vmtk-users Mailing List for Vascular Modeling Toolkit (Page 8)
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From: Luca A. <luc...@gm...> - 2013-04-01 21:01:04
|
Hello Adrian, in case of segmented sub-volumes of a larger volume, assuming the original larger volume is large.vti and the level set segmentations obtained from two smaller volumes (both extracted from large.vti) are ls1.vti and ls2.vti, you first need to resample the ls* volumes back onto the large.vti image grid: vmtkimagereslice -ifile ls1.vti -rfile large.vti -ofile ls1_resl.vti -background 5 vmtkimagereslice -ifile ls2.vti -rfile large.vti -ofile ls2_resl.vti -background 5 Here I specified background to an (arbitrary) positive value, assuming that level sets have the negative inside, positive outside convention. The background value is used for the regions of the larger volume that lies outside the extent of the smaller volume (which is assumed to be "outside" the segmented shape, hence the positive background value). At this point you have two compatible resampled ls* volumes and you can use vmtkimagecompose to merge the two segmentations. Cheers, Luca On Mar 31, 2013, at 6:39 PM, adrianrh wrote: > Hello Luca, > > Thank you for the answer, it is helpful. I actually need to combine > images from the same geometry and from different geometries at different > points in my work. I have some higher quality MR scans that are on a > smaller domain and would like to understand how to combine it with a > lower quality image of a bigger domain. So getting some more details > would really be nice. > > > > Best regards Adrian > > On 2013-03-29 13:53, Luca Antiga wrote: >> Hello Adrian, >> >> there is a way of combining level set files. After all, they are all >> image files, so here's how you do it: >> >> in case they are all produced from the same input image (i.e. they >> have the same geometry), you can go >> vmtkimagecompose -ifile ls1.vti -i2file ls2.vti -ofile ls_combined.vti >> If you have more than 2, you'll have to call another vmtkimagecompose >> on the result of the former; >> >> in case they are produced from different input images (hence they >> have different spatial extents) you'll first have to resample them >> onto >> a common grid using vmtkimagereslice; let me know if this is your case >> and I'll provide you with more details. >> >> Best, >> >> Luca >> >> On Mar 25, 2013, at 3:08 PM, adrianrh wrote: >> >>> Hi! >>> >>> I am working on segmenting water in the brain for simula research >>> laboratory. >>> >>> I am using the command >>> "vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile >>> level_sets.vti -ofile level_setsOut.vti" >>> to continue working on a project. >>> >>> what I would really like to be able to do is to make multiple >>> levelsets >>> files and then combine them. Like this; >>> >>> vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile >>> level_sets.vti -levelsetsfile level_sets2.vti -ofile >>> level_setsOut.vti >>> >>> is it possible to do this in the vmtk software? or possible to add >>> it? >>> >>> Adrian Hope >>> >>> ------------------------------------------------------------------------------ >>> 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 [1] >>> _______________________________________________ >>> vmtk-users mailing list >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> >> >> Links: >> ------ >> [1] http://p.sf.net/sfu/appdyn_d2d_mar > > ------------------------------------------------------------------------------ > Own the Future-Intel(R) Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. Compete > for recognition, cash, and the chance to get your game on Steam. > $5K grand prize plus 10 genre and skill prizes. Submit your demo > by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@or...> - 2013-04-01 20:46:23
|
Hi YiQiang, > 1)what difference are between InPlaneBifurcationVectorAngles and ICA angle? The InPlaneBifurcationVectorAngles are the angles between the up-normal vector and a branch vector projected onto the bifurcation plane. The ICA angle is the angle between the ICA and ECA vectors projected onto the bifurcation plane. So, by summing the angle between the ICA branch vector and the up-normal and the ECA branch vector and the up-normal you get the ICA angle. Note: here I wrote "sum" because I'm referring to the angles absolute value, but it's really the difference of the signed angles (since the ICA branch and the ECA branch are on opposite sides of the bifurcation up-normal, so one angle will come out positive and the other negative, by the convention used in vmtk). The reason why we don't spit the ICA angle directly is just our wish to make the tool generic and not specific to the carotid bifurcation. > 2)in the result of the vector (BifurcationVectors, InPlaneBifurcationVectors, OutOfPlaneBifurcationVectors) by VMTK (as an attachment), each part has three groups. and how to get the angle from the vector by VMTK? or do i need to use the other tools (such as Paraview) to caculate the angle value. You get both vectors and angles. In fact, the InPlaneBifurcationVectorAngles are angles in radians, while the InPlaneBifurcationVectors are the vector components from which the angle is computed. > 3)for the ICA angle, i need to get the difference between the two downstream inplane angles. but