<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:12pt"><div style="RIGHT: auto">Many thanks for the information.</div> <div style="RIGHT: auto"> </div> <div style="RIGHT: auto"> </div> <div style="RIGHT: auto"> </div> <div style="RIGHT: auto">Mike</div> <div> </div> <DIV style="FONT-FAMILY: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; FONT-SIZE: 12pt"> <DIV style="FONT-FAMILY: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; FONT-SIZE: 12pt"> <DIV style="RIGHT: auto" dir=ltr> <DIV style="BORDER-BOTTOM: #ccc 1px solid; BORDER-LEFT: #ccc 1px solid; PADDING-BOTTOM: 0px; LINE-HEIGHT: 0; MARGIN: 5px 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; HEIGHT: 0px; FONT-SIZE: 0px; BORDER-TOP: #ccc 1px solid; BORDER-RIGHT: #ccc 1px solid; PADDING-TOP: 0px" class=hr contentEditable=false readonly="true"></DIV>From: "gate-users-request@lists.opengatecollaboration.org" <gate-users-request@lists.opengatecollaboration.org> To: gate-users@lists.opengatecollaboration.org Sent: Tuesday, January 28, 2014 6:00 AM Subject: Gate-users Digest, Vol 92, Issue 35 </DIV> <DIV style="RIGHT: auto" class=y_msg_container> Send Gate-users mailing list submissions to <A href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</A> To subscribe or unsubscribe via the World Wide Web, visit <A href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target=_blank>http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</A> or, via email, send a message with subject or body 'help' to <A href="mailto:gate-users-request@lists.opengatecollaboration.org" ymailto="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</A> You can reach the person managing the list at <A href="mailto:gate-users-owner@lists.opengatecollaboration.org" ymailto="mailto:gate-users-owner@lists.opengatecollaboration.org">gate-users-owner@lists.opengatecollaboration.org</A> When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..." Today's Topics: 1. Re: Edep image output (thibaultmauxion) 2. Define scanning geometry (Stephen Yip) 3. Re: Define scanning geometry (Marc Chamberland) ---------------------------------------------------------------------- Message: 1 Date: Mon, 27 Jan 2014 11:31:29 -0500 From: thibaultmauxion <<A href="mailto:thibault.mauxion@gmail.com" ymailto="mailto:thibault.mauxion@gmail.com">thibault.mauxion@gmail.com</A>> To: <A href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</A> Subject: Re: [Gate-users] Edep image output Message-ID: <<A href="mailto:DB901663-D016-4803-970C-DE9C803D12D5@gmail.com" ymailto="mailto:DB901663-D016-4803-970C-DE9C803D12D5@gmail.com">DB901663-D016-4803-970C-DE9C803D12D5@gmail.com</A>> Content-Type: text/plain; charset="iso-8859-1" Hi Mike, Just had a quick look but seems you have a "geometry vs source" issue. The origin of the scale for the voxelized source is not set in the center of the geometry but at one corner (never remember which one). To match both scales, you need to shift your voxelized source by half of its total dimension using SetPosition) for more info, see <A href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6:Voxelized_Source_and_Phantom" target=_blank>http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6:Voxelized_Source_and_Phantom</A> under voxelized source section. I would also make sure the size of the voxels is consistent for the geometry and the voxelized source. Hope this helps Thibault Post-doctoral fellow Division of Medical Imaging Physics Johns Hopkins Medical Institutions JHOC 4260, 601 N. Caroline street, Baltimore, MD, 21287 Tel: +1 410 502 3772 Fax: +1 410 614 1060 <A href="http://www.hopkinsradiology.org/dmip/" target=_blank>http://www.hopkinsradiology.org/dmip/</A> On Jan 27, 2014, at 11:09 AM, Mike Tabriz <<A href="mailto:mtabriz@yahoo.com" ymailto="mailto:mtabriz@yahoo.com">mtabriz@yahoo.com</A>> wrote: > Dear GATE users, > In an attempt to simulate collection of dose in thyroid (target) from activity in lungs (source) I get the following images. Capture 4 shows a head slice from the Zubal phantom. Capture 5 shows the Edep image output file at the same exact slice. What is curious about this output image is that the head appears to be embedded in the lungs! > > Any opinions as to the cause of this phenomenon is greatly appreciated. > > With thanks in advance, > Mike > <Capture4.PNG><Capture5.PNG>_______________________________________________ > Gate-users mailing list > <A href="mailto:Gate-users@lists.opengatecollaboration.org" ymailto="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</A> > <A