[Castor-users] Issues about the List-mode normalization

Mon Mar 14 22:35:00 CET 2022

Thank you Dr. Merlin for your answers!

Best regards,

On Mon, Mar 14, 2022 at 12:26 PM tmerlin <Thibaut.Merlin at univ-brest.fr>
wrote:

> 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> 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> 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
>
>

-- 
Zipai Wang
Biomedical Engineering PhD student
Stony Brook University
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