[Gate-users] Gate-users Digest, Vol 89, Issue 7
Johannes Anderl
johannes.anderl at hotmail.com
Tue Oct 8 14:18:03 CEST 2013
Thank you for your help Kris and Claude :)
Johannes
> From: gate-users-request at lists.opengatecollaboration.org
> Subject: Gate-users Digest, Vol 89, Issue 7
> To: gate-users at lists.opengatecollaboration.org
> Date: Mon, 7 Oct 2013 12:00:01 +0200
>
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> Today's Topics:
>
> 1. How to view .hdr/.img files (Stathis Kamperis)
> 2. Re: ECAT7 output with user defined scanner (Kris Thielemans)
> 3. Re: How to view .hdr/.img files (D?vid V?lgyes)
> 4. Re: How to view .hdr/.img files (Stathis Kamperis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 6 Oct 2013 15:01:16 +0300
> From: Stathis Kamperis <ekamperi at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] How to view .hdr/.img files
> Message-ID:
> <CACYCkUvTDowjH7_CtsoEb_XNiQUztdy1UY9ukRD1kVwByQ=RbA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi everyone,
>
> I have enabled a dose actor in my simulation. The output for 3D images
> is .hdr/.img. Is there a program to view the resultant image ? Or an
> easy way to convert the raw pixel data into a format that a regular
> image viewer can display ?
>
> Thanks,
> Stathis
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 6 Oct 2013 13:36:56 +0100
> From: "Kris Thielemans" <kris.f.thielemans at gmail.com>
> To: <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] ECAT7 output with user defined scanner
> Message-ID: <000101cec290$bed36fd0$3c7a4f70$@gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Johannes,
> Claude is correct. One way to handle this is to use STIR's
> ifheaders_for_ecat7 utility to get Interfile headers "pointing" into your
> ECAT 7 header. You can then edit these by hand (or by script) to correct the
> info.
>
> You can find some info on the STIR wiki, including
> http://sourceforge.net/apps/mediawiki/stir/index.php?title=STIR_FAQ#How_do_I
> _add_my_own_scanner_to_STIR.3F
>
> Kris
>
> > -----Original Message-----
> > From: gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-
> > users-bounces at lists.opengatecollaboration.org] On Behalf Of COMTAT
> > Claude
> > Sent: 02 October 2013 10:21
> > To: gate-users at lists.opengatecollaboration.org
> > Subject: Re: [Gate-users] ECAT7 output with user defined scanner
> >
> > Hi Johannes,
> >
> >
> >
> > The problem is that some data that are required to reconstruct an image
> are
> > missing in the ECAT7 header. An example is the ring diameter. It is not
> > possible to store the ring diameter in a ECAT7 file (neither the number of
> > detectors per ring).
> >
> > As STIR requires this information, it has a database for each known
> scanner
> > model. What is printed at the end of your email is not the content of the
> > ECAT7 header, but the content of STIR database:
> >
> >
> >
> > WARNING: ECAT7 IO: Bin size from header.x_resolution (2.00714) does not
> > agree with expected value 2.25
> >
> > for scanner ECAT 962. Using bin size from header...
> >
> > Info for file yourSinogram.S
> >
> > ProjDataInfoCylindricalNoArcCorr :=
> >
> > Scanner parameters:=
> >
> > Scanner type := ECAT 962
> >
> > Number of rings := 32
> >
> > Number of detectors per ring := 576
> >
> > Inner ring diameter (cm) := 82.4
> >
> > Average depth of interaction (cm) := 0.7
> >
> > Distance between rings (cm) := 0.485
> >
> > Default bin size (cm) := 0.200714
> >
> > View offset (degrees) := 0
> >
> > Maximum number of non-arc-corrected bins := 288
> >
> > Default number of arc-corrected bins := 288
> >
> > Number of blocks per bucket in transaxial direction := 3
> >
> > Number of blocks per bucket in axial direction := 4
> >
> > Number of crystals per block in axial direction := 8
> >
> > Number of crystals per block in transaxial direction := 8
> >
> > Number of detector layers := 1
> >
> > Number of crystals per singles unit in axial direction := 8
> >
> > Number of crystals per singles unit in transaxial direction := 24
> >
> > end scanner parameters:=
> >
> >
> >
> > As you set the scanner model to zero in your ECAT7 file
> > (#/gate/output/ecat7/system 962 ), STIR does not recognize it. As a
> > consequence, STIR assumes it is an HR+ (default scanner):
> >
> >
> >
> > WARNING: ECAT7 IO: Couldn't determine the scanner
> >
> > (Main_header.system_type=0), defaulting to 962.