href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target=_blank>http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</A> -------------- next part -------------- An HTML attachment was scrubbed... URL: <<A href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140127/36731d1e/attachment-0001.html" target=_blank>http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140127/36731d1e/attachment-0001.html</A>> ------------------------------ Message: 2 Date: Mon, 27 Jan 2014 21:40:52 +0100 From: Stephen Yip <<A href="mailto:stephen.fyip1@gmail.com" ymailto="mailto:stephen.fyip1@gmail.com">stephen.fyip1@gmail.com</A>> To: gate-users <<A href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</A>> Subject: [Gate-users] Define scanning geometry Message-ID: <CADfqr+far8m4CF9C8+P=<A href="mailto:a8Zm7x3u8E5EZ7uiQd8wJV6KGpoAAA@mail.gmail.com" ymailto="mailto:a8Zm7x3u8E5EZ7uiQd8wJV6KGpoAAA@mail.gmail.com">a8Zm7x3u8E5EZ7uiQd8wJV6KGpoAAA@mail.gmail.com</A>> Content-Type: text/plain; charset="iso-8859-1" Hi, I am trying to create a sub-volume & insert material to it. For example: /gate/world/daughters/name cylindricalPET /gate/world/daughters/insert cylinder /gate/cylindricalPET/setMaterial Water It complained that /home/gate/Progs/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc .....GateMaterialDatabase: could not find the definition for material 'Water' in Material files.... It then kicked me out of vGate and closed OGLSX Does anyone know what I did wrong? Thanks, Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: <<A href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140127/20ab9f39/attachment-0001.html" target=_blank>http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140127/20ab9f39/attachment-0001.html</A>> ------------------------------ Message: 3 Date: Tue, 28 Jan 2014 00:25:34 +0000 From: Marc Chamberland <<A href="mailto:MarcChamberland@cmail.carleton.ca" ymailto="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</A>> To: Stephen Yip <<A href="mailto:stephen.fyip1@gmail.com" ymailto="mailto:stephen.fyip1@gmail.com">stephen.fyip1@gmail.com</A>> Cc: Gate Users <<A href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</A>> Subject: Re: [Gate-users] Define scanning geometry Message-ID: <<A href="mailto:AA9940EF-6CD7-4F2F-8626-B620B2665F94@cmail.carleton.ca" ymailto="mailto:AA9940EF-6CD7-4F2F-8626-B620B2665F94@cmail.carleton.ca">AA9940EF-6CD7-4F2F-8626-B620B2665F94@cmail.carleton.ca</A>> Content-Type: text/plain; charset="iso-8859-1" Hi Stephen, I've had something like that happen to me before. In my case, the culprit was either the wrong line endings (for example, Unix vs Windows line endings) in the material file, or some other invisible characters that threw off Gate when reading the file. I suggest you create a new blank text file and copy the material database to that new text file (all within vGate). Then use this new material file. And if this does not work, then I do not know what's going on. Good luck! Marc __________________________ Marc Chamberland, MSc PhD candidate Department of Physics Carleton University Ottawa (ON) On Jan 27, 2014, at 15:40, Stephen Yip <<A href="mailto:stephen.fyip1@gmail.com" ymailto="mailto:stephen.fyip1@gmail.com">stephen.fyip1@gmail.com</A><mailto:<A href="mailto:stephen.fyip1@gmail.com" ymailto="mailto:stephen.fyip1@gmail.com">stephen.fyip1@gmail.com</A>>> wrote: Hi, I am trying to create a sub-volume & insert material to it. For example: /gate/world/daughters/name cylindricalPET /gate/world/daughters/insert cylinder /gate/cylindricalPET/setMaterial Water It complained that /home/gate/Progs/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc<<A href="http://gatematerialdatabase.cc/" target=_blank>http://gatematerialdatabase.cc/</A>> .....GateMaterialDatabase: could not find the definition for material 'Water' in Material files.... It then kicked me out of vGate and closed OGLSX Does anyone know what I did wrong? Thanks, Stephen _______________________________________________ Gate-users mailing list <A href="mailto:Gate-users@lists.opengatecollaboration.org" ymailto="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</A><mailto:<A href="mailto:Gate-users@lists.opengatecollaboration.org" ymailto="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</A>> <A href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target=_blank>http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</A> -------------- next part -------------- An HTML attachment was scrubbed... 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