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

Mon Jan 3 13:39:47 CET 2022

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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