[Rtk-users] Cannot reconstruct the volume, what might be the problem?
Milan Manasijevic
milan-manasijevic at t-online.de
Tue Aug 21 17:28:55 EDT 2018
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 <mailto: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 <mailto:agravgaard at protonmail.com>
>
> Cell: +45 3165 8140
>
>
>
> On Mon, 20 Aug 2018 at 22:10, Milan Manasijevic
> <milan-manasijevic at t-online.de
> <mailto: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
>> <mailto:agravgaard at protonmail.com>
>>
>> Cell: +45 3165 8140
>>
>>
>>
>> On Sun, 19 Aug 2018 at 23:44, Milan Manasijevic
>> <milan-manasijevic at t-online.de
>> <mailto: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
>>
>>
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