the InPlaneBifurcationVectors has two downstream groups vector [(--0.27,0.18,2.60), (0.60, -0.50.0.89)] and how to distinguish and control these vectors. You should look at the InPlaneBifurcationVectorAngles and take the difference (see point above) between the angles for group 2 and 3 (which correspond to the ICA and ECA - assuming you selected the output target point of the ICA as first when extracting centerlines). So, in your case, ICA = 0.26687 - (- 0.608927) = 0.875797 (in radians) = 50.18 (in degrees) Hope this clarifies it. Luca On Mar 29, 2013, at 4:20 PM, qiang zeng wrote: > Hi Luca, > Thank you for your reply. > I have already saw the "Computing bifurcation geometry" section. but i have some doubt: > 1)what difference are between InPlaneBifurcationVectorAngles and ICA angle? > 2)in the result of the vector (BifurcationVectors, InPlaneBifurcationVectors, OutOfPlaneBifurcationVectors) by VMTK (as an attachment), each part has three groups. and how to get the angle from the vector by VMTK? or do i need to use the other tools (such as Paraview) to caculate the angle value. > 3)for the ICA angle, i need to get the difference between the two downstream inplane angles. but the InPlaneBifurcationVectors has two downstream groups vector [(--0.27,0.18,2.60), (0.60, -0.50.0.89)] and how to distinguish and control these vectors. > > Best, > YiQiang > > > --- 13年3月29日，周五, Luca Antiga <luc...@gm...> 写道： > > 发件人: Luca Antiga <luc...@gm...> > 主题: Re: [vmtk-users] How to calculate the ICA angle or planarity angle in VMTK or Paraview > 收件人: "qiang zeng" <zen...@ya...> > 抄送: vmt...@li... > 日期: 2013年3月29日,周五,下午9:35 > > Hi YiQiang, > the angles you get from vmtk are explained in http://www.vmtk.org/Tutorials/GeometricAnalysis/, > "Computing bifurcation geometry" section. > > The ICA angle is the difference between the two downstream inplane angles, while the planarity angle > is the difference between the upstream and downstream out of plane angles. > > Hope this gives you a hint > > > Luca > > > > On Mar 28, 2013, at 9:10 AM, qiang zeng wrote: > >> Dear VMTK users, >> In my works, I need to calculate the ICA angle and planarity angle like the Stroke 2005 paper. but I didn't get the result from the Paraview. >> Does anyone know a way to do this? >> >> Thanks in advance! >> Best wishes, >> YiQiang Zeng >> ------------------------------------------------------------------------------ >> Own the Future-Intel® Level Up Game Demo Contest 2013 >> Rise to greatness in Intel's independent game demo contest. >> Compete for recognition, cash, and the chance to get your game >> on Steam. $5K grand prize plus 10 genre and skill prizes. >> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________ >> vmtk-users mailing list >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > <data.jpg> |
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From: Luca A. <luc...@or...> - 2013-04-01 19:57:30
|
Hi Ben, try including the VMTKUse.cmake file in the vmtk build directory into your CMake project include(/path/to/VMTKUse.cmake) I just saw that the VMTKUse.cmake.in file needs an update, but it should work for most use cases. Best, Luca On Apr 1, 2013, at 7:21 PM, Berkowitz, Benjamin M wrote: > Hi, I'm interested in implementing some of the great functionality from the vtkvmtk C++ libraries into my programs. Is there a simple way to include all vtkvmtk libraries in my CMakeLists.txt file? > > Thanks > > Ben > ------------------------------------------------------------------------------ > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@gm...> - 2013-04-01 19:53:06
|
Hi Anouk, Ben,
right, although there might be a chance that just doing
system('vmtk vmtksurfaceviewer -ifile foo.vtp');
might work, i.e. just specify the pipe right after the call to the vmtk script - the one that makes pypepad show up (above I just wrote "vmtk", but whatever you used that launched pypepad is fine).
Luca
On Apr 1, 2013, at 7:55 PM, Berkowitz, Benjamin M wrote:
> Anouk,
>
> You would need to have vmtk command line functionality implemented in order to use the vmtkscripts with the system function (http://www.vmtk.org/Main/Installation/).
>
> Ben
>
>
> On Mar 29, 2013, at 7:58 AM, Anouk Post <ano...@gm...> wrote:
>
>> Hi Luca,
>>
>> Thanks!
>>
>> I do understand how I can open VMTK from MATLAB, but not how to actually run a VMTK 'script' from MATLAB. When I use the system function it just opens pypepad. Do you know how I can actually let it run a VMTK script?
>>
>> Best wishse,
>>
>> Anouk
>>
>> On 29 March 2013 12:56, Luca Antiga <luc...@gm...> wrote:
>> Hi Anouk,
>> you'll probably have to use the system() function in Matlab to call vmtk the way you call it from the command line.
>> It should work.
>>
>> Luca
>>
>> PS: a couple of random references on the system function
>>
>> http://stackoverflow.com/questions/6708760/non-blocking-call-to-external-program-without-losing-return-code
>> http://www.mathworks.com/matlabcentral/newsreader/view_thread/324084
>> http://www.perlmonks.org/?node_id=768159
>>
>> On Mar 25, 2013, at 6:06 PM, Anouk Post wrote:
>>
>>> Dear VMTK Users,
>>> I am using VMTK to calculate centerlines of stl files. This is part of a 3D reconstruction process for which I use MATLAB. I really want to incorporate the VMTK part of the process into my MATLAB code.
