<html> <head> <style></style></head> <body class='hmmessage'><div dir='ltr'>Thank you for your help Kris and Claude :) Johannes <div>> From: gate-users-request@lists.opengatecollaboration.org > Subject: Gate-users Digest, Vol 89, Issue 7 > To: gate-users@lists.opengatecollaboration.org > Date: Mon, 7 Oct 2013 12:00:01 +0200 > > Send Gate-users mailing list submissions to > gate-users@lists.opengatecollaboration.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users > or, via email, send a message with subject or body 'help' to > gate-users-request@lists.opengatecollaboration.org > > You can reach the person managing the list at > gate-users-owner@lists.opengatecollaboration.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gate-users digest..." > > > 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@gmail.com> > To: gate-users@lists.opengatecollaboration.org > Subject: [Gate-users] How to view .hdr/.img files > Message-ID: > <CACYCkUvTDowjH7_CtsoEb_XNiQUztdy1UY9ukRD1kVwByQ=RbA@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@gmail.com> > To: <gate-users@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@lists.opengatecollaboration.org [mailto:gate- > > users-bounces@lists.opengatecollaboration.org] On Behalf Of COMTAT > > Claude > > Sent: 02 October 2013 10:21 > > To: gate-users@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@lists.opengatecollaboration.org [mailto:gate- > > users-bounces@lists.opengatecollaboration.org] De la part de Johannes > > Anderl > > Envoy? : mercredi 2 octobre 2013 10:49 > > ? : gate-users@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@gmail.com> > To: Stathis Kamperis <ekamperi@gmail.com> > Cc: gate-users <gate-users@lists.opengatecollaboration.org> > Subject: Re: [Gate-users] How to view .hdr/.img files > Message-ID: > <CABwnx5hyJpygnn_akG+t3gGGwKO9DrpTMGgLxbjW=ttEjrJgxw@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@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@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@gmail.com> > To: D?vid V?lgyes <david.volgyes@gmail.com> > Cc: gate-users <gate-users@lists.opengatecollaboration.org> > Subject: Re: [Gate-users] How to view .hdr/.img files > Message-ID: > <CACYCkUu2EtzHDOxaNCJXFkpSm41G=T5ptf4XvZhctWN1QjbDCA@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@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@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@lists.opengatecollaboration.org > >> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users > > > ------------------------------ > > _______________________________________________ > Gate-users mailing list > Gate-users@lists.opengatecollaboration.org > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users > > End of Gate-users Digest, Vol 89, Issue 7 > ***************************************** </div> </div></body> </html>