[Castor-users] Issues about the List-mode normalization
tmerlin
Thibaut.Merlin at univ-brest.fr
Mon Mar 14 17:29:02 CET 2022
Dear Zipai,
I will answer to the mailing-list as well as it is an interesting
question and other users could have similar interrogations.
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 (https://doi.org/10.1109/TMI.2017.2761756 ). However implementing
this approach in CASToR would require substantial changes to optimize
the code performance, at the expense of genericity.
Many thanks for the kind words about the workshop, always good to know
it was useful to you and other attendees :)
Best regards,
Thibaut
On 11/03/2022 07:33, Zipai Wang wrote:
> Dear Dr. Merlin,
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> Best regards,
> Zipai
>
> On Mon, Feb 21, 2022 at 7:22 PM Thibaut Merlin
> <Thibaut.Merlin at univ-brest.fr <mailto:Thibaut.Merlin at univ-brest.fr>>
> wrote:
>
> Hi Zipai,
>
> 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 ?
>
> 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.
>
> Hope this helps!
>
> Best regards,
> Thibaut
>
> Zipai Wang <zipai.wang at stonybrook.edu
> <mailto:zipai.wang at stonybrook.edu>> a écrit :
>
>> Dear CASToR developers and users,
>> I am trying to apply normalization to a simulated PET scanner but
>> meet some issues, any help is highly appreciated!
>> 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.
>> However, the normalization doesn't work when I embed the factors
>> into the List-mode binary datafile:
>> 1. When I feed the list-mode data (with normalization factors and
>> flag on) to CASToR, it give me the following error:
>> /oSensitivityGenerator::InitializeNormalizationFiles() ->
>> Normalization correction is included in the data file while it is
>> not in the sensitivity computation!/
>> In order to bypass this error, I use /-sens/ 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?
>> 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.
>> The version I am using is CASToR v 3.0.1.
>> Here is one of the header files:
>> Data filename: PET_Sim_LMNorm.Cdf
>> Number of events: 13755984
>> Data mode: list-mode
>> Data type: PET
>> Start time (s): 0
>> Normalization correction flag: 1
>> Duration (s): 1500
>> Scanner name: D04_sim_1ring
>> Calibration factor: 1
>> Isotope: unknown
>> Here is some examples of the I generated list-mode data: (I
>> assgin all the time frames to 0 and norm factors to 1)
>> 0000 0000 0000 803f ba22 0000 c005 0000
>> 0000 0000 0000 803f 9a15 0000 9e19 0000
>> 0000 0000 0000 803f e20e 0000 fa0b 0000
>> 0000 0000 0000 803f f51f 0000 6a05 0000
>> 0000 0000 0000 803f 971a 0000 1203 0000
>> 0000 0000 0000 803f e91f 0000 d719 0000
>> 0000 0000 0000 803f 211d 0000 3721 0000
>> 0000 0000 0000 803f f906 0000 7105 0000
>> 0000 0000 0000 803f 4c20 0000 f014 0000
>> 0000 0000 0000 803f 8e1e 0000 a607 0000
>> 0000 0000 0000 803f a821 0000 1a19 0000
>> 0000 0000 0000 803f e81a 0000 8514 0000
>> 0000 0000 0000 803f 6913 0000 e525 0000
>> Thank you very much!
>> --
>> Zipai Wang
>> Biomedical Engineering PhD student
>> Stony Brook University
>
>
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>
> --
> Zipai Wang
> Biomedical Engineering PhD student
> Stony Brook University
--
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
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