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

Wed Nov 9 16:41:59 UTC 2022

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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>
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