a specific bin
> projection ID: 0 (uint32_t) it's the angle ID between 0 and 63 in this 
> example
> binID: 0 (uint32_t) it's the bin ID between 0 and (64x64 – 1) in this 
> example
>
> We don't provide a SPECT/PET data converter, but the easiest way to 
> create a correct Cdf file (I consider you are using C/C++) is to 
> create a struct like this:
>
> struct SPECT_CASTOR_EVENT_FORMAT {
>    uint32_t     time;
>    float          data;
>    uint32_t    projectionID;
>    uint32_t    binID;
> };
>
> and store each bin from your data in the CASToR event format.
>
> Kind Regards,
> Didier Benoit
>
> On 04/14/2017 05:34 PM, Michael Ljungberg wrote:
>
>     Dear Castor developers
>
>     I ran into this release a week ago and it is really a nice
>     contribution you have made. I have been working with Monte Carlo
>     simulations for many years developing the program simind and often
>     I get this question of supplying reconstruction software since
>     simind only produce projections. So being able to direct to your
>     webpage would be natural.
>
>     However, I dont understand how to read data into castor-recon. I
>     also use Interfile and float values so when reading in the manual
>     at you are using interfile for both input data and output gave me
>     confidence for a smooth connection. But I dont see how to actual
>     do this. I checked the spect benchmark file but the cdh format is
>     different. So my question is how I can read in for example a 64x64
>     float matrices for 64 angles stored in a data file and with an
>     associated interfile header file.
>
>     Hälsningar / Best regards
>
>     Michael Ljungberg
>
>     Lund University
>
>     Sweden
>
>
>
>
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>
>
>
> -- 
> -------------------------------------------------------------------------------
> Didier BENOIT, PhD,
> Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)
> CHRU Morvan, bâtiment 1, étage 1
> 5 Avenue Foch
> 29609 Brest
> FRANCE
> E-mail:
> didier.benoit at univ-brest.fr <mailto:didier.benoit at univ-brest.fr>
> didier.benoit at inserm.fr <mailto:didier.benoit at inserm.fr>
> Tél: +33 (0)2 98 01 81 96
> -------------------------------------------------------------------------------

-- 
-------------------------------------------------------------------------------
Didier BENOIT, PhD,
Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)
CHRU Morvan, bâtiment 1, étage 1
5 Avenue Foch
29609 Brest
FRANCE

E-mail:
didier.benoit at univ-brest.fr
didier.benoit at inserm.fr

Tél: +33 (0)2 98 01 81 96
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