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 >
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