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<p>Dear Zipai,</p>
<p>I will answer to the mailing-list as well as it is an interesting
question and other users could have similar interrogations.<br>
There is unfortunately no way to do that with CASToR. However I do
think the optimal approach would be to rebin the LORs before
reconstruction and directly provide to castor-recon a list-mode
with the repositioned LORs and adjusted normalization factors. I
believe the main interest to integrate even-by-event motion
correction during reconstruction would be to perform non-rigid
deformation as in the approach developed by Yale group (<span
lang="en-US"><a class="moz-txt-link-freetext" href="https://doi.org/10.1109/TMI.2017.2761756">https://doi.org/10.1109/TMI.2017.2761756</a> ). However
implementing this approach in CASToR would require substantial
changes to optimize the code performance, at the expense of
genericity.</span></p>
<p><span lang="en-US">Many thanks for the kind words about the
workshop, always good to know it was useful to you and other
attendees :) <br>
</span></p>
<p><span lang="en-US">Best regards,<br>
Thibaut<br>
</span></p>
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<div class="moz-cite-prefix">On 11/03/2022 07:33, Zipai Wang wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CABOvga-4O6at6YH+uL4O927NBVQb_j8THdaSiOM0u+2-r+kPGw@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Dear Dr. Merlin,
<div><br>
</div>
<div>Thank you very much for your reply. I now understand why I
got the same images even I force the normalization factors to
be different.</div>
<div><br>
</div>
<div>I have a further question. In my case (motion correction),
I need to move a LOR from its original location to another
location and rebin it to corresponding channels. But I think
the rebinned event should be normalized with the normalization
factor of its original channels. Is there a way to achieve
this in CASToR? Like manually assigning a normalization factor
to an event during the reconstruction.</div>
<div><br>
</div>
<div>I understand that the CASToR can perform the motion
correction by distorting the sensitivity image, but it will be
great for us if it is possible to do it in a list-mode way. </div>
<div><br>
</div>
<div>By the way, the CASToR works incredibly well and we learned
a lot in the CASToR workshop we attended last year! Thank you
very much, and I hope it is ok to send you a direct email to
ask questions.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Zipai</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Feb 21, 2022 at 7:22
PM Thibaut Merlin <<a
href="mailto:Thibaut.Merlin@univ-brest.fr"
moz-do-not-send="true">Thibaut.Merlin@univ-brest.fr</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="font-family:Arial;font-size:14px">
<p> Hi Zipai,<br>
<br>
You will get the error described in 1. when you try to
reconstruct the list-mode with a datafile containing
normalization correction factors without providing a
normalization datafile containing these factors. The
normalization correction factors must be included in both
the regular datafile (using -df option) and the
normalization datafile (using -norm option). Is it what
you did ?<br>
<br>
Regarding 2., the factors in your normalization datafile
will contribute to the correction in the image (through
the sensitivity image which is generated before the
reconstruction itself), while the correction factors in
the datafile are used to normalize the additive background
(scatter/random) during reconstruction. As your data does
not contain scatter or random correction factors (and as
you use a precomputed sensitivity image), there will be no
difference in the resulting image.<br>
<br>
Hope this helps!<br>
<br>
Best regards,<br>
Thibaut<br>
<br>
Zipai Wang <<a href="mailto:zipai.wang@stonybrook.edu"
target="_blank" moz-do-not-send="true">zipai.wang@stonybrook.edu</a>>
a écrit :</p>
<blockquote style="border-left:2px solid
blue;margin-left:2px;padding-left:12px" type="cite">
<div dir="ltr"> Dear CASToR developers and users,
<div> </div>
<div> I am trying to apply normalization to a simulated
PET scanner but meet some issues, any help is
highly appreciated!</div>
<div> </div>
<div> First I successfully applied the normalization by
feeding the normalization file (all LORs with
norm&attenuation factors) into the CASToR for the
computation of the sensitivity image. The CASToR gives
me artefact free images in this way.</div>
<div> </div>
<div> However, the normalization doesn't work when I
embed the factors into the List-mode binary datafile:</div>
<div> </div>
<div> 1. When I feed the list-mode data (with
normalization factors and flag on) to CASToR, it give
me the following error:</div>
<div> <i>oSensitivityGenerator::InitializeNormalizationFiles()
-> Normalization correction is included in the
data file while it is not in the sensitivity
computation!</i></div>
<div> In order to bypass this error, I use <i>-sens</i>
to provide a precomputed sensitivity image (Not
normalized) to CASToR. Is this the proper way to do
it? If not, what should I feed to CASToR instead?</div>
<div> </div>
<div> 2. After feeding precomputed sensitivity image,
the CASToR can run reconstruction with no issues, but
the image with embedded LM normalization factors is
identical to the image without normalization factors.
Then I assign all the events with the same
normalization factor of 0.1,1,10, respectively. But
the reconstructed images have the same pixel
intensities, which means I did something wrong and the
LM normalization factors is not doing its job at all
in my case.</div>
<div> </div>
<div> The version I am using is CASToR v 3.0.1.</div>
<div> </div>
<div> Here is one of the header files:</div>
<div> Data filename: PET_Sim_LMNorm.Cdf<br>
Number of events: 13755984<br>
Data mode: list-mode<br>
Data type: PET<br>
Start time (s): 0<br>
Normalization correction flag: 1<br>
Duration (s): 1500<br>
Scanner name: D04_sim_1ring<br>
Calibration factor: 1<br>
Isotope: unknown</div>
<div> </div>
<div> Here is some examples of the I generated list-mode
data: (I assgin all the time frames to 0 and norm
factors to 1)</div>
0000 0000 0000 803f ba22 0000 c005 0000<br>
0000 0000 0000 803f 9a15 0000 9e19 0000<br>
0000 0000 0000 803f e20e 0000 fa0b 0000<br>
0000 0000 0000 803f f51f 0000 6a05 0000<br>
0000 0000 0000 803f 971a 0000 1203 0000<br>
0000 0000 0000 803f e91f 0000 d719 0000<br>
0000 0000 0000 803f 211d 0000 3721 0000<br>
0000 0000 0000 803f f906 0000 7105 0000<br>
0000 0000 0000 803f 4c20 0000 f014 0000<br>
0000 0000 0000 803f 8e1e 0000 a607 0000<br>
0000 0000 0000 803f a821 0000 1a19 0000<br>
0000 0000 0000 803f e81a 0000 8514 0000<br>
<div> 0000 0000 0000 803f 6913 0000 e525 0000</div>
<div> </div>
<div> </div>
<div> Thank you very much!</div>
<div> --</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr"> Zipai Wang</div>
<div dir="ltr"> Biomedical Engineering PhD
student
<div> Stony Brook University </div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
<br>
</div>
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">Zipai Wang</div>
<div dir="ltr">Biomedical Engineering PhD student
<div>Stony Brook University </div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
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