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

Simon Rit simon.rit at creatis.insa-lyon.fr
Wed Aug 22 07:36:47 EDT 2018 

Hi,
To be honest, it's quite hard to guess the meaning of YS in test.pcj
but I would be suprised if it corresponds to source_y... Maybe you
should find the documentation regarding the meaning of YS and we can
help in relating it to RTK's geometry parameters.
Best regards,
Simon
On Tue, Aug 21, 2018 at 11:35 PM Milan Manasijevic
<milan-manasijevic at t-online.de> wrote:
>
> Hi Simon,
>
> my understanding of origin in this context was wrong. Your advise makes sense and I ran the reconstruction succesfully by setting the values --proj_iso_x=-202.3 --proj_iso_y=-202.3. I didn't investigate the result further, but at first glance it is a big step ahead for me. Regarding the source_y value, It is given in the test.pca and also in the test.pcj file (please check the dropbox).
> Similar to the value of the ZSample=180.611687 (which is SID) the value of YSample is given by YSample=-16.412937. My understanding is that this should be the SourceOfsetY. However, in my first attempt today, I didn't use that argument.
>
> Many thanks for helping me.
>
> Best Regards,
> Milan
>
>
>
> Am 21.08.2018 um 13:25 schrieb Simon Rit:
>
> 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 )
>>> 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
>>>
>>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> https://public.kitware.com/mailman/listinfo/rtk-users
>
>

More information about the Rtk-users mailing list