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<p>Hi Ruoyan,</p>
<p><br>
</p>
<p>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.<br>
</p>
<p><br>
</p>
<p>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. <br>
</p>
<p>First, you can open your shroud image using Matlab, for example
with the function read_mhd() provided in MITK. See
<a class="moz-txt-link-freetext" href="http://mitk.org/wiki/The_Medical_Imaging_Interaction_Toolkit_(MITK)">http://mitk.org/wiki/The_Medical_Imaging_Interaction_Toolkit_(MITK)</a>
. 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. <br>
</p>
<br>
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.<br>
<br>
I hope it helps,<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 11/01/2018 07:54, ry.meng wrote:<br>
</div>
<blockquote type="cite"
cite="mid:66E4352A-AC64-4CFD-8DA0-E22BC5168E07@siat.ac.cn">
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<div><span>Hi </span><span style="line-height: 1.6;">Cyril,</span></div>
<div><br>
</div>
<div>
<div>The new code works fine, I still got some questions
about sphase.txt file.</div>
<div>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. </div>
</div>
<div><br>
</div>
<div>
<blockquote type="cite"
cite="mid:ea92b94b-4d36-76c7-86e6-7ab94351b44c@creatis.insa-lyon.fr"
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<div
style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On
<span class="mail-date">1/10/2018 00:33</span>，<a
class="mail-to"
style="text-decoration:none;color:#2a83f2;"
href="mailto:cyril.mory@creatis.insa-lyon.fr"
moz-do-not-send="true">Cyril
Mory<cyril.mory@creatis.insa-lyon.fr></a> wrote： </div>
</div>
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<blockquote type="cite"
cite="mid:ea92b94b-4d36-76c7-86e6-7ab94351b44c@creatis.insa-lyon.fr">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<p>Ruoyan,</p>
<p><br>
</p>
<p>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:</p>
<p><a class="moz-txt-link-freetext"
href="https://www.creatis.insa-lyon.fr/%7Emory/showPeaksOverShroud.py"
moz-do-not-send="true">https://www.creatis.insa-lyon.fr/~mory/showPeaksOverShroud.py</a></p>
<p><br>
</p>
<p>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 <br>
</p>
<pre class="de1">rtkamsterdamshroud <span class="re5">--path</span> . \
<span class="re5">--regexp</span> <span class="st_h">'.*.his'</span> \
<span class="re5">--output</span> shroud.mha \
<span class="re5">--unsharp</span> <span class="nu0">650)
</span></pre>
<span class="nu0">Change "shroud.mha" into "shroud.mhd",
re-run all command lines except the ROOSTER
reconstruction, and then run <br>
<br>
</span>"showPeaksOverShroud.py <span class="nu0">shroud.mhd
sphase.txt"</span><br>
<span class="nu0"></span><span class="nu0"></span><br>
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. <br>
<br>
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.<br>
<br>
Regards,<br>
<span style="line-height: 1.6;">Cyril</span></blockquote>
<blockquote type="cite"
cite="mid:ea92b94b-4d36-76c7-86e6-7ab94351b44c@creatis.insa-lyon.fr">
<br>
<div class="moz-cite-prefix">On 09/01/2018 15:47, ry.meng
wrote:<br>
</div>
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cite="mid:5D207BEE-6153-4D53-BD0C-6CD67BE69149@siat.ac.cn">
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<div>
<div style="line-height: 22.4px;">Hi <span
style="line-height: 22.4px;">Cyril, </span></div>
<div style="line-height: 22.4px;"><span
style="line-height: 22.4px;"><br>
</span></div>
<div style="line-height: 22.4px;"><span
style="font-family: Verdana, 微软雅黑, 宋体,
sans-serif; line-height: 22.4px;">The attachment
is our </span><span style="line-height: 1.6;">projections.mhd</span><span
style="line-height: 1.6;"> <font face="Verdana,
微软雅黑, 宋体, sans-serif">file and we are running
the latest RTK, </font></span><span
style="line-height: 1.6;">example data works
well.</span></div>
<div style="line-height: 22.4px;"><font
face="Verdana, 微软雅黑, 宋体, sans-serif">I have
another question about our sphase.txt file. As
my understanding of 4D reconstruction process, </font><font
face="Verdana, 微软雅黑, 宋体, sans-serif">spase.txt
file should be the optimal fit </font><span
style="line-height: 1.6;">respiration signals.
