Sorry, I checked the doc <http://www.openrtk.org/Doxygen/DocGeo3D.html> 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 proj_iso_x and proj_iso_y in my email. One source of confusion here (to me too) is that I refer here to "origin" as point "(0,0)" and not to m_Origin in the itk::Image object... Any suggestion to improve this is welcome. On the other hand, you seem to suggest that source offsets and projection offsets are redundant which is not true in a divergent geometry (or I did not get you). Thanks a lot for your correction. Simon
On Tue, Aug 21, 2018 at 3:28 PM Chao Wu <[email protected]> wrote: > 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 arguments). > > Therefore in the above case I would give --proj_iso_x=-202.3 > --proj_iso_y=-202.3 if the image origin is at pixel (0,0) and the +x and +y > directions are aligned with the i and j indices of projection images, > respectively, which is the normal case when reading from TIFF files. > > In rtk::ThreeDCircularProjectionGeometry::AddProjectionInRadians() this > two arguments are named as projOffsetX and projOffsetY, similar to the ones > for the source sourceOffsetX and sourceOffsetY, implying that the argument > description is problematic. The way of calculation of > submatrix AddProjectionTranslationMatrix( > ComputeTranslationHomogeneousMatrix(sourceOffsetX-projOffsetX, > sourceOffsetY-projOffsetY) ) also supports that they are projection origin > wrt isocenter instead of isocenter wrt projection origin. > > Best regards, > Chao > > > Simon Rit <[email protected]> 于2018年8月21日周二 下午1:26写道： > >> 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 is also a bit surprising but you can check if the >> assigned GantryAngle is the correct one for each projection. >> Finally, in rtkfdk, setting origin (this time for the volume) to a >> y-value equal 0 means that you only look at the part above the source >> trajectory. I would leave the default values (centered volume around the >> center of rotation). >> Best regards, >> Simon >> >> >> On Tue, Aug 21, 2018 at 12:01 AM Andreas Andersen <[email protected]> >> wrote: >> >>> 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 is not the isocenter, it is the offset of the image origin, >>> i.e. index 0,0,0, in relation to the isocenter (AFAIK). >>> Just a guess: Try with an offset of: -0.03840368 * {421,0,471} / 2 => >>> "--origin -8.08,0,-9.04" >>> (I forget the definition of the y-axis, so I'm unsure about the "0", if >>> it doesn't work also try -10.23, 10.23, multiplying it by 2, and 0.) >>> >>> Best regards >>> Andreas >>> >>> __________________________________ >>> >>> Andreas Gravgaard Andersen >>> >>> Department of Oncology, >>> >>> Aarhus University Hospital >>> >>> Nørrebrogade 44, >>> >>> 8000, Aarhus C >>> >>> Mail: [email protected] >>> >>> Cell: +45 3165 8140 >>> >>> >>> On Mon, 20 Aug 2018 at 22:10, Milan Manasijevic < >>> [email protected]> wrote: >>> >>>> 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 mm and this is near to the object >>>> measures. >>>> >>>> 2) The second try was to check if the " -o fdk.raw" works. >>>> Unfortunately not, I get such exception: >>>> itk::ImageFileWriterException (000000C71D4FE5D0) >>>> Location: "void __cdecl itk::ImageFileWriter<class itk::Image<float,3> >>>> >::Write(void)" >>>> File: >>>> d:\reconstruction_rtk\itk\modules\io\imagebase\include\itkImageFileWriter.hxx >>>> Line: 151 >>>> Description: Could not create IO object for writing file fdk.raw >>>> Tried to create one of the following: >>>> NiftiImageIO >>>> NrrdImageIO >>>> GiplImageIO >>>> HDF5ImageIO >>>> JPEGImageIO >>>> BMPImageIO >>>> LSMImageIO >>>> PNGImageIO >>>> TIFFImageIO >>>> VTKImageIO >>>> StimulateImageIO >>>> BioRadImageIO >>>> MetaImageIO >>>> MRCImageIO >>>> GE4ImageIO >>>> GE5ImageIO >>>> HndImageIO >>>> XimImageIO >>>> HisImageIO >>>> ImagXImageIO >>>> DCMImagXImageIO >>>> EdfImageIO >>>> XRadImageIO >>>> OraImageIO >>>> GDCMImageIO >>>> You probably failed to set a file suffix, or >>>> set the suffix to an unsupported type. >>>> >>>> >>>> 3) Regarding the "--origin argument" and refering to my context (see >>>> attached files please), what would you suggest, what should I pass as the >>>> origin values? The detecetor origin is at 0,0 but for the Volume I am not >>>> quit sure if I should provide some values and which (actually