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

Simon Rit simon.rit at creatis.insa-lyon.fr
Tue Aug 21 09:44:37 EDT 2018 

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
>>>>>
>>>>
>>>> _______________________________________________
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>>> Rtk-users at public.kitware.com
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