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

Mon Jan 3 13:36:06 CET 2022

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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