>>> Does anyone know how I can call VMTK from MATLAB and execute a VMTK script?
>>> Thanks!
>>> Best wishes,
>>> Anouk
>>>
>>> P.S. My VMTK code is:
>>> vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>>
>> --
>> Best Wishes,
>>
>> Anouk
>> ------------------------------------------------------------------------------
>> Own the Future-Intel(R) Level Up Game Demo Contest 2013
>> Rise to greatness in Intel's independent game demo contest. Compete
>> for recognition, cash, and the chance to get your game on Steam.
>> $5K grand prize plus 10 genre and skill prizes. Submit your demo
>> by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
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From: Gawlitza, M. <Mat...@me...> - 2013-04-01 19:49:06
|
cool, thanks guys, it`s working now! Greetings from GER ________________________________________ Von: Berkowitz, Benjamin M [ben...@ui...] Gesendet: Montag, 1. April 2013 19:33 An: Luca Antiga Cc: Gawlitza, Matthias; vmt...@li... Betreff: ***SPAM*** Re: [vmtk-users] Problem: Interactor? Cannot move image planes in the renderer Looks like Luca's trick with the Alt key works too. Good to know. Ben On Mar 29, 2013, at 7:48 AM, Luca Antiga <luc...@gm...> wrote: > Hi Mat, > I'm not sure about the problem you're experiencing. I'm developing vmtk on a OSX 10.7 machine and I've never > bumped into this problem. > Did you try holding the Alt key while pressing the left mouse button to move the planes? > > Luca > > On Mar 24, 2013, at 7:52 PM, Gawlitza, Matthias wrote: > >> 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: vmt...@li... [vmt...@li...] >> Gesendet: Donnerstag, 21. März 2013 18:17 >> An: vmt...@li... >> Betreff: vmtk-users Digest, Vol 65, Issue 19 >> >> Send vmtk-users mailing list submissions to >> vmt...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> or, via email, send a message with subject or body 'help' to >> vmt...@li... >> >> You can reach the person managing the list at >> vmt...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of vmtk-users digest..." >> >> >> 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 <gre...@gm...> >> Subject: [vmtk-users] conformal/parametrized mapping ( 3D surface mesh >> to 2D plane ) with vmtk ? >> To: vmt...@li... >> Message-ID: >> <CAF...@ma...> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 21 Mar 2013 18:03:48 +0100 >> From: Luca Antiga <luc...@gm...> >> Subject: Re: [vmtk-users] vmtklevelsetsegmentation >> To: Ric...@we... >> Cc: vmt...@li... >> Message-ID: <B07...@gm...> >> 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, Ric...@we... 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 >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ >>> vmtk-users mailing list >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 21 Mar 2013 18:15:50 +0100 >> From: Luca Antiga <luc...@or...> >> Subject: Re: [vmtk-users] Computing centerline geometry >> To: qiang zeng <zen...@ya...> >> Cc: vmt...@li... >> Message-ID: <F39...@or...> >> 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 >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: foobar.vtp >> Type: application/octet-stream >> Size: 370380 bytes >> Desc: not available >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Screen Shot 2013-03-21 at 6.13.26 PM.png >> Type: image/png >> Size: 97833 bytes >> Desc: not available >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> >> End of vmtk-users Digest, Vol 65, Issue 19 >> ****************************************** >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > ------------------------------------------------------------------------------ > Own the Future-Intel(R) Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. Compete > for recognition, cash, and the chance to get your game on Steam. > $5K grand prize plus 10 genre and skill prizes. Submit your demo > by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Berkowitz, B. M <ben...@ui...> - 2013-04-01 17:55:36
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Anouk, You would need to have vmtk command line functionality implemented in order to use the vmtkscripts with the system function (http://www.vmtk.org/Main/Installation/). Ben On Mar 29, 2013, at 7:58 AM, Anouk Post <ano...@gm...> wrote: > Hi Luca, > > Thanks! > > I do understand how I can open VMTK from MATLAB, but not how to actually run a VMTK 'script' from MATLAB. When I use the system function it just opens pypepad. Do you know how I can actually let it run a VMTK script? > > Best wishse, > > Anouk > > On 29 March 2013 12:56, Luca Antiga <luc...@gm...> wrote: > Hi Anouk, > you'll probably have to use the system() function in Matlab to call vmtk the way you call it from the command line. > It should work. > > Luca > > PS: a couple of random references on the system function > > http://stackoverflow.com/questions/6708760/non-blocking-call-to-external-program-without-losing-return-code > http://www.mathworks.com/matlabcentral/newsreader/view_thread/324084 > http://www.perlmonks.org/?node_id=768159 > > On Mar 25, 2013, at 6:06 PM, Anouk Post wrote: > >> Dear VMTK Users, >> I am using VMTK to calculate centerlines of stl files. This is part of a 3D reconstruction process for which I use MATLAB. I really want to incorporate the VMTK part of the process into my MATLAB code. >> Does anyone know how I can call VMTK from MATLAB and execute a VMTK script? >> Thanks! >> Best wishes, >> Anouk >> >> P.S. My VMTK code is: >> vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > > > -- > Best Wishes, > > Anouk > ------------------------------------------------------------------------------ > Own the Future-Intel(R) Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. Compete > for recognition, cash, and the chance to get your game on Steam. > $5K grand prize plus 10 genre and skill prizes. Submit your demo > by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Berkowitz, B. M <ben...@ui...> - 2013-04-01 17:34:01
