[Castor-users] Scatter rate estimation for LM-TOF-MLEM

[STUTE Simon]

Hi Jakub,

I am confused as you give two different legends for the cuboid data in your two latest emails.

OK for being both simulated data, indeed, otherwise you could not perform your SSRB-like scatter estimation... Sorry.

Your frame duration is significant. As you take it into account when computing the scatter estimation (with your method), I do not understand why you initially forced it to be ignored in the reconstruction ? You should always take it into account.

The way you estimate the scatter seems to be in agreement with what is expected into CASToR.

For the cuboid data, I still do not understand how CASToR is including a scatter correction. It may be that the real scatter count of each LOR is written as a rate in the scatter correction term. If so, then, it is not in agreement with the model used in CASToR as the scatter rate is included in the forward model (in other words, it is not subtracted). Anyway, if it is done this way, then it should not be done this way and you should not take this as a reference or so. You should definitely prefer your SSRB-like method of smoothing the scatter estimate.

About your cdh file, everything looks fine.

About what to look for in the datafile, I would like to see the total number of prompts VS total number of scatters, based on the CASToR datafile, and also the total number of corrected counts. You will be able to check if the scatter fraction is in agreement with the data coming out from GATE.

Best
Simon
________________________________________
De : jbaran <jbaran at ifj.edu.pl>
Envoyé : lundi 3 janvier 2022 13:39
À : STUTE Simon
Cc : Castor Users
Objet : Re: [Castor-users] Scatter rate estimation for LM-TOF-MLEM

Hi Simon,

I forget to add the proper legend to the cuboid.png file:

The legend for the plot (cuboid_fdur.png) is as follows:
TOP LEFT: true coincidences
TOP RIGHT: true + scatter coincidences
BOTTOM LEFT: true + scatter coincidences scatter corrected
BOTTOM RIGHT: profiles along the orange line from previous plots.

