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

Simon Rit simon.rit at creatis.insa-lyon.fr
Wed Aug 22 07:42:02 EDT 2018 

Hi,
I have made some amendments to the documentation to try to clarify this:
https://github.com/SimonRit/RTK/commit/fea8e136b7248f42be29ef2d5fbaf3d26e12cfbb
http://www.openrtk.org/Doxygen/DocGeo3D.html
Any suggestion to improve this is welcome.
Best regards,
Simon


On Tue, Aug 21, 2018 at 4:39 PM Chao Wu <wuchao04 at gmail.com> wrote:

> Thank you for the clarification and confirmation of the minus sign here.
>
> To me the source of confusion is the description of --proj_iso_x and
> --proj_iso_x in the command line (or from the GGO file):
>
>> option "proj_iso_x"  - "X coordinate on the projection image of
>> isocenter"     double no  default="0"
>> option "proj_iso_y"  - "Y coordinate on the projection image of
>> isocenter"     double no  default="0"
>
> If one read this, he may give positive values to the two arguments since
> "the coordinates of isocenter in the projection image coordinate system"
> are positive.
>
> I did not suggest the redundance. I meant the way how the tranlation is
> calculated (source_# - proj_iso_#) proves that proj_iso_# is projection
> origin wrt isocenter, not the other way around (then the right form will be
> source_# + proj_iso_#).
>
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> 于2018年8月21日周二 下午3:44写道：
>
>> Sorry, I checked the doc <http://www.openrtk.org/Doxygen/DocGeo3D.html>
>> and you're right,
>> "(ProjectionOffsetX,ProjectionOffsetY,SourceToIsocenterDistance-SourceToDetectorDistance)
>> are the coordinates of the detector origin in the rotated coordinated
>> system". So yes, add minus signs in front of proj_iso_x and proj_iso_y in
>> my email.
>> One source of confusion here (to me too) is that I refer here to "origin"
>> as point "(0,0)" and not to m_Origin in the itk::Image object... Any
>> suggestion to improve this is welcome.
>> On the other hand, you seem to suggest that source offsets and projection
>> offsets are redundant which is not true in a divergent geometry (or I did
>> not get you).
>> Thanks a lot for your correction.
>> Simon
>>
>>
>> On Tue, Aug 21, 2018 at 3:28 PM Chao Wu <wuchao04 at gmail.com> wrote:
>>
>>> Hi Simon,
>>>
>>> The --proj_iso_x and --proj_iso_y arguments are confusing to me.
>>>
>>> Their explanation states that they are the X/Y coordinates on the
>>> projection image of isocenter, but in practice I found them to be the
>>> projection offset in X/Y wrt to central ray (similar to --source_x and
>>> --source_y arguments).
>>>
>>> Therefore in the above case I would give --proj_iso_x=-202.3
>>> --proj_iso_y=-202.3 if the image origin is at pixel (0,0) and the +x and +y
>>> directions are aligned with the i and j indices of projection images,
>>> respectively, which is the normal case when reading from TIFF files.
>>>
>>> In rtk::ThreeDCircularProjectionGeometry::AddProjectionInRadians() this
>>> two arguments are named as projOffsetX and projOffsetY, similar to the ones
>>> for the source sourceOffsetX and sourceOffsetY, implying that the argument
>>> description is problematic. The way of calculation of
>>> submatrix AddProjectionTranslationMatrix(
>>> ComputeTranslationHomogeneousMatrix(sourceOffsetX-projOffsetX,
>>> sourceOffsetY-projOffsetY) ) also supports that they are projection origin
>>> wrt isocenter instead of isocenter wrt projection origin.
>>>
>>> Best regards,
>>> Chao
>>>
>>>
>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> 于2018年8月21日周二 下午1:26写道：
>>>
>>>> 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
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
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>>>>>
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