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

Tue Aug 21 07:25:53 EDT 2018

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 <andreasga22 at gmail.com>
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:     agravgaard at protonmail.com
>
> Cell:      +45 3165 8140
>
>
> On Mon, 20 Aug 2018 at 22:10, Milan Manasijevic <
> milan-manasijevic at t-online.de> 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:     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
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
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