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<p>Hi Philip,</p>
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<p>In (2), you said that you provide an attenuation image but no attenuation factor in the CASToR datafile.</p>
<p>Does it means that you input the pifa using -attn option, that you do not input a normalization file and that in the list-mode file, there is no attenuation factor ?</p>
<p>If yes, then the corrections for scatters and randoms are severely underestimated.<br>
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<p>Could you compare (1) with the following case: the attenuation map provided with -attn, no normalization file at all, attenuation correction factors included in the list-mode file ?</p>
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<p>In the SIGNA, there is span 3 (indirect planes between rings are summed) for the first segment (copolar angle 0).</p>
<p>Is there any span in the acquired sinograms ?</p>
<p>I think there is some, from the image (4).</p>
<p>So it may be that you do not take this axial compression into account.</p>
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<p>Simon<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>De :</b> Castor-users <castor-users-bounces@lists.castor-project.org> de la part de Philip Kalaitzidis <kalaitzidis.philip@gmail.com><br>
<b>Envoyé :</b> vendredi 25 septembre 2020 19:07<br>
<b>À :</b> castor-users@lists.castor-project.org<br>
<b>Objet :</b> [Castor-users] Reconstructing with normalization</font>
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<div>Dear CASToR developers and users,</div>
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<div>I have been facing an issue when trying to reconstruct PET data (a 18F measurement with the NEMA IQ Body Phantom) acquired on a G.E. Discovery MI with CASToR, in particular when reconstructing with normalization correction factors embedded in the file.
The correction terms (attenuation, scatter, random, normalization, dead-time, and pile-up) that I am using when reconstructing with CASToR have been extracted with the G.E. PET Toolbox. I am converting the G.E. PET list-file to a CASToR list-file, embedding
all aforementioned correction terms in that file. Additionally, I am also constructing the CASToR normalization file by looping over all (unique) crystal-pairs and embedding the attenuation- and normalization correction factors as is suggested in the general
documentation.</div>
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<div>When performing the reconstruction (in my case OSEM with a 4 mm axial and transaxial FWHM post-filtering) with normalization factors embedded in both the list-file and the normalization file, every other slice has a reduced intensity - this does not appear
if I do not use the CASToR normalization file (and thus not embedding attenuation- and/or normalization correction factors in the list-file). This can be seen in the attached image, (1) shows the reconstructed images (summed) with CASToR including attenuation
and normalization correction embedded in the file, (2) shows the reconstructed images (summed) when using the pifa obtained from the PET Toolbox to account for attenuation correction and not including attenuation and normalization correction factors in the
CASToR file, and (3) is when the reconstruction is performed with the PET Toolbox.</div>
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<div>Now, if I look at the sinograms extracted from the PET Toolbox I can see that for the first axial indices (0-70) there is a notable difference in the number of counts, something that I am expecting to be corrected for by the normalization correction. So,
I tried to look at the prompts sinogram by subtracting the randoms and scattered coincidences, and then multiplying each sinogram bin by the attenuation- and normalization correction factors. From this I get a smooth sinogram (summed over all views) which
can be seen as (4) in the attached image. If I would do the same thing again, but this time not multiply with the normalization correction factors, this differing intensity becomes apparent in the first axial slices in the sinogram (ring difference 0 for the
DMI with four axial units), seen to the left in (5) in the attached image. <br>
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<div>This made me think that the error lies in the CASToR normalization file. So, to be on the safe side that I constructed the CASToR normalization file correctly, I looked at the normalization file in the benchmark of the G.E. SIGNA data event by event and
could not find any discrepancy between how I constructed the normalization file and the organization to that of the benchmark normalization file.</div>
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<div>I have tried changing the projector but the issue remains (although less apparent with the distance-driven projector).
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<div>Is there something obvious, or less obvious, that I might have missed? Is there something that you could point out that might be wrong?</div>
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<div>I hope to hear from you!</div>
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<div>Best regards,</div>
<div><i>Philip</i><br>
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