attenuation correction and normalization

General Discussions
1

Dear CASToR users

I simulated an IEC NEMA phantom on a PET using GATE and reconstructed it using CASTOR without any correction (random, scatter, attenuation and normalization). The reconstructed image was undesirable. I found that for random and scatter correction I can write “-t” on the castor-GATERootToCastor to convert only trues (is it right?). But, how can I perform the attenuation correction (and also normalization)?
I used bellow commands for convert to CASTOR and reconstructed it.
./castor-GATERootToCastor -i output.root -m mymacfile.mac -o IEC -s IEC -geo -k
./castor-recon -df IEC_df.Cdh -dout IEC -opti MLEM -it 10:20 -th 40 -dim 512,512,1655 -fov 600,600,1940
I attached the reconstructed image here. I would therefore appreciate it if anyone could help me to apply any correction on it.
Best regards
Hadi

IEC.png

2

Hi Hadi,

You can provide an attenuation map to castor-recon if you use list-mode format with the -atn option (or directly to castor-GATERootToCastor if you want to get an histogram) .

castor-GATERootToCastor doesn’t perform normalization correction, so normalization correction coefficients would have to be computed manually and inserted directly in the datafiles, as indicated in the documentation section 6.1.

Looking at your image, it is not easy to know what is wrong without details about the simulation and the image values, but it seems it was reconstructed from a simulation with very low statistics.

Hope this helps,
Thibaut

3

Hi Tmerlin
Thank you for your answer.
I provided an attenuation map using mu map actor in GATE using the following commands:

4

Hi Hadi,

Could you share the header of your mumap (myMapFileName-MuMap.hdr) ? It looks like the problem comes from some interfile keys.

Best,
Thibaut

5

Hi Thibaut
Thank you for your answer.

I shared it. I got it from GATE directly.

Thank you

myMapFileName-MuMap.hdr (348 Bytes)

6

Hi Hadi,

Could you check if there is an issue with the file ? I couldn’t open it using regular text editors.

Best,
Thibaut

7

Hi Thibaut
I am sorry for the delay.

Could you share a sample of the header (.hdr) file ??
Thank you so much.

Hadi

8

Hi Hadi,

Here is a umap example.

Best,
Thibaut

mumapblur_p1_128x83x47_atn_cm.hdr (750 Bytes)

mumapblur_p1_128x83x47_atn_cm.raw (1.9 MB)

9

Thank you very much.