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] <mailto:[email protected]>
Cell: +45 3165 8140
On Sun, 19 Aug 2018 at 23:44, Milan Manasijevic
<[email protected] <mailto:[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
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