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Looks like Luca's trick with the Alt key works too. Good to know. Ben On Mar 29, 2013, at 7:48 AM, Luca Antiga <luc...@gm...> wrote: > Hi Mat, > I'm not sure about the problem you're experiencing. I'm developing vmtk on a OSX 10.7 machine and I've never > bumped into this problem. > Did you try holding the Alt key while pressing the left mouse button to move the planes? > > Luca > > On Mar 24, 2013, at 7:52 PM, Gawlitza, Matthias wrote: > >> 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: vmt...@li... [vmt...@li...] >> Gesendet: Donnerstag, 21. März 2013 18:17 >> An: vmt...@li... >> Betreff: vmtk-users Digest, Vol 65, Issue 19 >> >> Send vmtk-users mailing list submissions to >> vmt...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> or, via email, send a message with subject or body 'help' to >> vmt...@li... >> >> You can reach the person managing the list at >> vmt...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of vmtk-users digest..." >> >> >> 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 <gre...@gm...> >> Subject: [vmtk-users] conformal/parametrized mapping ( 3D surface mesh >> to 2D plane ) with vmtk ? >> To: vmt...@li... >> Message-ID: >> <CAF...@ma...> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 21 Mar 2013 18:03:48 +0100 >> From: Luca Antiga <luc...@gm...> >> Subject: Re: [vmtk-users] vmtklevelsetsegmentation >> To: Ric...@we... >> Cc: vmt...@li... >> Message-ID: <B07...@gm...> >> 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, Ric...@we... 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 >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ >>> vmtk-users mailing list >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 21 Mar 2013 18:15:50 +0100 >> From: Luca Antiga <luc...@or...> >> Subject: Re: [vmtk-users] Computing centerline geometry >> To: qiang zeng <zen...@ya...> >> Cc: vmt...@li... >> Message-ID: <F39...@or...> >> 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 >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: foobar.vtp >> Type: application/octet-stream >> Size: 370380 bytes >> Desc: not available >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Screen Shot 2013-03-21 at 6.13.26 PM.png >> Type: image/png >> Size: 97833 bytes >> Desc: not available >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> >> End of vmtk-users Digest, Vol 65, Issue 19 >> ****************************************** >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > ------------------------------------------------------------------------------ > Own the Future-Intel(R) Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. Compete > for recognition, cash, and the chance to get your game on Steam. > $5K grand prize plus 10 genre and skill prizes. Submit your demo > by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Berkowitz, B. M <ben...@ui...> - 2013-04-01 17:31:10
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Mat, I tried to do that with the Magic Mouse and BetterTouchTool. I couldn't get it to work. If you shell out a few bucks for a simple scroll-wheel mouse you can use that mouse specifically to move the image planes and the Magic Mouse for everything else. It's clunky but it works. Ben On Mar 29, 2013, at 7:48 AM, Luca Antiga <luc...@gm...> wrote: > Hi Mat, > I'm not sure about the problem you're experiencing. I'm developing vmtk on a OSX 10.7 machine and I've never > bumped into this problem. > Did you try holding the Alt key while pressing the left mouse button to move the planes? > > Luca > > On Mar 24, 2013, at 7:52 PM, Gawlitza, Matthias wrote: > >> 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: vmt...@li... [vmt...@li...] >> Gesendet: Donnerstag, 21. März 2013 18:17 >> An: vmt...@li... >> Betreff: vmtk-users Digest, Vol 65, Issue 19 >> >> Send vmtk-users mailing list submissions to >> vmt...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> or, via email, send a message with subject or body 'help' to >> vmt...@li... >> >> You can reach the person managing the list at >> vmt...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of vmtk-users digest..." >> >> >> 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 <gre...@gm...> >> Subject: [vmtk-users] conformal/parametrized mapping ( 3D surface mesh >> to 2D plane ) with vmtk ? >> To: vmt...@li... >> Message-ID: >> <CAF...@ma...> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 21 Mar 2013 18:03:48 +0100 >> From: Luca Antiga <luc...@gm...> >> Subject: Re: [vmtk-users] vmtklevelsetsegmentation >> To: Ric...@we... >> Cc: vmt...@li... >> Message-ID: <B07...@gm...> >> 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, Ric...@we... 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 >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ >>> vmtk-users mailing list >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 21 Mar 2013 18:15:50 +0100 >> From: Luca Antiga <luc...@or...> >> Subject: Re: [vmtk-users] Computing centerline geometry >> To: qiang zeng <zen...@ya...> >> Cc: vmt...@li... >> Message-ID: <F39...@or...> >> 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 >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: foobar.vtp >> Type: application/octet-stream >> Size: 370380 bytes >> Desc: not available >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Screen Shot 2013-03-21 at 6.13.26 PM.png >> Type: image/png >> Size: 97833 bytes >> Desc: not available >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> >> End of vmtk-users Digest, Vol 65, Issue 19 >> ****************************************** >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > ------------------------------------------------------------------------------ > Own the Future-Intel(R) Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. Compete > for recognition, cash, and the chance to get your game on Steam. > $5K grand prize plus 10 genre and skill prizes. Submit your demo > by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Berkowitz, B. M <ben...@ui...> - 2013-04-01 17:22:11
