[Rtk-users] About Kaiser-Bessel Filter

Guangming Zang guangming.zang at kaust.edu.sa
Wed Nov 19 08:50:48 EST 2014


Yes, thanks for your prompt reply.
 what i want is  to figure out how to set -f and -b to get i fastest
reconstruction  (not -p,sorry for my mistake.). and in -b. which one is
related to our trilinear interpolation, CudaRayCast??   thanks
Best

*Guangming Zang (Alex)*
*King Abdullah University of Science and Technology(KAUST)*
*University of Chinese Academy of Sciences(UCAS)*


2014-11-19 16:40 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:

> Hi,
> I think you are looking at the code generated by gengetopt for the rtksart
> application. In general, it's simpler to simply do "rtksart --help" when
> you want to find out how to use a parameter. You will then find the
> following help section
> Projectors:
>   -f, --fp=ENUM             Forward projection method  (possible
>                               values="Joseph", "RayCastInterpolator",
>                               "CudaRayCast" default=`Joseph')
>   -b, --bp=ENUM             Back projection method  (possible
>                               values="VoxelBasedBackProjection", "Joseph",
>                               "CudaVoxelBased", "NormalizedJoseph"
>                               default=`VoxelBasedBackProjection')
> That should answer your question rtksart -b CudaVoxelBased. -p is the
> option for the path where the program will look for your projection images.
> Simon
>
> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang <
> guangming.zang at kaust.edu.sa> wrote:
>
>> Hi,Simon and Chao,
>> i want to test the cuda performance in SART algorithm.
>> but when i looked in the parameters in forwardprojection and
>> backprojection. i got the  enum:
>>
>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0,
>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast };
>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0,
>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph };
>>
>> So if i want to use the trilinear intrtpolation forwardprojection you
>> mentioned , how should i set the -b and -p in SART? or how to choose -b and
>> -p that  i  can get a fastest reconstruction in SART in this case??
>>
>> thanks for your help in advance.
>> Best
>> Guangming
>>
>> *Guangming Zang (Alex)*
>> *King Abdullah University of Science and Technology(KAUST)*
>> *University of Chinese Academy of Sciences(UCAS)*
>>
>>
>> 2014-11-18 19:47 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>>
>>> The trilinear version is available with CUDA:
>>>
>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html
>>> Simon
>>>
>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang <
>>> guangming.zang at kaust.edu.sa> wrote:
>>>
>>>> Hi Chao,
>>>> Thanks very much for your prompt and so kind reply.
>>>> I will recheck the process of setting carefully with your suggestions
>>>> and  a short report may be given later.
>>>>  BTW, do you have any plan recently to add other interpolation
>>>> filter(e.g.Kaiser-Bessel or Trilinear)??
>>>> Thanks for your time.
>>>> Regards
>>>> Guangming
>>>>
>>>>
>>>>
>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu <wuchao04 at gmail.com>:
>>>>
>>>>> Hi Guangming,
>>>>>
>>>>> To reconstruct a volume from a series of tiff files you have to let
>>>>> the algorithm know the geometrical relationship among the source, the
>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK
>>>>> uses projection matrices and image coordinates to understand the
>>>>> positioning of those projections. The projection matrices are based on a
>>>>> lot of geometrical parameters like gantry angle, source position, detector
>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I
>>>>> won't go though all since most of them have no differences if you use tiff
>>>>> files or whatever format as input. I focus on some tiff tips.
>>>>>
>>>>> In the simplest situation, the tiff files contain correct resolution
>>>>> (DPI) information, then you need to do nothing on these files. You have to
>>>>> specify the correct detector offset though, since in the tiff image
>>>>> coordinates the origin is the first pixel (corner pixel) which is
>>>>> apparently not the intersection of the central ray and the detector. The
>>>>> detector offsets in x and y actually mean the position of the image origin
>>>>> (the first pixel) in the coordinate system centred at the intersection.
>>>>> Since the direction cosines is an identity matrix and pixel sizes are
>>>>> positive, the detector offsets in x and y will be negative.
>>>>>
>>>>> If the resolution information of the tiff files is not correct, you
>>>>> have to rewrite this information. You can of course perform a
>>>>> pre-processing to change the DPI of all tiff files with a third-party
>>>>> software, or you can alter the RTK code to allow such changes after reading
>>>>> the images, by using a itk::ChangeInformationImageFilter filter.
>>>>>
>>>>> Another non-geometrical issue with tiff files is that when their
>>>>> integer pixel values are converted into attenuation, the maximum possible
>>>>> integer is used as the reference value. This may not be correct in
>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no
>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical
>>>>> fluctuation. If for instance you only use the lower 14 bits for your data
>>>>> then this problem is more severe. For sure you can correct this by changing
>>>>> the code and specify the correct reference value.
>>>>>
>>>>> Hope these can help.
>>>>>
>>>>> Regards,
>>>>> Chao
>>>>>
>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang <guangming.zang at kaust.edu.sa
>>>>> >:
>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> *Guangming Zang (Alex)*
>>>>>> *King Abdullah University of Science and Technology(KAUST)*
>>>>>> *University of Chinese Academy of Sciences(UCAS)*
>>>>>>
>>>>>>
>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang <
>>>>>> guangming.zang at kaust.edu.sa>:
>>>>>>
>>>>>>> Hi,
>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for
>>>>>>> your great work.
>>>>>>> and i was wondering do you have any plan to add other filters except
>>>>>>> Joseph, such as Kaiser-Bessel???  ( described here
>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf)
>>>>>>> BTW, i have read the messages sent by other users(
>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html
>>>>>>> )
>>>>>>> but i still can not make it. can u help me and explain again about
>>>>>>> using a series of .tiff images ans sart algorithms to get the volume.
>>>>>>> Thanks in advance
>>>>>>> Best
>>>>>>> *King Abdullah University of Science and Technology(KAUST)*
>>>>>>> *University of Chinese Academy of Sciences(UCAS)*
>>>>>>>
>>>>>>>
>>>>>>
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