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

[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

Cell:      +45 3165 8140


On Sun, 19 Aug 2018 at 23:44, Milan Manasijevic <
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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