[Rtk-users] Cannot reconstruct the volume, what might be the problem?
Chao Wu
wuchao04 at gmail.com
Tue Aug 21 10:38:52 EDT 2018
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
>>>>>>
>>>>>
>>>>> _______________________________________________
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