Dear Vacular Modelers,
I am experiencing strange problems with the VMTK Image Viewer and the other
render windows - if I load a 3D data set (e.g. CT-angiography) into it can zoom
or rotate the images and I can adjust window levels, but no matter what I try I
can not move the image planes.
Maybe anybody of you has an idea how to fix this problem? I am using a Mac
(Intel) with OsX 10.7 (middle mouse button is assigned via BetterTouchTool to
my Magic Mouse). If I try this in a virtual machine in Ubuntu 12.04 [precise]
the thing works (okay there are some other problems but that is another
story...)
Maybe anyone has an idea or has experienced the same problem and found a way to
fix it?
Greetings, Mat
________________________________________
Von: vmtk-users-requ...@lists.sourceforge.net
[vmtk-users-requ...@lists.sourceforge.net]
Gesendet: Donnerstag, 21. März 2013 18:17
An: vmtk-users@lists.sourceforge.net
Betreff: vmtk-users Digest, Vol 65, Issue 19
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Today's Topics:
1. conformal/parametrized mapping ( 3D surface mesh to 2D plane
) with vmtk ? (Greg Fokum)
2. Re: vmtklevelsetsegmentation (Luca Antiga)
3. Re: Computing centerline geometry (Luca Antiga)
----------------------------------------------------------------------
Message: 1
Date: Wed, 20 Mar 2013 20:44:17 -0400
From: Greg Fokum <gregthom...@gmail.com>
Subject: [vmtk-users] conformal/parametrized mapping ( 3D surface mesh
to 2D plane ) with vmtk ?
To: vmtk-users@lists.sourceforge.net
Message-ID:
<cafh_-on1xgcgs9-0-tvuzifc8khpooyqngicobwdc-uxug-...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello everyone,
I just came across vmtk and was wondering if I could you it for my work. My
question is this:
I have a tubular 3d surface ( length of colon) similar to the vessels you
show in the tutorials except that there is not branching only bending.
I would like to map this 3D surface to a plane (or regular cylinder) using
VMTK so that I can then create try to subdivide my tubular 3d surface (
volume) in to sections ( alond the central axis direction) of equal volume
based on mapping uniform strips on the mapped plane back to the 3D surface.
I see a two step procedure:
1) first create a mapping from the 3D surface to a plane ( or in fact a
regular cylinder such that volume is conserved)
2) cut sections of the cylinder and relate them to sections on the mesh.
Is that possible with tools in VMTK ? If not please help me with some
suggestions. I can send a sample of my mesh in wrl/vrml format.
thank you
GT
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Message: 2
Date: Thu, 21 Mar 2013 18:03:48 +0100
From: Luca Antiga <luca.ant...@gmail.com>
Subject: Re: [vmtk-users] vmtklevelsetsegmentation
To: richschm...@web.de
Cc: vmtk-users@lists.sourceforge.net
Message-ID: <b07dfe7e-6498-4d00-bc3c-9f563534e...@gmail.com>
Content-Type: text/plain; charset="us-ascii"
Hi Regine,
did you try inverting with vmtkimageshiftscale?
vmtkimageshiftscale -ifile input.mha -scale -1.0
If you need to re-obtain positive intensity levels for some reason, you need to
pipe another shift scale for the shift part:
vmtkimageshiftscale -ifile input.mha -scale -1.0 --pipe vmtkimageshiftscale
-shift 4000
Hope this helps.
Luca
On Mar 18, 2013, at 10:39 PM, richschm...@web.de wrote:
> Dear all,
>
> a friend of mine came up with a dicom data set of the lung. She wants to
> extract the trachea which is represented with a lower intensity as compared
> to their environment (since it is filled with air). We tried to use
> vmtklevelsetsegmentation, but it didn't work due to the inverted intensity
> distribution, I guess. I tried to invert the dicom data set and read it into
> vmtk afterwards, but I wasn't successful.
> Did anybody have the same problem and could tell me how he/she solved it?
> Thank you for any help!
> Bye,
> Regine
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
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Message: 3
Date: Thu, 21 Mar 2013 18:15:50 +0100
From: Luca Antiga <luca.ant...@orobix.com>
Subject: Re: [vmtk-users] Computing centerline geometry
To: qiang zeng <zengqiang2...@yahoo.com.cn>
Cc: vmtk-users@lists.sourceforge.net
Message-ID: <f397cc31-b034-4913-9e38-5bd4bb578...@orobix.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Qiang,
the script works, I'm attaching the result and a Paraview screenshot where the
Glyph filter has been applied to the Frenet normals.
Note that I specified a higher number of iterations and factor than the
default, to diminish the effect of noise on the finite difference approximation
of derivatives.
vmtkcenterlinegeometry -ifile wf2011.8.31-20080918-L-3-1-3.18_centerlines.vtp
-smoothing 1 -ofile foobar.vtp -iterations 1000 -factor 0.5
Luca
On Mar 20, 2013, at 11:47 AM, qiang zeng wrote:
> Dear all,
> When I am following the script "vmtkcenterlinegeometry -ifile foo_cl.vtp
> -smoothing 1 -ofile foo_clgm.vtp", I cannot get any centerline geometry. But
> I am dealing with split centerlines, the script "vmtkcenterlines -ifile
> foo.vtp -seedselector openprofiles --pipe vmtkbranchextractor --pipe
> vmtkbranchgeometry -ofile foo_clcg.vtp" is OK for the same vessel (as an
> attachment).
> Did anybody have the same problem and could tell me how he/she solved it?
> Thanks.
>
> Qiang
> <wf2011.8.31-20080918-L-3-1-3.18_centerlines.vtp><wf2011.8.31-20080918-L-3-1-3.18_model_cl.vtp>------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________
> vmtk-users mailing list
> vmtk-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/vmtk-users
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Everyone hates slow websites. So do we.
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Download AppDynamics Lite for free today:
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