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I've tested reproducibility of the results either using ASEG (therefore via recon-all -all) and also SAMSEG (via run_samseg).
The methods are different either in terms of reproducibility of results.
Multiple runs of ASEG (recon-all -all) provide the same result but it requires 8+ hours to be executed (each). By comparing the results of multiple runs using the file from a single patient, such results are exactly the same, no changes at all.
If I use SAMSEG (which is a lot faster, execution time is less than 1h using multi-thread execution), I get overall slightly similar results (when compared to ASEG) except for the CSF which is very different.
The problem I've found is that if I run SAMSEG on the same patient data and evaluate the results, these results (which I would expect they should be exactly the same), are slightly different. I've done multiple test, whether using single-thread or multi-thread execution. Every time I execute run_samseg the results express variability. I think this is because multiple calls to numpy.random in the python code of samseg. This problem should be fixed to ensure reproducibility of the data.
I hope to be clear now.
I just wanted to understand is the results from ASEG and SAMSEG (which is again, a lot faster) could be compared in terms of reproducibility, even if these results are not equivalent per se.
Regards