[Castor-users] SPECT reading Interfile
Carlier Thomas
thomas.carlier at chu-nantes.fr
Mon Apr 24 18:34:24 CEST 2017
Dear Michael,
The attenuation coefficient is in cm-1 as explicitly specified in the
manual. The attenuation map was extracted directly from the Siemens
computation which uses (as you assume) a wide beam approach. The correct
value should be the one you mention for the methodology used by CASToR.
I apologize for this misunderstanding and a correct mu-map will be
uploaded soon.
Thanks for pointing out this small error.
Best regards
Thomas Carlier
Le 19/04/2017 à 16:42, Michael Ljungberg a écrit :
>
> Dear Simon and Didier
>
> Thank you for your comments and information. I have now written a
> conversion program between simind interfiles and castor and I can
> reconstruct images :-) . I have a final question for the moment and
> that concerns the units of the mu map. I assume it is mu (cm-1) for
> the current photon energy. When I looked at the SPECT benchmark file
> the average value in a ROI is however, around 0.128 cm-1 instead of
> 0.154 which is this the linear attenuation coefficient for water. Is
> this an ‘effective attenuation coefficient map’ with lower values with
> the purpose of compensate for presence of scatter? I just want to be
> clear about what values the mu-map should reflect.
>
> Hälsningar / Best regards
>
> Michael
>
> *From: *Castor-users <castor-users-bounces at lists.castor-project.org>
> on behalf of Simon Stute <simon.stute at cea.fr>
> *Date: *Tuesday, 18 April 2017 at 17:26
> *To: *"castor-users at lists.castor-project.org"
> <castor-users at lists.castor-project.org>
> *Subject: *Re: [Castor-users] SPECT reading Interfile
>
> Hello,
>
> The castor configuration folder also contains other configuration
> files, so it is not only related to the scanner geometries.
>
> However, a third possibility is to copy the whole 'config' folder (it
> is light) into your working directory, put your geom files inside the
> 'scanner' sub-folder and then you can use the '-conf
> ./your_config_folder' option to overload the path of the configuration
> directory at run-time.
>
> The '-conf' option is described when calling 'castor-recon -help-misc'.
>
> Regards
> Simon
>
>
> Le 18/04/2017 à 17:13, Didier Benoit a écrit :
>
> In our software, we didn't plan to read the .geom files in 2 or
> more folders. I think you have 2 solutions :
>
> 1- You can copy all your .geom files for each different kind of
> scanners in the CASTOR_CONFIG folder
>
> 2- Or creating a "castor_test" folder, where you write all your
> .geom files (and the .geom files provided by CASToR) and set
> CASTOR_CONFIG to the location of "castor_test" during the
> installation.
>
> Kind regards,
> Didier
>
> On 04/18/2017 04:36 PM, Michael Ljungberg wrote:
>
> Sorry Didier
>
> I meant the CASTOR_CONFIG folder. That was my question - if it
> would be possible for your software to search first in the
> local directory for a scanner name before looking in the
> CASTOR_CONFIG folder. Sometimes one do simulations as function
> of different camera geometries and I can then imagine I would
> need one .geom file for each of them. If the search for the
> scanner name is first made in the local directory and then in
> the CASTOR_CONFIG folder then these local .geom files could be
> isolated from the more permanent scanner system files, stored
> in the CASTOR_CONFIG folder.
>
> Hälsningar / Best regards
>
> Michael
>
> *From: *Didier Benoit <didier.benoit at inserm.fr>
> <mailto:didier.benoit at inserm.fr>
> *Date: *Tuesday, 18 April 2017 at 16:07
> *To: *Michael Ljungberg <michael.ljungberg at med.lu.se>
> <mailto:michael.ljungberg at med.lu.se>,
> "castor-users at lists.castor-project.org"
> <mailto:castor-users at lists.castor-project.org>
> <castor-users at lists.castor-project.org>
> <mailto:castor-users at lists.castor-project.org>
> *Subject: *Re: [Castor-users] SPECT reading Interfile
>
> 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>
> <mailto:castor-users-bounces at lists.castor-project.org> on
> behalf of Didier Benoit <didier.benoit at inserm.fr>
> <mailto:didier.benoit at inserm.fr>
> *Date: *Tuesday, 18 April 2017 at 14:52
> *To: *"castor-users at lists.castor-project.org"
> <mailto:castor-users at lists.castor-project.org>
> <castor-users at lists.castor-project.org>
> <mailto: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 <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 <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
>
> -------------------------------------------------------------------------------
>
>
>
>
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