[Rtk-users] problem while determining the interpolation weights in 4D ROOSTER Reconstruction
Cyril Mory
cyril.mory at creatis.insa-lyon.fr
Tue Jan 9 11:33:43 EST 2018
> Ruoyan,
>
>
> From the shroud image, the signal extraction sometimes fails to find
> the period of the motion of the diaphragm, which results in incorrect
> phase detection. The easiest way to make sure your respiratory phase
> has been correctly detected is to used the following python script:
>
> https://www.creatis.insa-lyon.fr/~mory/showPeaksOverShroud.py
>
>
> You have to save your shroud image with .mhd extension, because
> simpleRTK can't read .mha (I think), so modify the command line that
> generates it (in the 4DROOSTER wiki page, that would be
>
> rtkamsterdamshroud--path . \
> --regexp '.*.his' \
> --output shroud.mha \
> --unsharp 650)
> Change "shroud.mha" into "shroud.mhd", re-run all command lines except
> the ROOSTER reconstruction, and then run
>
> "showPeaksOverShroud.py shroud.mhd sphase.txt"
>
> It will generate an RGB image named "peaksOverShroud.png", which shows
> the shroud, and overlays the detected extrema of the phase. If your
> detection is wrong, you'll see it. The script requires SimpleRTK,
> python and a few python libs.
>
> If your peaks detection is indeed incorrect, you can try cropping the
> shroud to the region where the periodic signal is most visible. This
> is usually sufficient. If you need more help, send over your
> shroud.mhd and shroud.raw file.
>
> Regards,
> Cyril
>
> On 09/01/2018 15:47, ry.meng wrote:
>> Hi Cyril,
>>
>> The attachment is our projections.mhdfile and we are running the
>> latest RTK, example data works well.
>> I have another question about our sphase.txt file. As my
>> understanding of 4D reconstruction process, spase.txt file should be
>> the optimal fit respiration signals. But in our file, it only has 6
>> cycles, which is impossible, it confused me.
>> I'm now testing your new code with our data, hope it works!
>> Thanks for your help.
>>>>
>>>>
>>>> Regards
>>>>
>>>> Ruoyan Meng
>>>>
>> On 1/9/2018 20:48，Cyril Mory<cyril.mory at creatis.insa-lyon.fr>
>> <mailto:cyril.mory at creatis.insa-lyon.fr> wrote：
>>
>> Hi again Ruoyan,
>>
>>
>> I have investigated further and found the source of the problem:
>> the code performs a rounding of the phase signal to two digits,
>> which for some values of your phase ended up to be 1. And the
>> rest of the code assumes that the phase belongs to [0; 1[, i.e.
>> there should never be a value 1.
>> The rounding is useful for optimization: projections with
>> identical phases can be forward and backprojected together, which
>> is faster than one-by-one, and with high-precision phase values,
>> there are never two equal phase values.
>>
>>
>> So I just fixed the bug by setting the phase to 0 when its
>> rounding is equal to 1, which should do the trick. The pull
>> request is being tested, it should be merged soon.
>>
>>
>> Thanks for reporting your issue.
>>
>> Regards,
>>
>> Cyril
>>
>>
>> On 09/01/2018 11:31, Cyril Mory wrote:
>>>
>>> Hi Ruoyan,
>>>
>>>
>>> I've had a look at your file sphase.txt, it looks perfectly fine
>>> to me. The problem must lie elsewhere. Does the application 4D
>>> ROOSTER work with the example data provided on the wiki ? If it
>>> does, then the problem lies in your data. In that case, please run
>>>
>>>
>>> rtkprojections --path D:\bd\20171116 --regexp .*.his
>>> -oD:\bd\20171116\projections.mhd
>>>
>>>
>>> and send us the "projections.mhd" file. It will contain only the
>>> metadata of your projections, and we'll be able to run the same
>>> command line as you and try to reproduce the problem.
>>>
>>>
>>> If, on the other hand, it doesn't even work with the example
>>> data provided on the wiki, it is a software problem. In that
>>> case, can you first update to the latest RTK (the git master
>>> branch), recompile and test again ?
>>>
>>>
>>> Best regards,
>>>
>>> Cyril
>>>
>>>
>>> On 26/12/2017 10:47, ry.meng wrote:
>>>> Hi
>>>>
>>>> Thank you for your reply. I have checked the value in
>>>> sphase.txt and don't have any value larger or equal to 5. Maybe
>>>> the problem lies elsewhere? Thanks.
>>>>
>>>> Regards
>>>>
>>>> Ruoyan Meng
>>>>
>>>> On 12/26/2017 17:14，Simon Rit<simon.rit at creatis.insa-lyon.fr>
>>>> <mailto:simon.rit at creatis.insa-lyon.fr> wrote：
>>>>
>>>> Hi,
>>>> If you look at the code
>>>> <https://github.com/SimonRit/RTK/blob/master/code/rtkPhasesToInterpolationWeights.hxx#L154>,
>>>> you'll see that the error message corresponds to the case
>>>> where you have a phase which equals the number of frames.
>>>> This cannot be since it is 0-based. In other words, with
>>>> the option "--frames 5", you cannot have a value larger or
>>>> equal to 5 in your file sphase.txt.
>>>> Simon
>>>>
>>>> On Mon, Dec 25, 2017 at 9:36 AM, ry.meng
>>>> <ry.meng at siat.ac.cn <mailto:ry.meng at siat.ac.cn>> wrote:
>>>>
>>>>
>>>> Hi:
>>>> When I tried the application of 4D ROOSTER
>>>> Reconstruction with my own data, it will stop for the
>>>> following reason: problem while determining the
>>>> interpolation weights. Maybe you guys have met this
>>>> problem before and have a solution for it. Thank you
>>>> very much and I hope to receive your reply soon.
>>>>
>>>>
>>>> Happy Holidays!
>>>>
>>>>
>>>> Regards
>>>>
>>>> Ruoyan Meng
>>>>
>>>> ------------------------------------------------------------------------------------------
>>>>
>>>> Research Center for Medical Robotics and Minimally
>>>> Invasive Surgical Devices,
>>>> Institute of Biomedical and Health Engineering,
>>>> Shenzhen Institutes of Advanced Technology, Chinese
>>>> Academy of Sciences
>>>> Tel: +86-18576617767 <tel:+86%20185%207661%207767>
>>>> Email: ry.meng at siat.ac.cn <mailto:qs.zhu at siat.ac.cn>
>>>> Zip: 518055
>>>> Add: No. 1068 Xueyuan Avenue, Nanshan, Shenzhen, China
>>>> <https://maps.google.com/?q=No.+1068+Xueyuan+Avenue,+Nanshan,+Shenzhen,+China&entry=gmail&source=g>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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