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Hi, I'm interested in implementing some of the great functionality from the vtkvmtk C++ libraries into my programs. Is there a simple way to include all vtkvmtk libraries in my CMakeLists.txt file? Thanks Ben |
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From: adrianrh <adr...@st...> - 2013-03-31 16:39:16
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Hello Luca, Thank you for the answer, it is helpful. I actually need to combine images from the same geometry and from different geometries at different points in my work. I have some higher quality MR scans that are on a smaller domain and would like to understand how to combine it with a lower quality image of a bigger domain. So getting some more details would really be nice. Best regards Adrian On 2013-03-29 13:53, Luca Antiga wrote: > Hello Adrian, > > there is a way of combining level set files. After all, they are all > image files, so here's how you do it: > > in case they are all produced from the same input image (i.e. they > have the same geometry), you can go > vmtkimagecompose -ifile ls1.vti -i2file ls2.vti -ofile ls_combined.vti > If you have more than 2, you'll have to call another vmtkimagecompose > on the result of the former; > > in case they are produced from different input images (hence they > have different spatial extents) you'll first have to resample them > onto > a common grid using vmtkimagereslice; let me know if this is your case > and I'll provide you with more details. > > Best, > > Luca > > On Mar 25, 2013, at 3:08 PM, adrianrh wrote: > >> Hi! >> >> I am working on segmenting water in the brain for simula research >> laboratory. >> >> I am using the command >> "vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile >> level_sets.vti -ofile level_setsOut.vti" >> to continue working on a project. >> >> what I would really like to be able to do is to make multiple >> levelsets >> files and then combine them. Like this; >> >> vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile >> level_sets.vti -levelsetsfile level_sets2.vti -ofile >> level_setsOut.vti >> >> is it possible to do this in the vmtk software? or possible to add >> it? >> >> Adrian Hope >> >> ------------------------------------------------------------------------------ >> 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 [1] >> _______________________________________________ >> vmtk-users mailing list >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > > Links: > ------ > [1] http://p.sf.net/sfu/appdyn_d2d_mar |
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From: Luca A. <luc...@gm...> - 2013-03-29 13:35:39
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Hi YiQiang, the angles you get from vmtk are explained in http://www.vmtk.org/Tutorials/GeometricAnalysis/, "Computing bifurcation geometry" section. The ICA angle is the difference between the two downstream inplane angles, while the planarity angle is the difference between the upstream and downstream out of plane angles. Hope this gives you a hint Luca On Mar 28, 2013, at 9:10 AM, qiang zeng wrote: > Dear VMTK users, > In my works, I need to calculate the ICA angle and planarity angle like the Stroke 2005 paper. but I didn't get the result from the Paraview. > Does anyone know a way to do this? > > Thanks in advance! > Best wishes, > YiQiang Zeng > ------------------------------------------------------------------------------ > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@or...> - 2013-03-29 13:28:40
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Hi Anouk, this is what I'd expect from -seedselector idlist, not -seedselector profileidlist. Are you sure it was the latter and not the former? Luca On Mar 29, 2013, at 2:07 PM, Anouk Post wrote: > Hi Luca, > > I already tried that and it didn't work. It gave me only a partial reconstruction of the centerline (a very short one). > > Best, > > Anouk > > On 29 March 2013 13:04, Luca Antiga <luc...@or...> wrote: > Hi Anouk, > try with > -seedselector profileidlist -sourceids 0 -targetids 1 > > (hoping you have a recent enough version of vmtk) > > Best, > > > Luca > > > On Mar 25, 2013, at 7:36 PM, Anouk Post wrote: > >> Dear VMTK users, >> >> I am using VMTK centerline to calculate the centerline of an stl file as follows: >> >> vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat >> >> >> >> For all the different input files I use, the seedselector option always leads to me pressing 'q' '0' '1' and then it works. So I close the viewer, and I think I set the source id as 0 and the target id as 1. >> >> Is there a way to make this an automatic process so I don't have to type q, 0, 1 each time? I've tried using seedselector idlist but I'm not sure how to use it (it does not give me the right answer when I use -sourceids 0 -targetids 1. >> >> Does anyone know a way to do this? >> >> >> Thanks in advance! >> >> >> Best wishes, >> >> >> Anouk >> >> ------------------------------------------------------------------------------ >> 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > > > -- > Best Wishes, > > Anouk > ------------------------------------------------------------------------------ > Own the Future-Intel(R) Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. Compete > for recognition, cash, and the chance to get your game on Steam. > $5K grand prize plus 10 genre and skill prizes. Submit your demo > by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Anouk P. <ano...@gm...> - 2013-03-29 13:07:40
