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 ------------------------------------------------------------------------------ _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
