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<p>Sorry, I made a mistake in the attached files. Ignore
peaksOverShroud.png, I intended to send
peaksOverOriginalShroud.png instead (the shroud.mhd you sent,
overlaid with the sphase.txt you sent) so you can see how I
cropped the shroud to improve the results of
rtkextractshroudsignal.</p>
<p><br>
Regards</p>
<p>Cyril<br>
</p>
<br>
<div class="moz-cite-prefix">On 11/01/2018 09:57, Cyril Mory wrote:<br>
</div>
<blockquote type="cite"
cite="mid:3dff8cae-3131-f9ce-6fc9-2ee1bc7f400b@creatis.insa-lyon.fr">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<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_%28MITK%29"
moz-do-not-send="true">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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cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr"
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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">1/10/2018 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>
<blockquote id="ntes-pcmail-quote" style="margin: 0; padding:
0; font-size: 14px; font-family: '微软雅黑';">
<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>
<blockquote type="cite"
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;">
<blockquote type="cite"
cite="mid:88BEDC3F-802B-4D7D-A627-C28A26D68ED5@siat.ac.cn">
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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>
</div>
<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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</div>
<div style="line-height: 22.4px;
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sans-serif;">
<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
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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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Surgical Devices,<br
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Institute of Biomedical
and Health Engineering,<br
style="font-family:Verdana,微软雅黑,宋体,sans-serif!important">
Shenzhen Institutes of
Advanced Technology,
Chinese Academy of
Sciences<br
style="font-family:Verdana,微软雅黑,宋体,sans-serif!important">
Tel: <a
href="tel:+86%20185%207661%207767"
value="+8618576617767"
target="_blank"
moz-do-not-send="true">+86-18576617767</a><br
style="font-family:Verdana,微软雅黑,宋体,sans-serif!important">
Email: <a
href="mailto:qs.zhu@siat.ac.cn"
style="color:purple;font-family:Verdana,微软雅黑,宋体,sans-serif!important"
target="_blank"
moz-do-not-send="true">ry.meng@siat.ac.cn</a><br
style="font-family:Verdana,微软雅黑,宋体,sans-serif!important">
Zip: 518055<br
style="font-family:Verdana,微软雅黑,宋体,sans-serif!important">
Add: <a
href="https://maps.google.com/?q=No.+1068+Xueyuan+Avenue,+Nanshan,+Shenzhen,+China&entry=gmail&source=g"
moz-do-not-send="true">No.
1068 Xueyuan Avenue,
Nanshan, Shenzhen,
China</a></font></span></p>
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