Hi, The anatomical orientation is not used by RTK. Simon On Fri, Nov 11, 2022 at 11:43 AM Isuru Suranga Wijesinghe < isurusuranga.wijesin...@gmail.com> wrote:
> Hi Simon, > > I cannot change the format of the image volume since I use another tool to > generate these nifti image volumes and corresponding DVFs in the same > format. > I want to use RTK to generate DRRs for these nifti instances with differnt > projection angles. > > Therefore I first reorient the CT volme to have RAS orientation which is > now the direction matrix is preserved and the point (0,0,0) mm is in the > image . > > However, the genreted DRRs do not appear correctly. > > The previous example code you provided works correctly, but the origin is > reordered. > > If I use this RAS-oriented new CT, the DRRs should be in the correct > versions. What could be the cause ? > RAS_oriented_ref_CT.nii.gz > <https://drive.google.com/file/d/1ypdqeQQpbvjy7k4T_zxY3e8g3-fhmI5q/view?usp=drive_web> > > > > On Thu, Nov 10, 2022 at 7:22 AM Simon Rit <simon....@creatis.insa-lyon.fr> > wrote: > >> Hi, >> ref_CT_updated.nii.gz is still not oriented correctly, please check the >> RTK geometry doc more carefully. If I use the following lines >> CTDirection=np.zeros([3,3]) >> CTDirection[0,0]=1. >> CTDirection[1,2]=1. >> CTDirection[2,1]=1. >> CT.SetDirection(itk.matrix_from_array(CTDirection)) >> CT.SetOrigin([CT.GetOrigin()[0],CT.GetOrigin()[2],-CT.GetOrigin()[1]]) >> CTarray = itk.array_view_from_image(CT) >> CTarray += 1000 >> >> and set the outOfPlaneAngle to 0, the result looks more as expected. I >> advise you to avoid the nifti file format which has many issues according >> to ITK discussions on github, prefer mha or mhd. >> Simon >> >> On Wed, Nov 9, 2022 at 5:42 PM Isuru Suranga Wijesinghe < >> isurusuranga.wijesin...@gmail.com> wrote: >> >>> Hi Simon, >>> >>> Many thanks. I'm in need of some assistance once more please. >>> >>> First, I reoreinted the CT volume and used the field of view origin in >>> the corresponding real kV dicom file (i.e. with projection angle zero) to >>> adjust the correct field of view for projection angle zero (FOV origin >>> [116.368270874, 3.837730408]). I simply replace the default values of >>> projOffsetX and projOffsetY with the values shown below. >>> projOffsetY = -3.837730408 >>> >>> I simply rotated around the x-axis by setting the outOfPlaneAngle >>> parameter to 90 degrees. >>> >>> However, If I project through a 324 (degrees) projection angle (with FOV >>> origin [117.085998535, 3.948999882]), it will rotate in the worng axis. >>> For this step, I simply replace the gantryAngle parameter with 324 and >>> set the new projOffsetX and projOffsetY. >>> >>> I've attached the updated code, the reoriented CT volume, the correct >>> DRR at projection angle zero, and the incorrect DRR at projection angle 324. >>> >>> Can you assist me in resolving that error ? >>> >>> drr_0.png >>> <https://drive.google.com/file/d/1qOoMQ6jvOSY-7KivjmcLuAoIIMhBafmE/view?usp=drive_web> >>> drr_324.png >>> <https://drive.google.com/file/d/1RjT6_hGF2vkog3YNUfv-03RAmTClrSbK/view?usp=drive_web> >>> ref_CT_updated.nii.gz >>> <https://drive.google.com/file/d/1BntJvZ7JRF9kTxQsycB5JoipWVFESNQ_/view?usp=drive_web> >>> rtk_drr_projection_code.txt >>> <https://drive.google.com/file/d/1mEaIbj9NjuU5BZB4NKlmv0S9CUN0FME3/view?usp=drive_web> >>> >>> >>> >>> >>> On Wed, Nov 9, 2022 at 2:26 PM Simon Rit <simon....@creatis.insa-lyon.fr> >>> wrote: >>> >>>> Hi, >>>> The first input of JosephForwardProjectionImageFilter is the image in >>>> which you'll calculate the DRR, typically an empty projection (filled with >>>> zeros). In your code, this is computed with constantImageSource but you're >>>> setting the volume origin, spacing size which is probably wrong. For an >>>> Elekta projection (you showed an Elekta drawing), this would be >>>> constantImageSource.SetOrigin( [-204.4,-204.4,0] ) >>>> constantImageSource.SetSpacing( [0.8,0.8,0.8] ) >>>> constantImageSource.SetSize( [512, 512,1] ) >>>> Besides, for the CT volume you sent, point (0,0,0) mm is not in the >>>> image and this is the default center of rotation in RTK (see doc >>>> <http://www.openrtk.org/Doxygen/DocGeo3D.html>). Moreover the >>>> orientation is wrong. So either you change the origin and the direction to >>>> use RTK convention or you build your geometry differently, e.g. by setting >>>> source center, detector origin position and detector u v coordinates: >>>> geometry.AddProjection([-57.,20.+sid,25.],[-57+115.,20.