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

Mon Aug 20 18:01:39 EDT 2018

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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