Hi,
It's not clear to me how you came up with your source_y value.
Assuming that the origin of your projections is 0,0,0, I would advise
to set the geometry with --proj_iso_x=202.3 --proj_iso_y=202.3 (or,
equivalently, set a new origin to the projection equal to
-202.3,-202.3,0).
The --arc value is also a bit surprising but you can check if the
assigned GantryAngle is the correct one for each projection.
Finally, in rtkfdk, setting origin (this time for the volume) to a
y-value equal 0 means that you only look at the part above the source
trajectory. I would leave the default values (centered volume around
the center of rotation).
Best regards,
Simon
On Tue, Aug 21, 2018 at 12:01 AM Andreas Andersen
<[email protected] <mailto:[email protected]>> wrote:
Hi Milan
1) OK, I guess it makes sense with the source/detector geometry.
2) I forgot to check which group RawImageIO was in; it's own
apparently.
So you'll have to re-compile ITK with the CMake option:
Module_ITKIORAW=ON
(You'll have to add the entry manually if you use a CMake GUI)
3) Origin is not the isocenter, it is the offset of the image
origin, i.e. index 0,0,0, in relation to the isocenter (AFAIK).
Just a guess: Try with an offset of: -0.03840368 * {421,0,471} / 2
=> "--origin -8.08,0,-9.04"
(I forget the definition of the y-axis, so I'm unsure about the
"0", if it doesn't work also try -10.23, 10.23, multiplying it by
2, and 0.)
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 Mon, 20 Aug 2018 at 22:10, Milan Manasijevic
<[email protected]
<mailto:[email protected]>> wrote:
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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