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<[email protected]>
<mailto:[email protected]> 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<[email protected]>
<mailto:[email protected]> 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
<[email protected] <mailto:[email protected]>> 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
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