Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

What I tried to give is the physical position of the origin in an ITK image: a vector shift of -m_Origin from the center of the first pixel. I didn't mean the position represented by indices. I should say "... In ITK this is at Pixel(0,0)−m_Origin in 2D or Voxel(0,0,0)−m_Origin in 3D in physical

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

It's actually more complex than that. The index to mm conversion is m_Direction*m_Spacing*index+m_Origin so point with all mm coordinates at 0 has index (that's what you're trying to give ?) -m_Spacing^-1*m_Direction^-1*m_Origin. I find it a bit too complex for this documentation which is not

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Looks great. Now I understand you story about point (0,0) and the itk m_Origin. I read point (0,0) as pixel (0,0) yesterday so I was confused. "point (0,0)" followed by "mm" is much less ambiguous. Maybe instead of saying "... (and not to m_Origin in ITK)", you can write down the actual

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi, I have made some amendments to the documentation to try to clarify this: https://github.com/SimonRit/RTK/commit/fea8e136b7248f42be29ef2d5fbaf3d26e12cfbb http://www.openrtk.org/Doxygen/DocGeo3D.html Any suggestion to improve this is welcome. Best regards, Simon On Tue, Aug 21, 2018 at 4:39 PM

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi, To be honest, it's quite hard to guess the meaning of YS in test.pcj but I would be suprised if it corresponds to source_y... Maybe you should find the documentation regarding the meaning of YS and we can help in relating it to RTK's geometry parameters. Best regards, Simon On Tue, Aug 21,

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi Simon, my understanding of origin in this context was wrong. Your advise makes sense and I ran the reconstruction succesfully by setting the values --proj_iso_x=-202.3 --proj_iso_y=-202.3. I didn't investigate the result further, but at first glance it is a big step ahead for me. Regarding

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Thank you for the clarification and confirmation of the minus sign here. To me the source of confusion is the description of --proj_iso_x and --proj_iso_x in the command line (or from the GGO file): > option "proj_iso_x" - "X coordinate on the projection image of > isocenter" double no

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Sorry, I checked the doc and you're right, "(ProjectionOffsetX,ProjectionOffsetY,SourceToIsocenterDistance-SourceToDetectorDistance) are the coordinates of the detector origin in the rotated coordinated system". So yes, add minus signs in front of

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi Simon, The --proj_iso_x and --proj_iso_y arguments are confusing to me. Their explanation states that they are the X/Y coordinates on the projection image of isocenter, but in practice I found them to be the projection offset in X/Y wrt to central ray (similar to --source_x and --source_y

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi, It's not clear to me how you came up with your source_y value. Assuming that the origin of your projections is 0,0,0, I would advise to set the geometry with --proj_iso_x=202.3 --proj_iso_y=202.3 (or, equivalently, set a new origin to the projection equal to -202.3,-202.3,0). The --arc value

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi Milan 1) OK, I guess it makes sense with the source/detector geometry. 2) I forgot to check which group RawImageIO was in; it's own apparently. So you'll have to re-compile ITK with the CMake option: Module_ITKIORAW=ON (You'll have to add the entry manually if you use a CMake GUI) 3) Origin

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi Andreas, I am really grateful that you've found time to response so quickly. 1) Following your suggestions I first checked the spacing. I suppose, you refer to the value of 0.03840368. I am confident, this is the correct value in the correct unit (mm). The 4D Slicer shows the dimensions in

Re: [Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi Milan I didn't open the dropbox link, but I think in general one should take an extra look at the rtkfdk arguments if nothing "meaningful" comes out: Is your spacing in the correct unit (mm)? it seems quite small in relation to the dimensions. Also try adding the --origin argument.

[Rtk-users] Cannot reconstruct the volume, what might be the problem?

Hi RTK-users, I am trying to reconstruct a sample scanned using the CBCT. Rtk seems to be the best chioce for that, but unfortenately I have no success. Hopefully, some of you guys can help. The outcome of the scanning are 2500 projections (each 2024x2024 pixels). The increasement of the