Hi Caspar, the strange think is that if I create a smooth surface everything seems to be fine (from loading to segmentation to generation of the polygon everything is consisten), but I checked with a doctor who told that the generated surface is flipped.
He gave to me an example of what should I get to compare it. The folowing two images are, in order, the example one and the one generated with MITK. https://www.dropbox.com/s/us08dqzbyz8yol6/RightWay.png?dl=0 https://www.dropbox.com/s/4e1a8k5kryn3sth/MITKSmoothPolygon.png?dl=0 Hope this will be helpful :) Cheers, Yari Il 16.06.2015 16:57, Goch, Caspar Jonas ha scritto: > Hi Yari, > > good to hear. Nonetheless If you happen to acquire data which can be shared > and reproduces that error we would be happy to take a look at it and find the > cause of the bug. > > Best, > Caspar > > -----Ursprüngliche Nachricht----- > Von: yari mattei [mailto:[email protected]] > Gesendet: Dienstag, 16. Juni 2015 15:40 > An: [email protected] > Betreff: Re: [mitk-users] Mirror image > > Hi Caspar, > > sorry I am freaking out. The flipping filter (which was always there) > actually solve the problem. > After flipping across axis 1, I create the segmentation and then the smoothed > polygon model which is finally at in the right orientation. > > Thanks a lot. > > Cheers, > Yari > > Il 16.06.2015 15:18, Goch, Caspar Jonas ha scritto: >> Hi Yari, >> >> if you select an image and open the "choose an operation" dropdown box >> there should be a scrollbar on the right. At the very bottom should be >> a section "Misc" which, among others, contains a "Flipping" Filter >> >> Best, >> Caspar >> >> -----Ursprüngliche Nachricht----- >> Von: yari mattei [mailto:[email protected]] >> Gesendet: Dienstag, 16. Juni 2015 14:42 >> An: [email protected] >> Betreff: Re: [mitk-users] Mirror image >> >> Hi Caspar, >> >> I am trying to do what you suggest but on the "basic image processing" I >> cannot find anything to flip image (just denoising and morphological filters >> and arithmetic to do on 2 images) I also tried to look around in the other >> view but I didn't find anything. >> >> Am I making some mistake? >> >> Thanks >> Yari >> >> Il 16.06.2015 14:00, Goch, Caspar Jonas ha scritto: >>> Hi Yari, >>> >>> as far as I am aware there is no button for it in the MITK binary release. >>> However... the MITK Diffusion 2014.10.02 binary release contains the "basic >>> image processing" view, which is able to flip images (no surface though) so >>> you could flip the image to match the surface. This might not be what you >>> want, depending on your use case. >>> >>> Does this help? >>> >>> Best, >>> Caspar >>> >>> -----Ursprüngliche Nachricht----- >>> Von: yari mattei [mailto:[email protected]] >>> Gesendet: Dienstag, 16. Juni 2015 13:32 >>> An: [email protected] >>> Betreff: Re: [mitk-users] Mirror image >>> >>> Hi Caspar, >>> >>> thanks for the answer, at the moment I have only real image that I cannot >>> share but I asked for a sherable sample. >>> So there is no way to mirror the coordinate - of one of the three >>> views >>> - directly in the binary release? >>> >>> Do you know perhaps another way to do that? >>> >>> Cheers, >>> Yari >>> >>> Il 15.06.2015 17:15, Goch, Caspar Jonas ha scritto: >>>> Hi Yari, >>>> >>>> I just tried the same pipeline on some image we had here using the 2014.10 >>>> binary release and I cannot reproduce that behavior. Would it be possible >>>> for you to provide a test data set on which the error occurs so we can try >>>> and narrow it down? The details look ok to me. >>>> >>>> Best, >>>> Caspar >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: yari mattei [mailto:[email protected]] >>>> Gesendet: Montag, 15. Juni 2015 15:54 >>>> An: [email protected] >>>> Betreff: Re: [mitk-users] Mirror image >>>> >>>> Hi Caspar, >>>> >>>> Yes the pipeline is exactely the one you describe. Yes the surface is >>>> already mirrored in step 3 (after "create smoothed polygon model" a can >>>> see that the surface is mirrored). >>>> >>>> Because I was not sure about the data you asked me I paste the whole image >>>> details : >>>> >>>> Image (000000000A307E30) >>>> Dimension: 4 >>>> Dimensions: 256 224 208 9 >>>> Channel: Unnamed [] >>>> PixelType: >>>> BytesPerElement: 1 >>>> ComponentType: unsigned_char >>>> NumberOfComponents: 1 >>>> BitsPerComponent: 8 >>>> >>>> TimeGeometry: ProportionalTimeGeometry (000000000A7489E0) >>>> TimeSteps: 9 >>>> FirstTimePoint: 0 >>>> StepDuration: 1 ms >>>> Time Bounds: 0 - 9 >>>> >>>> GetGeometryForTimeStep(0): SlicedGeometry3D (000000000A45BB00) >>>> IndexToWorldTransform: >>>> Matrix: >>>> 0.343466 0 0 >>>> 0 0.346719 0 >>>> 0 0 0.198195 >>>> Offset: [0, 0, 0] >>>> Center: [0, 0, 0] >>>> Translation: [0, 0, 0] >>>> Inverse: >>>> 2.91149 0 0 >>>> 0 2.88418 0 >>>> 0 0 5.04553 >>>> Scale : 1 1 1 >>>> BoundingBox: ( 0,256 0,224 0,208 ) >>>> Origin: [0, 0, 0] >>>> ImageGeometry: 1 >>>> Spacing: [0.343466, 0.346719, 0.198195] >>>> EvenlySpaced: 1 >>>> DirectionVector: [0, 0, 1] >>>> Slices: 208 >>>> >>>> GetPlaneGeometry(0): PlaneGeometry (000000000A0882E0) >>>> IndexToWorldTransform: >>>> Matrix: >>>> 0.343466 0 0 >>>> 0 0.346719 0 >>>> 0 0 0.198195 >>>> Offset: [0, 0, 0] >>>> Center: [0, 0, 0] >>>> Translation: [0, 0, 0] >>>> Inverse: >>>> 2.91149 0 0 >>>> 0 2.88418 0 >>>> 0 0 5.04553 >>>> Scale : 1 1 1 >>>> BoundingBox: ( 0,256 0,224 0,1 ) >>>> Origin: [0, 0, 0] >>>> ImageGeometry: 1 >>>> Spacing: [0.343466, 0.346719, 0.198195] >>>> ScaleFactorMMPerUnitX: 0.343466 >>>> ScaleFactorMMPerUnitY: 0.346719 >>>> Normal: [0, 0, 0.198195] >>>> >>>> At the moment I am using the build-in functionality and I would like to >>>> know how to do it in the binary application. >>>> >>>> Cheers >>>> >>>> Yari >>>> >>>> Il 15.06.2015 14:45, Goch, Caspar Jonas ha scritto: >>>>> Hi Yari, >>>>> >>>>> just to be clear, your workflow is: >>>>> 1. Load a dicom file >>>>> 2. Do a segmentation >>>>> 3. create surface from segmentation 4. Save surface as stl 5. Load >>>>> as stl >>>>> >>>>> Is the stl already mirrored in step 3 or do you need steps 4 and 5? What >>>>> coordinate system is the dicom file in? Could you give the >>>>> matrix/spacing? (right click on image -> Details) Are you using build-in >>>>> MITK functionality for step 3 or do you create the surface yourself? >>>>> >>>>> Are you looking for ways to mirror the surface in the binary application >>>>> or how to do it in code? >>>>> >>>>> Best, >>>>> Caspar >>>>> >>>>> -----Ursprüngliche Nachricht----- >>>>> Von: yari mattei [mailto:[email protected]] >>>>> Gesendet: Freitag, 12. Juni 2015 14:00 >>>>> An: [email protected] >>>>> Betreff: [mitk-users] Mirror image >>>>> >>>>> Hi everybody, >>>>> >>>>> I am using the MITK workbench to produce some stl file from a DICOM file, >>>>> but I have a problem. >>>>> >>>>> I can create the segmentation and save the stl file and it looks good >>>>> besides the fact that is mirrored (just to be clear with mirrored I mean >>>>> that if the image should be AAABBB it appears as BBBAAA). >>>>> >>>>> There is a way to mirror sagital, axial or coronal view in the workbench? >>>>> Or any other way to solve this problem? >>>>> >>>>> I hope that my explanation is clear, if not just let me know. >>>>> >>>>> Best, >>>>> >>>>> Yari >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------- >>>>> - >>>>> - >>>>> - >>>>> -------- _______________________________________________ >>>>> mitk-users mailing list >>>>> [email protected] >>>>> https://lists.sourceforge.net/lists/listinfo/mitk-users >>>> -------------------------------------------------------------------- >>>> - >>>> - >>>> -------- _______________________________________________ >>>> mitk-users mailing list >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/mitk-users >>> --------------------------------------------------------------------- >>> - >>> -------- _______________________________________________ >>> mitk-users mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/mitk-users >> ---------------------------------------------------------------------- >> -------- _______________________________________________ >> mitk-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/mitk-users > > ------------------------------------------------------------------------------ > _______________________________________________ > mitk-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mitk-users ------------------------------------------------------------------------------ Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