All the best
Jakub

On 2022-01-03 13:36, jbaran wrote:
> Hi Simon,
>
> Happy New Year for you also.
>
> All datasets which I shown are from the simulation datasets.
>
> On 2022-01-03 12:47, STUTE Simon wrote:
>> Hi Jakub,
>>
>> Happy new year to you and your project !
>>
>> About real data, what is the scan duration ? Could you share the
>> header of the datafile ?
>
> I assumed that you mean the data from NEMA IEC siulation. The header
> looks as follows:
>
> Data filename: factor_20000_df.Cdf
> Number of events: 298175691
> Data mode: list-mode
> Data type: PET
> Start time (s): 0
> Duration (s): 500
> Scanner name: TB_JPET_2nd_gen
> Calibration factor: 1
> Isotope: unknown
> TOF information flag: 1
> TOF resolution (ps): 230
> List TOF measurement range (ps): 3000
> List TOF quantization bin size (ps): 100
> Scatter correction flag: 1
>
>
>> I will try to modify as soon as possible the DatafileExplorer toolkit
>> to display the total corrected counts in addition to the total number
>> of counts, that that you will be able to see if everything is globally
>> correct in the datafile.
>
> We developed such a toolkit (more like dumping the data to the
> external file). Could you please tell me what I should look like for?
>
>>
>> About simulated data, CASToR does not perform any scatter correction,
>> so there is something I do not understand.
>> I am not used to the Gate2CASToR toolkit, sorry.
>> Anyway, in the figure you attached, I cannot believe that bottom left
>> is true coincidences only, there should be something wrong.
>
> I am sorry I made a mistake in the description of the cuboid.png file.
> It should be as follows:
>
> The legend for the plot (cuboid_fdu.png) is as follows:
> TOP LEFT: true + scatter coincidences scatter corrected
> TOP RIGHT: true + scatter coincidences
> BOTTOM LEFT: true coincidences
> BOTTOM RIGHT: profiles along the orange line from previous plots.
>
>> How many iterations/subsets are you using in the reconstructions ?
>
> We used 20 iterations. The results which I sent are for the 15th
> iteration.
>
>>
>> Best
>> Simon
>> ________________________________________
>> De : jbaran <jbaran at ifj.edu.pl>
>> Envoyé : lundi 20 décembre 2021 10:08
>> À : STUTE Simon
>> Cc : Castor Users
>> Objet : Re: [Castor-users] Scatter rate estimation for LM-TOF-MLEM
>>
>> Hi Simon,
>>
>> thanks for your prompt reply. and sorry for the late response.
>>
>> I did as you suggest. I remove the -ignore-corr fdur flag from the
>> reconstruction. I attached the results for both, NEMA IEC phantom
>> (scatter fraction calculated by ourselves) - NEMA_IEC_fdur.png - and
>> the
>> cuboid phantom (scatter correction calculated by CASToR) -
>> cuboid_fdur.png.
>>
>> For the NEMA IEC plot, all presented images are reconstructed with
>> scatter correction implemented and tested by ourselves. The difference
>> is in an applied -ignore-corr fdur flag and scaling factor of the
>> scatter rates and the legend is as follows:
>> TOP LEFT: scalling factor = 20000 with -ignore-corr fdur
>> TOP RIGHT: scalling factor = 1  (without -ignore-corr fdur frame
>> duration is incorporated)
>> BOTTOM LEFT: scalling factor = 20000 superimposed on scalling factor =
>> 1
>> with -ignore-corr fdur (the images looks the same)
>> BOTTOM RIGHT: profiles along the orange line from previous plots
>>
>> You can see that three of the reconstructed images looks very similar.
>> The most significant difference is in the image on TOP LEFT so the one
>> with scalling factor = 20000 with -ignore-corr fdur. But still the
>> effect of the scatters is observable.
>>
>> Regarding the way of scatter rate estimation we did in principle as
>> follows. We calculate the scatter corrections for each TOF bin. Then
>> we
>> merge some LORs to calculate the let say downsampled scatter rate.
>> Then
>> we divided this number by the number of LORs and time. In principle
>> you
>> can find some similarity to the SSRB procedure.
>>
>> For the cuboid study where the CASToR calculate the scatter rate
>> factors
>> internally, the results doesn't change. For this case I reconstruct
>> images once again but without -ignore-corr fdur flag. Incorporation of
>> the scatter rate does not give any improvement of the image quality.
>> It
>> seems that even with nonTOF data these is something wrong with scatter
>> correction.
>>
>> The legend for the plot (cuboid_fdu.png) is as follows:
>> TOP LEFT: true + scatter coincidences scatter corrected
>> TOP RIGHT: true + scatter coincidences
>> BOTTOM LEFT: true coincidences
>> BOTTOM RIGHT: profiles along the orange line from previous plots.
>>
>> All the best,
>> Jakub
>>
>>
>>
>> On 2021-12-07 11:51, STUTE Simon wrote:
>>> Hi,
>>>
>>> OK thanks for the explanations.
>>>
>>> Why ignoring the frame duration in the reconstruction ?
>>>
>>> As the scatter correction is supplied as a rate, you really need the
>>> frame duration to rescale the scatters to the prompt coincidences.
>>>
>>> Could you try to reconstruct with the frame duration taken into
>>> account
>>> ?
>>>
>>> How did you translate the estimation of the scatter rates based on a
>>> sinogram to the list-mode data ? Did you take the binning size into
>>> account ? You need to divide your scatter rate for a TOF bin by the
>>> size of the TOF bin to get an "almost" continuous measurement.
>>>
>>> Simon
>>>
>>> ________________________________________
>>> De : jbaran <jbaran at ifj.edu.pl>
>>> Envoyé : mardi 7 décembre 2021 10:59
>>> À : STUTE Simon
>>> Cc : Castor Users
>>> Objet : Re: [Castor-users] Scatter rate estimation for LM-TOF-MLEM
>>>
>>> Hi Simon,
>>>
>>> many thanks for the quick response. The answers are as follows:
>>>
>>>
>>> On 2021-12-07 09:56, STUTE Simon wrote:
>>>> Hello Jakub,
>>>>
>>>> Thanks for the detailed email !
>>>>
>>>> Do you take the scan duration into account in the datafile header ?
>>>
>>> Yes, I added the information about the scan duration in the header.
>>> On
>>> the other hand in the reconstruction I used -ignore-corr fdur option.
>>>
>>>>
>>>> You say that you estimated the scatter rate for each TOF bin
>>>> independently to be 1-2. Is it "1 or 2" (which would be insanely
>>>> high)
>>>> or "e-2" ?
>>>
>>> I was not explicit here. The scatter rate passed to the castor lm is
>>> ranging from 0 to 2. However most values are in the range from 1e-3
>>> to
>>> 1e-1.
>>>
>>>>
>>>> How did you compute this estimated scatter rate ?
>>>
>>> We made basic estimation based on Monte Carlo simulations - NEMA IEC
>>> study. For the cubic study we use -sc flag during the conversion of
>>> the
>>> ROOT data to CASToR. For this the scatter rate is at the level of
>>> about
>>> 1e-4.
>>>
>>>>
>>>> And how did you translate this information into your list-mode file
>>>> ?
>>>
>>> We adapt the CASToR code to read the scatter correction rate factor
>>> from
>>> the matrix provided by ourselves.
>>>
>>>>
>>>> Best
>>>> Simon
>>>
>>> All the best,
>>> Jakub
>>> _______________________________________________
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