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

Sat Nov 12 06:06:16 UTC 2022

Hi,
The anatomical orientation is not used by RTK.
Simon

On Fri, Nov 11, 2022 at 11:43 AM Isuru Suranga Wijesinghe <
isurusuranga.wijesinghe at 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.rit at 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.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()
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>> Rtk-users mailing list
>>>>> Rtk-users at public.kitware.com
>>>>> https://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>>>>
>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/rtk-users/attachments/20221112/431cc55f/attachment-0001.htm>