[Rtk-users] problem while determining the interpolation weights in 4D ROOSTER Reconstruction
Cyril Mory
cyril.mory at creatis.insa-lyon.fr
Thu Jan 11 03:57:22 EST 2018
Hi Ruoyan,
The original sphase.txt you sent a few days earlier does not look like
the Matlab plot you just sent. I guess you modified it in the meantime.
It does not matter much, but for one of the images I'm sending, I've
used your old sphase.txt.
I am not the best person to help you with your SimpleRTK problem. If
you're used to Matlab, let's go for that way.
First, you can open your shroud image using Matlab, for example with the
function read_mhd() provided in MITK. See
http://mitk.org/wiki/The_Medical_Imaging_Interaction_Toolkit_(MITK) .
Second, to crop it using Matlab, simply keep the part where the
diaphragm motion is most visible (I removed the whole top part, wide 285
pixels), then save the file back to croppedShroud.mhd, then rerun phase
extraction.
I have used another tool than Matlab to crop the image, but it shouldn't
matter. And I have rerun phase extraction, and generated the overlay of
peaks over shroud image in both cases. See the attached pictures. Note
that a few respiratory cycles have been missed by the algorithm. You can
try playing with parameters of rtkextractshroudsignal, but those cycles
will be hard to detect anyway, since they correspond to irregular
breathing (it looks like the patient coughed). You can live with that,
or modify the phase file manually to add those cycles: the phase is
nothing more than a number that goes linearly from 0 to 1 between one
peak and the next.
I hope it helps,
Cyril
On 11/01/2018 07:54, ry.meng wrote:
> Hi Cyril,
>
> The new code works fine, I still got some questions about sphase.txt file.
> When building simpleRTK, I met an error "error MSB6006:
> “cmd.exe”exit，code 1", and I didn't find a solution. So I just plot
> sphase.txt with Matlab and compare it with respiration signals
> provided by raw data. They are quite different. I am not very clear
> about how to crop the shroud, can you share the method? Thanks a lot.
>
>>>>> Regards
>>>>>
>>>>> Ruoyan Meng
>>>>>
>
> On 1/10/2018 00:33，Cyril Mory<cyril.mory at creatis.insa-lyon.fr>
> <mailto:cyril.mory at creatis.insa-lyon.fr> wrote：
>
>> 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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>>>>> <mailto:Rtk-users at public.kitware.com>
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>>>>> <https://public.kitware.com/mailman/listinfo/rtk-users>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>
>>>>
>>>>
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>
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