But in our file, it only has 6 cycles, which is
impossible, </span>it confused me.</div>
<div style="line-height: 22.4px;">I'm now testing
your new code with our data, hope it works!</div>
<div style="line-height: 22.4px;">Thanks for your
help.</div>
<div style="line-height: 22.4px;">
<blockquote type="cite"
cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr"
style="line-height: 22.4px;">
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<p class="MsoNormal" style="margin: 0cm
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<div
style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On
<span class="mail-date">1/9/2018 20:48</span>，<a
class="mail-to"
style="text-decoration:none;color:#2a83f2;"
href="mailto:cyril.mory@creatis.insa-lyon.fr"
moz-do-not-send="true">Cyril
Mory<cyril.mory@creatis.insa-lyon.fr></a>
wrote： </div>
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<blockquote id="ntes-pcmail-quote" style="margin: 0;
padding: 0; font-size: 14px; font-family: '微软雅黑';">
<p>Hi again Ruoyan,</p>
<p><br>
</p>
<p>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. <br>
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. </p>
<p><br>
</p>
<p>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. <br>
</p>
<p><br>
</p>
<p>Thanks for reporting your issue.<br>
</p>
<p>Regards,</p>
<p>Cyril<br>
</p>
<br>
<div class="moz-cite-prefix">On 09/01/2018 11:31,
Cyril Mory wrote:<br>
</div>
<blockquote type="cite"
cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<p>Hi Ruoyan,</p>
<p><br>
</p>
<p>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</p>
<p><br>
</p>
<p>rtkprojections --path D:\bd\20171116 --regexp
.*.his -o<span style="line-height: 1.6;">D:\bd\20171116\</span><span
style="line-height: 1.6;">projections.mhd </span></p>
</blockquote>
<blockquote type="cite"
cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr">
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>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 ?</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Cyril<br>
</p>
<br>
<div class="moz-cite-prefix">On 26/12/2017 10:47,
ry.meng wrote:<br>
</div>
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cite="mid:88BEDC3F-802B-4D7D-A627-C28A26D68ED5@siat.ac.cn">
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<div><span>Hi</span></div>
<div><span><br>
</span></div>
<div><span>Thank you for your reply. I have
checked the value in sphase.txt and don't
have any value </span><span
style="font-family: Verdana, 微软雅黑, 宋体,
sans-serif; line-height: 22.4px;">larger
or equal to 5. </span><font face="Verdana,
微软雅黑, 宋体, sans-serif">Maybe the problem
lies elsewhere? Thanks.</font></div>
<div><br>
</div>
<div>
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<p class="MsoNormal" style="margin: 0cm
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<div
style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On
<span class="mail-date">12/26/2017 17:14</span>，<a
class="mail-to"
style="text-decoration:none;color:#2a83f2;"
href="mailto:simon.rit@creatis.insa-lyon.fr" moz-do-not-send="true">Simon
Rit<simon.rit@creatis.insa-lyon.fr></a>
wrote： </div>
</div>
<blockquote id="ntes-pcmail-quote"
style="margin: 0; padding: 0; font-size: 14px;
font-family: '微软雅黑';">
<div dir="ltr">
<div>
<div>Hi,<br>
</div>
If you look at the <a
href="https://github.com/SimonRit/RTK/blob/master/code/rtkPhasesToInterpolationWeights.hxx#L154"
moz-do-not-send="true">code</a>, 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.<br>
</div>
Simon<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Dec 25,
2017 at 9:36 AM, ry.meng <span dir="ltr"><<a
href="mailto:ry.meng@siat.ac.cn"
target="_blank" moz-do-not-send="true">ry.meng@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div>
<div
style="font-family:"\005fae\008f6f\0096c5\009ed1";line-height:1.6">
<div><span><br>
</span></div>
<div><span>Hi:</span></div>
<div><span> </span></div>
<div>When I tried the application
of 4D ROOSTER Reconstruction with
my own data, it will stop for the
following reason: <span
style="line-height:22.4px">problem
while determining the
interpolation weights</span><span
style="line-height:1.6">. 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.</span></div>
<div>
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