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

Mon Aug 20 16:10:12 EDT 2018

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: agravgaard at protonmail.com <mailto:agravgaard at protonmail.com>
>
> Cell: +45 3165 8140
>
>
>
> On Sun, 19 Aug 2018 at 23:44, Milan Manasijevic 
> <milan-manasijevic at t-online.de <mailto:milan-manasijevic at t-online.de>> 
> 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
>
>
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