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

[Milan Manasijevic]

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