+sid-sdd >>>> ,25.],[1.,1.,0.],[0.,0.,1.]) >>>> where the coordinates (-57,28,25) are those of a point somewhere in the >>>> center of the patient. This will give you line integrals, I don't know what >>>> is the content of your png file but you might have to take the exponential >>>> to have something close to real data. you also have to add 1000 to yourCT >>>> numbers to put air at 0. >>>> In short, read the geometry doc and don't expect us to be able to match >>>> exactly the DRR you sent... This will require some work on your side >>>> Cheers, >>>> Simon >>>> >>>> On Wed, Nov 9, 2022 at 11:32 AM Isuru Suranga Wijesinghe < >>>> isurusuranga.wijesin...@gmail.com> wrote: >>>> >>>>> Can I ask any possible solution to my issue please (I just want to get >>>>> the DRR with the limited FOV based on the machine parameters attached >>>>> above) ??? >>>>> >>>>> On Tue, Nov 8, 2022 at 2:12 PM Isuru Suranga Wijesinghe < >>>>> isurusuranga.wijesin...@gmail.com> wrote: >>>>> >>>>>> In addition to that I want to generate DRRs with a limited field of >>>>>> view as attached in the sample real kV Xray image. >>>>>> I've included a sample CT volume that I'm currently using to generate >>>>>> such DRR images using the machine parameters. Please assist in resolving >>>>>> this matter. Thank you in advance for your consideration and time. >>>>>> >>>>>> ref_CT_volume.nii.gz >>>>>> <https://drive.google.com/file/d/1PilfGAhqWe-NFD4Up1CYwSHqDXns04CV/view?usp=drive_web> >>>>>> sample_real_kv_xray.png >>>>>> <https://drive.google.com/file/d/1zX2HUEEL4-lGxS4daDrhXuhTy1uFBY89/view?usp=drive_web> >>>>>> >>>>>> >>>>>> On Tue, Nov 8, 2022 at 11:23 AM Isuru Suranga Wijesinghe < >>>>>> isurusuranga.wijesin...@gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I have a 3D-CT volume and want to obtain the DRR projection by >>>>>>> adjusting the machine parameters as shown in the image below. >>>>>>> >>>>>>> Here's my code, and I didn't get the expected DRRs with the limited >>>>>>> FOV. Is there anything missing from the parameter setup? >>>>>>> >>>>>>> Could you please assist me in resolving this issue? Any code level >>>>>>> assistance or advice would be greatly appreciated. >>>>>>> >>>>>>> # Loading 3D CT image >>>>>>> CT = itk.imread("./ct.nii.gz", pixel_type=itk.F) >>>>>>> >>>>>>> # Defines the image type >>>>>>> Dimension_CT = 3 >>>>>>> PixelType = itk.F >>>>>>> ImageType = itk.Image[PixelType, Dimension_CT] >>>>>>> >>>>>>> origin_x, origin_y, origin_z = CT.GetOrigin() >>>>>>> space_x, space_y, space_z = CT.GetSpacing() >>>>>>> >>>>>>> # Define origin, sizeOutput and spacing (still need to change these) >>>>>>> origin = [origin_x, origin_y, origin_z] >>>>>>> spacing = [space_x, space_y, space_z] >>>>>>> >>>>>>> sizeOutput = [ 512, 512, 1] >>>>>>> >>>>>>> # Create a stack of empty projection images >>>>>>> ConstantImageSourceType = rtk.ConstantImageSource[ImageType] >>>>>>> constantImageSource = ConstantImageSourceType.New() >>>>>>> >>>>>>> constantImageSource.SetOrigin( origin ) >>>>>>> constantImageSource.SetSpacing( spacing ) >>>>>>> constantImageSource.SetSize( sizeOutput ) >>>>>>> constantImageSource.SetConstant(0.) >>>>>>> >>>>>>> # Defines the RTK geometry object >>>>>>> geometry = rtk.ThreeDCircularProjectionGeometry.New() >>>>>>> firstAngle = 0. >>>>>>> angularArc = 360. >>>>>>> sid = 1000 # source to isocenter distance >>>>>>> sdd = 1536 # source to detector distance >>>>>>> gantryAngle = 0. # rot around y-axis >>>>>>> projOffsetX = 0. >>>>>>> projOffsetY = 0. >>>>>>> outOfPlaneAngle = 90. # rot around x-axis >>>>>>> inPlaneAngle = 0. # rot around z-axis >>>>>>> sourceOffsetX = 0. >>>>>>> sourceOffsetY = 0. >>>>>>> geometry.AddProjection(sid, sdd, gantryAngle) >>>>>>> >>>>>>> REIType = rtk.JosephForwardProjectionImageFilter[ImageType, >>>>>>> ImageType] >>>>>>> rei = REIType.New() >>>>>>> >>>>>>> rei.SetGeometry( geometry ) >>>>>>> rei.SetInput(0, constantImageSource.GetOutput()) >>>>>>> rei.SetInput(1, CT) >>>>>>> rei.Update() >>>>>>> >>>>>>> Dimension = 3 >>>>>>> OutputPixelType = itk.UC >>>>>>> OutputImageType = itk.Image[OutputPixelType, Dimension] >>>>>>> >>>>>>> RescaleType = itk.RescaleIntensityImageFilter[ImageType, >>>>>>> OutputImageType] >>>>>>> rescaler = RescaleType.New() >>>>>>> rescaler.SetOutputMinimum(0) >>>>>>> rescaler.SetOutputMaximum(255) >>>>>>> rescaler.SetInput(rei.GetOutput()) >>>>>>> rescaler.Update() >>>>>>> >>>>>>> WriteType = itk.ImageFileWriter[OutputImageType] >>>>>>> writer = WriteType.New() >>>>>>> writer.SetFileName('./drr_0.png') >>>>>>> writer.SetInput(rescaler.GetOutput()) >>>>>>> writer.Update() >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users@public.kitware.com >>>>> https://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >>>>> >>>>
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