> >
> > This might give dramatic problems.
> >
> >
> >
> > You should define a new scanner model ID in GATE, like
> > /gate/output/ecat7/system 492, and create in STIR the corresponding
> > database. I do not know how to create your own database in STIR.
> >
> >
> >
> > Claude
> >
> >
> >
> > De : gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-
> > users-bounces at lists.opengatecollaboration.org] De la part de Johannes
> > Anderl
> > Envoy? : mercredi 2 octobre 2013 10:49
> > ? : gate-users at lists.opengatecollaboration.org
> > Objet : [Gate-users] ECAT7 output with user defined scanner
> >
> >
> >
> > Dear all,
> >
> > I have a problem concerning the ECAT7 Output.
> > I would like to simulate a user defined scanner and not the E962 scanner
> > type.
> > The created yourSinogram.S file still contains the default values (ring
> > diameter, detectors per ring,...) for the E962 scanner model.
> > Is there a possbility to get this ECAT7 *.S output with the user defined
> > scanner values?
> >
> > The code for the user defined scanner type can be seen below:
> >
> > /gate/world/daughters/name ecat
> > /gate/world/daughters/insert cylinder
> > /gate/ecat/setMaterial Air
> > /gate/ecat/geometry/setRmax 44.1 cm
> > /gate/ecat/geometry/setRmin 42.1 cm
> > /gate/ecat/geometry/setHeight 21.7685 cm
> > /gate/ecat/vis/forceWireframe
> >
> > # B L O C K
> > /gate/ecat/daughters/name block
> > /gate/ecat/daughters/insert box
> > /gate/block/placement/setTranslation 431.0 0.0 0.0 mm
> > /gate/block/geometry/setXLength 20.0 mm
> > /gate/block/geometry/setYLength 52.17127 mm
> > /gate/block/geometry/setZLength 52.17127 mm
> > /gate/block/setMaterial Air
> > /gate/block/vis/forceWireframe
> >
> > # C R Y S T A L
> > /gate/block/daughters/name crystal
> > /gate/block/daughters/insert box
> > /gate/crystal/geometry/setXLength 20.0 mm
> > /gate/crystal/geometry/setYLength 4 mm
> > /gate/crystal/geometry/setZLength 4 mm
> > /gate/crystal/setMaterial LSO
> > /gate/crystal/vis/setColor yellow
> >
> > # R E P E A T C R Y S T A L
> > /gate/crystal/repeaters/insert cubicArray
> > /gate/crystal/cubicArray/setRepeatNumberX 1
> > /gate/crystal/cubicArray/setRepeatNumberY 13
> > /gate/crystal/cubicArray/setRepeatNumberZ 13
> > /gate/crystal/cubicArray/setRepeatVector 0. 4.0142725 4.0142725 mm
> >
> > # R E P E A T BLOCK (reproduziert die Box entlang eines Rings)
> > /gate/block/repeaters/insert linear
> > /gate/block/linear/setRepeatNumber 4
> > /gate/block/linear/setRepeatVector 0. 0. 55.17127 mm
> > /gate/block/repeaters/insert ring
> > /gate/block/ring/setRepeatNumber 48
> >
> > The ecat7 code can be seen below:
> >
> > /gate/output/ecat7/enable
> > /gate/output/ecat7/verbose 2
> > /gate/output/ecat7/setFileName yourSinogram
> > /gate/output/ecat7/describe
> > /gate/output/ecat7/mashing 2
> > /gate/output/ecat7/span 103
> > /gate/output/ecat7/maxringdiff 51
> > #/gate/output/ecat7/system 962
> >
> > Looking at the values from the yoursinogram.S using list_projdata_info
> from
> > STIR shows:
> >
> >
> > WARNING: ECAT7 IO: Couldn't determine the scanner
> > (Main_header.system_type=0), defaulting to 962.
