[Rtk-users] DRR with limited FOV from 3D-CT

Thu Nov 10 07:22:11 UTC 2022

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.wijesinghe at 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.rit at 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.wijesinghe at 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.wijesinghe at 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.wijesinghe at 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()
>>>>>
>>>>>
>>>>> _______________________________________________
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>>> Rtk-users at public.kitware.com
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>>>
>>
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