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Hi Luca, I already tried that and it didn't work. It gave me only a partial reconstruction of the centerline (a very short one). Best, Anouk On 29 March 2013 13:04, Luca Antiga <luc...@or...> wrote: > Hi Anouk, > try with > -seedselector profileidlist -sourceids 0 -targetids 1 > > (hoping you have a recent enough version of vmtk) > > Best, > > > Luca > > > On Mar 25, 2013, at 7:36 PM, Anouk Post wrote: > > Dear VMTK users, > > I am using VMTK centerline to calculate the centerline of an stl file as > follows: > > vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f > "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles > --pipe vmtkcenterlinegeometry -ofile > /Users/.../Phantom_Best_Catheter_now_output.dat > > > For all the different input files I use, the seedselector option always > leads to me pressing 'q' '0' '1' and then it works. So I close the viewer, > and I think I set the source id as 0 and the target id as 1. > > Is there a way to make this an automatic process so I don't have to type > q, 0, 1 each time? I've tried using seedselector idlist but I'm not sure > how to use it (it does not give me the right answer when I use -sourceids 0 > -targetids 1. > > Does anyone know a way to do this? > > > Thanks in advance! > > > Best wishes, > > > Anouk > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > -- Best Wishes, Anouk |
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From: Luca A. <luc...@or...> - 2013-03-29 13:04:54
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Hi Anouk, try with -seedselector profileidlist -sourceids 0 -targetids 1 (hoping you have a recent enough version of vmtk) Best, Luca On Mar 25, 2013, at 7:36 PM, Anouk Post wrote: > Dear VMTK users, > > I am using VMTK centerline to calculate the centerline of an stl file as follows: > > vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat > > > > For all the different input files I use, the seedselector option always leads to me pressing 'q' '0' '1' and then it works. So I close the viewer, and I think I set the source id as 0 and the target id as 1. > > Is there a way to make this an automatic process so I don't have to type q, 0, 1 each time? I've tried using seedselector idlist but I'm not sure how to use it (it does not give me the right answer when I use -sourceids 0 -targetids 1. > > Does anyone know a way to do this? > > > Thanks in advance! > > > Best wishes, > > > Anouk > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Anouk P. <ano...@gm...> - 2013-03-29 12:58:40
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Hi Luca, Thanks! I do understand how I can open VMTK from MATLAB, but not how to actually run a VMTK 'script' from MATLAB. When I use the system function it just opens pypepad. Do you know how I can actually let it run a VMTK script? Best wishse, Anouk On 29 March 2013 12:56, Luca Antiga <luc...@gm...> wrote: > Hi Anouk, > you'll probably have to use the system() function in Matlab to call vmtk > the way you call it from the command line. > It should work. > > Luca > > PS: a couple of random references on the system function > > > http://stackoverflow.com/questions/6708760/non-blocking-call-to-external-program-without-losing-return-code > http://www.mathworks.com/matlabcentral/newsreader/view_thread/324084 > http://www.perlmonks.org/?node_id=768159 > > On Mar 25, 2013, at 6:06 PM, Anouk Post wrote: > > Dear VMTK Users, > > I am using VMTK to calculate centerlines of stl files. This is part of a 3D reconstruction process for which I use MATLAB. I really want to incorporate the VMTK part of the process into my MATLAB code. > > Does anyone know how I can call VMTK from MATLAB and execute a VMTK script? > > Thanks! > > Best wishes, > > Anouk > > > P.S. My VMTK code is: > > vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat > > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > -- Best Wishes, Anouk |
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From: Luca A. <luc...@gm...> - 2013-03-29 12:56:51
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Hi Anouk, you'll probably have to use the system() function in Matlab to call vmtk the way you call it from the command line. It should work. Luca PS: a couple of random references on the system function http://stackoverflow.com/questions/6708760/non-blocking-call-to-external-program-without-losing-return-code http://www.mathworks.com/matlabcentral/newsreader/view_thread/324084 http://www.perlmonks.org/?node_id=768159 On Mar 25, 2013, at 6:06 PM, Anouk Post wrote: > Dear VMTK Users, > I am using VMTK to calculate centerlines of stl files. This is part of a 3D reconstruction process for which I use MATLAB. I really want to incorporate the VMTK part of the process into my MATLAB code. > Does anyone know how I can call VMTK from MATLAB and execute a VMTK script? > Thanks! > Best wishes, > Anouk > > P.S. My VMTK code is: > vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@gm...> - 2013-03-29 12:53:24
