[Castor-users] Attenuation correction and normalization for list-mode reconstruction

[tmerlin]

Dear Jakub,

Maybe I am wrong about this, but I don't think you could skip a 
retro-projection step over all the system LORs at some point in order to 
compute the attenuation factors in the image space. This is required by 
the (list-mode) MLEM equation.

Best,
Thibaut

On 23/05/2022 11:52, jbaran wrote:
> Dear Thibaut,
>
> is there a possibility to apply the above mentioned attenuation 
> factors directly to the reconstruction (not sensitivity map 
> production). Let say I have a one sensitivity map for my scanner 
> (sensitivity without any phantom put inside the FOV) and I just want 
> to calculate the attenuation in-fly (which will vary from subject to 
> subject) during the regular (MLEM, OSEM, ...) reconstruction.
>
> Is it somehow hard to adapt the CASToR for that?
>
> All the best,
> Jakub
>
>
> On 2022-05-18 17:31, tmerlin wrote:
>> Dear Zipai,
>>
>> I advice to proceed as Simon suggested, but just for information there
>> is a way to compute the ACFs with _castor-GATERootToCastor_ using the
>> _-atn_ option. They will be incorporated in the generated CASToR
>> datafile. The projector must be the same that the one used for
>> reconstruction.
>>
>> Best,
>>
>> Thibaut
>>
>> On 16/05/2022 14:08, STUTE Simon wrote:
>>
>>> Hi Zipai Wang,
>>>
>>> When you use a normalization datafile to guide the computation of
>>> the sensitivity image, you can input attenuation correction factor
>>> in the normalization datafile but you can still simply supply an
>>> attenuation image with the option "-atn". Both are compatible.
>>>
>>> To compute the attenuation coefficients, I personally use the
>>> following database
>>>
>>> https://physics.nist.gov/PhysRefData/Xcom/html/xcom1.html
>>>
>>> It is very convenient, you just supply the different compounds of
>>> the material from the GATE material database, ask for an energy, and
>>> get the attenuation factor.
>>>
>>> Then you can build an image where you replace each label of your
>>> phantom by the attenuation factor in cm-1, and this is what you
>>> supply to castor using the option "-atn".
>>>
>>> Simon
>>>
>>> -------------------------
>>>
>>> DE : Castor-users <castor-users-bounces at lists.castor-project.org> de
>>> la part de Zipai Wang <zipai.wang at stonybrook.edu>
>>> ENVOYÉ : lundi 18 avril 2022 22:01
>>> À : castor-users at lists.castor-project.org
>>> OBJET : [Castor-users] Attenuation correction and normalization for
>>> list-mode reconstruction
>>>
>>> Dear CASToR users and developers,
>>>
>>> I have simulated a digital phantom in GATE and reconstructed the
>>> GATE list-mode using CASToR. In order to perform the normalization I
>>> manually calculated the normalization factors and fed the
>>> normalization datafile into the CASToR for the calculation of
>>> Sensitivity image.
>>>
>>> In this case, in order to apply the attenuation correction, I
>>> believe I need to calculate the attenuation coefficient for each
>>> LORs and feed it within the normalization datafile. However this is
>>> not straightforward for me because the phantom contains multiple
>>> types of material and tissues.
>>>
>>> So my question is: 1. I know we can feed atn image to CASToR during
>>> the reconstruction, but in this way how can I apply the
>>> normalization?
>>>
>>> 2. Can the CASToR generate the atten coefficient and output the
>>> information so that I can combine it with the norm factors to form
>>> the datafile?
>>>
>>> Thank you very much for your help! --
>>>
>>> Zipai Wang
>>> Biomedical Engineering PhD student
>>> Stony Brook University
>>>
>>> _______________________________________________
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>>>
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>>> box at:
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>>
>> -- 
>> 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
>> _______________________________________________
>> Castor-users mailing list
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>>
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-- 
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