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 >
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