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Hello Adrian, there is a way of combining level set files. After all, they are all image files, so here's how you do it: in case they are all produced from the same input image (i.e. they have the same geometry), you can go vmtkimagecompose -ifile ls1.vti -i2file ls2.vti -ofile ls_combined.vti If you have more than 2, you'll have to call another vmtkimagecompose on the result of the former; in case they are produced from different input images (hence they have different spatial extents) you'll first have to resample them onto a common grid using vmtkimagereslice; let me know if this is your case and I'll provide you with more details. Best, Luca On Mar 25, 2013, at 3:08 PM, adrianrh wrote: > Hi! > > I am working on segmenting water in the brain for simula research > laboratory. > > I am using the command > "vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile > level_sets.vti -ofile level_setsOut.vti" > to continue working on a project. > > what I would really like to be able to do is to make multiple levelsets > files and then combine them. Like this; > > vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile > level_sets.vti -levelsetsfile level_sets2.vti -ofile level_setsOut.vti > > is it possible to do this in the vmtk software? or possible to add it? > > Adrian Hope > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@or...> - 2013-03-29 12:48:59
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Hello Greg, first of all thanks for your patience. Replies are inline: On Mar 21, 2013, at 1:44 AM, Greg Fokum wrote: > 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. Ok. > 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. Note that we don't have full conformal mapping in vmtk: we can create a longitudinal harmonic map, but the missing part is the harmonic mapping in the circumferential direction. (I'm just mentioning this in case you are looking for a fully conformal map as in the literature). > 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. It's quite easy to create a mapping to the plane of a cylindrical structure in vmtk. Just follow this tutorial http://www.vmtk.org/Tutorials/MappingAndPatching/ and even if you have no branchings, just try running the scripts the same way. For a mapping to the cylinder, then you'll have to code a bit. Actually a lot of the basic tools are there in vmtk already (differential geometry classes for the mappings etc), but it would require you to code, you can't just do it from the command line. Feel free to seek more specific inputs on the list. Thanks Luca > thank you > > GT > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@gm...> - 2013-03-29 12:48:37
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Hi Mat, I'm not sure about the problem you're experiencing. I'm developing vmtk on a OSX 10.7 machine and I've never bumped into this problem. Did you try holding the Alt key while pressing the left mouse button to move the planes? Luca On Mar 24, 2013, at 7:52 PM, Gawlitza, Matthias wrote: > 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: vmt...@li... [vmt...@li...] > Gesendet: Donnerstag, 21. März 2013 18:17 > An: vmt...@li... > Betreff: vmtk-users Digest, Vol 65, Issue 19 > > Send vmtk-users mailing list submissions to > vmt...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/vmtk-users > or, via email, send a message with subject or body 'help' to > vmt...@li... > > You can reach the person managing the list at > vmt...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of vmtk-users digest..." > > > 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 <gre...@gm...> > Subject: [vmtk-users] conformal/parametrized mapping ( 3D surface mesh > to 2D plane ) with vmtk ? > To: vmt...@li... > Message-ID: > <CAF...@ma...> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Thu, 21 Mar 2013 18:03:48 +0100 > From: Luca Antiga <luc...@gm...> > Subject: Re: [vmtk-users] vmtklevelsetsegmentation > To: Ric...@we... > Cc: vmt...@li... > Message-ID: <B07...@gm...> > 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, Ric...@we... 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 >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ >> vmtk-users mailing list >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Thu, 21 Mar 2013 18:15:50 +0100 > From: Luca Antiga <luc...@or...> > Subject: Re: [vmtk-users] Computing centerline geometry > To: qiang zeng <zen...@ya...> > Cc: vmt...@li... > Message-ID: <F39...@or...> > 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 >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: foobar.vtp > Type: application/octet-stream > Size: 370380 bytes > Desc: not available > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Screen Shot 2013-03-21 at 6.13.26 PM.png > Type: image/png > Size: 97833 bytes > Desc: not available > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users > > > End of vmtk-users Digest, Vol 65, Issue 19 > ****************************************** > > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@or...> - 2013-03-29 12:43:32