isocenter >>>> should be at 0,0,0 and if I provide these values I still get no result ). >>>> Probably this would solve my problem. >>>> >>>> Again, many thanks for your time and thank you for your help. >>>> >>>> Best regards, >>>> Milan >>>> >>>> >>>> >>>> >>>> Am 20.08.2018 um 14:26 schrieb Andreas Andersen: >>>> >>>> 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. >>>> >>>> Additional 1: >>>> Slicer is a good tool for exactly that. >>>> ( I have also made a similar tool with some reconstruction options, >>>> mainly for scatter correction: cbctrecon >>>> <https://gitlab.com/agravgaard/cbctrecon/wikis/Installation> ) >>>> Additional 2: >>>> try giving " -o fdk.raw" instead of "-o fdk.mha", the default output >>>> value type is 32-bit floating point. >>>> >>>> Best regards >>>> Andreas >>>> >>>> __________________________________ >>>> >>>> Andreas Gravgaard Andersen >>>> >>>> Department of Oncology, >>>> >>>> Aarhus University Hospital >>>> >>>> Nørrebrogade 44, >>>> >>>> 8000, Aarhus C >>>> >>>> Mail: [email protected] >>>> >>>> Cell: +45 3165 8140 >>>> >>>> >>>> On Sun, 19 Aug 2018 at 23:44, Milan Manasijevic < >>>> [email protected]> wrote: >>>> >>>>> 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 rotation angle is 0.144 degree >>>>> To reduce the reconstruction time I use just 79 projection images and >>>>> angle increasement is 4.608 degree. >>>>> >>>>> The data regarding the scanning process are (test.pca, test.pcj and >>>>> test.pcr) dropped >>>>> here: >>>>> https://www.dropbox.com/sh/on7c049aqx5ep1r/AAA7THDCkIHPF_9DBRl7MwROa?dl=0 >>>>> >>>>> From these three files I have the following values required for the >>>>> reconstruction: >>>>> [Geometry] >>>>> FDD=940.59570922 >>>>> FOD=180.61168750 >>>>> VoxelSizeX=0.03840368 >>>>> VoxelSizeY=0.03840368 >>>>> >>>>> [VolumeData] >>>>> Volume_SizeX=421 >>>>> Volume_SizeY=533 >>>>> Volume_SizeZ=471 >>>>> >>>>> [Detector] >>>>> PixelsizeX=0.20000000 >>>>> PixelsizeY=0.20000000 >>>>> NrPixelsX=2024 >>>>> NrPixelsY=2024 >>>>> >>>>> Finally, these are commands that I used to reconstruct the volume: >>>>> >>>>> >>>>> ========================================================================================================================================== >>>>> rtksimulatedgeometry --output="geometry.xml" --nproj=79 --arc=364.032 >>>>> --sdd=940.59570922 --sid=180.611687 --source_y=-16.412937 >>>>> rtkprojections --path "d:\data\test\tiffs" --output "projections.mha" >>>>> --regexp .tif --newspacing 0.2 >>>>> rtkfdk -p . -r projections.mha -o fdk.mha -g geometry.xml >>>>> --spacing=0.03840368,0.03840368,0.03840368 --dimension=421,533,471 >>>>> >>>>> ========================================================================================================================================== >>>>> >>>>> I use the VV, the 4D Slicer to check the results fro both, >>>>> projections.mha and fdk.mha. The first one looks fine and shows tha >>>>> sample correctly, but fdk.mha does not show any meaningfull >>>>> information. >>>>> The jpgs that show that, you can also find in the dropbox. >>>>> >>>>> Probably, I need to include the ROI values given in the test.pcr file >>>>> but I am not sure how. Would that be the neworigin value. (I have >>>>> tried >>>>> but no success). >>>>> >>>>> Any help on that is highly appreciated! >>>>> >>>>> >>>>> In addition I would have another two questions: >>>>> 1. Can anyone advice a proper tool to check the reconstruction result >>>>> (the reconstructed volume)? >>>>> 2. I am using the Voreen (https://www.uni-muenster.de/Voreen/) and >>>>> would >>>>> rather have the reconstruction result in a raw file format (containing >>>>> intensities as a 32-Bit floats). How can I convert mha into raw? (I >>>>> tried to split the mha into mhd and raw, but no success) >>>>> >>>>> Best Regards, >>>>> Milan >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> [email protected] >>>>> https://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>>> >>>> _______________________________________________ >>> Rtk-users mailing list >>> [email protected] >>> https://public.kitware.com/mailman/listinfo/rtk-users >>> >> _______________________________________________ >> Rtk-users mailing list >> [email protected] >> https://public.kitware.com/mailman/listinfo/rtk-users >> >
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