> > This might give dramatic problems.
> >
> >
> > WARNING: ECAT7 IO: Bin size from header.x_resolution (2.00714) does not
> > agree with expected value 2.25
> > for scanner ECAT 962. Using bin size from header...
> > Info for file yourSinogram.S
> > ProjDataInfoCylindricalNoArcCorr :=
> > Scanner parameters:=
> > Scanner type := ECAT 962
> > Number of rings := 32
> > Number of detectors per ring := 576
> > Inner ring diameter (cm) := 82.4
> > Average depth of interaction (cm) := 0.7
> > Distance between rings (cm) := 0.485
> > Default bin size (cm) := 0.200714
> > View offset (degrees) := 0
> > Maximum number of non-arc-corrected bins := 288
> > Default number of arc-corrected bins := 288
> > Number of blocks per bucket in transaxial direction := 3
> > Number of blocks per bucket in axial direction := 4
> > Number of crystals per block in axial direction := 8
> > Number of crystals per block in transaxial direction := 8
> > Number of detector layers := 1
> > Number of crystals per singles unit in axial direction := 8
> > Number of crystals per singles unit in transaxial direction := 24
> > end scanner parameters:=
> >
> >
> > Thanks in advance,
> >
> > Johannes
> >
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 6 Oct 2013 15:00:31 +0200
> From: D?vid V?lgyes <david.volgyes at gmail.com>
> To: Stathis Kamperis <ekamperi at gmail.com>
> Cc: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] How to view .hdr/.img files
> Message-ID:
> <CABwnx5hyJpygnn_akG+t3gGGwKO9DrpTMGgLxbjW=ttEjrJgxw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Most of the viewers can open it, for example, Amide is a basic,
> cross-platform viewer which works fine with hdr/img.
>
> Best,
> David
>
> On Sun, Oct 6, 2013 at 2:01 PM, Stathis Kamperis <ekamperi at gmail.com> wrote:
> > Hi everyone,
> >
> > I have enabled a dose actor in my simulation. The output for 3D images
> > is .hdr/.img. Is there a program to view the resultant image ? Or an
> > easy way to convert the raw pixel data into a format that a regular
> > image viewer can display ?
> >
> > Thanks,
> > Stathis
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 6 Oct 2013 16:30:32 +0300
> From: Stathis Kamperis <ekamperi at gmail.com>
> To: D?vid V?lgyes <david.volgyes at gmail.com>
> Cc: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] How to view .hdr/.img files
> Message-ID:
> <CACYCkUu2EtzHDOxaNCJXFkpSm41G=T5ptf4XvZhctWN1QjbDCA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks David,
>
> amide works fine, just like VV viewer as suggested by Yahya@
>
> -Stathis
>
> On Sun, Oct 6, 2013 at 4:00 PM, D?vid V?lgyes <david.volgyes at gmail.com> wrote:
> > Hi,
> >
> > Most of the viewers can open it, for example, Amide is a basic,
> > cross-platform viewer which works fine with hdr/img.
> >
> > Best,
> > David
> >
> > On Sun, Oct 6, 2013 at 2:01 PM, Stathis Kamperis <ekamperi at gmail.com> wrote:
> >> Hi everyone,
> >>
> >> I have enabled a dose actor in my simulation. The output for 3D images
> >> is .hdr/.img. Is there a program to view the resultant image ? Or an
> >> easy way to convert the raw pixel data into a format that a regular
> >> image viewer can display ?
> >>
> >> Thanks,
> >> Stathis
> >> _______________________________________________
> >> Gate-users mailing list
> >> Gate-users at lists.opengatecollaboration.org
> >> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
> ------------------------------
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
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>
> End of Gate-users Digest, Vol 89, Issue 7
> *****************************************
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