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Hi Evan, On Mar 22, 2013, at 9:48 PM, Evan Kao wrote: > Hello, > > I am trying to segment a particular set of 3D-cine images with vmtklevelsetsegmentation, but the perhaps due to the shape of the vessel and/or quality of the images, the suggested settings of 300 0 0 1 isn't working well. I've tried playing around with the level set deformation parameters, but the resultant shapes feel just as arbitrary as if I had simply used thresholds directly. Can you recommend any guides or references that can explain in more depth (i.e. quantitatively) how the parameters affect the deformation, and/or also provide an explanation of the additional options available in vmtklevelsetsegmentation that weren't covered in the tutorials? The level set parameters are those of itkGeodesicActiveContourLevelSetImageFilter and itkGeodesicActiveContourLevelSetFunction. http://www.itk.org/Doxygen/html/classitk_1_1GeodesicActiveContourLevelSetImageFilter.html http://www.itk.org/Doxygen/html/classitk_1_1GeodesicActiveContourLevelSetFunction.html The main reference for level set methods is J. A. Sethian, "Level Set Methods and Fast Marching Methods", Cambridge University Press, 1996. but you can find a lot of material around. You may want to take a look at my PhDThesis (good old times) at lantiga.github.com/about/ If you have noise issues, I suggest you to use a non-zero featurederivativesigma , which expresses the width of the gaussian kernel used for performing partial derivatives for the feature image. It's expressed in physical spatial units (e.g. mm) and it's roughly related to the minimum scale that you'll end up detecting in the image - i.e. the noise below that spatial scale is going to be filtered out, thus not affecting the evolution of level sets (again, roughly speaking). Feel free to post a couple of screenshots of the problem you're having, so that replies can be more to the point. Best, Luca > Thank you, > Evan Kao > ------------------------------------------------------------------------------ > 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 > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: qiang z. <zen...@ya...> - 2013-03-28 08:10:36
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Dear VMTK users, In my works, I need to calculate the ICA angle and planarity angle like the Stroke 2005 paper. but I didn't get the result from the Paraview. Does anyone know a way to do this? Thanks in advance! Best wishes, YiQiang Zeng |
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From: Anouk P. <ano...@gm...> - 2013-03-25 18:36:07
|
Dear VMTK users, I am using VMTK centerline to calculate the centerline of an stl file as follows: vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat For all the different input files I use, the seedselector option always leads to me pressing 'q' '0' '1' and then it works. So I close the viewer, and I think I set the source id as 0 and the target id as 1. Is there a way to make this an automatic process so I don't have to type q, 0, 1 each time? I've tried using seedselector idlist but I'm not sure how to use it (it does not give me the right answer when I use -sourceids 0 -targetids 1. Does anyone know a way to do this? Thanks in advance! Best wishes, Anouk |
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From: Anouk P. <ano...@gm...> - 2013-03-25 17:07:05
|
Dear VMTK Users, I am using VMTK to calculate centerlines of stl files. This is part of a 3D reconstruction process for which I use MATLAB. I really want to incorporate the VMTK part of the process into my MATLAB code. Does anyone know how I can call VMTK from MATLAB and execute a VMTK script? Thanks! Best wishes, Anouk P.S. My VMTK code is: vmtksurfacereader -ifile /Users/.../Phantom_Best_Catheter_now.stl -f "stl" --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile /Users/.../Phantom_Best_Catheter_now_output.dat |
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From: adrianrh <adr...@st...> - 2013-03-25 14:27:06
|
Hi! I am working on segmenting water in the brain for simula research laboratory. I am using the command "vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile level_sets.vti -ofile level_setsOut.vti" to continue working on a project. what I would really like to be able to do is to make multiple levelsets files and then combine them. Like this; vmtklevelsetsegmentation -ifile image_volume_voi.vti -levelsetsfile level_sets.vti -levelsetsfile level_sets2.vti -ofile level_setsOut.vti is it possible to do this in the vmtk software? or possible to add it? Adrian Hope |
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From: Gawlitza, M. <Mat...@me...> - 2013-03-24 18:53:01
|
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: vmt...@li... [vmt...@li...]
Gesendet: Donnerstag, 21. März 2013 18:17
An: vmt...@li...
Betreff: vmtk-users Digest, Vol 65, Issue 19
Send vmtk-users mailing list submissions to
vmt...@li...
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/vmtk-users
or, via email, send a message with subject or body 'help' to
vmt...@li...
You can reach the person managing the list at
vmt...@li...
When replying, please edit your Subject line so it is more specific
than "Re: Contents of vmtk-users digest..."
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 <gre...@gm...>
Subject: [vmtk-users] conformal/parametrized mapping ( 3D surface mesh
to 2D plane ) with vmtk ?
To: vmt...@li...
Message-ID:
<CAF...@ma...>
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
-------------- next part --------------
An HTML attachment was scrubbed...
------------------------------
Message: 2
Date: Thu, 21 Mar 2013 18:03:48 +0100
From: Luca Antiga <luc...@gm...>
Subject: Re: [vmtk-users] vmtklevelsetsegmentation
To: Ric...@we...
Cc: vmt...@li...
Message-ID: <B07...@gm...>
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, Ric...@we... 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
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________
> vmtk-users mailing list
> vmt...@li...
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Message: 3
Date: Thu, 21 Mar 2013 18:15:50 +0100
From: Luca Antiga <luc...@or...>
Subject: Re: [vmtk-users] Computing centerline geometry
To: qiang zeng <zen...@ya...>
Cc: vmt...@li...
Message-ID: <F39...@or...>
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>------------------------------------------------------------------------------
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