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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
# Measure Unknown, 938678.804563, mm^3
# Measure Skull, 70514.097706, mm^3
# Measure Soft_Nonbrain_Tissue, 1117216.914116, mm^3
# Measure Brain-Stem, 19382.400237, mm^3
# Measure CSF, 510336.929212, mm^3
# Measure Left-Cerebellum-Cortex, 46227.404805, mm^3
# Measure Right-Cerebellum-Cortex, 46954.827348, mm^3
# Measure 4th-Ventricle, 1927.249860, mm^3
# Measure Fluid_Inside_Eyes, 10681.567722, mm^3
# Measure Left-Cerebral-Cortex, 194854.703127, mm^3
# Measure Right-Cerebral-Cortex, 198395.911108, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.296942, mm^3
# Measure Right-Cerebellum-White-Matter, 13442.628195, mm^3
# Measure Right-Cerebral-White-Matter, 200768.332902, mm^3
# Measure Left-Cerebral-White-Matter, 199392.351036, mm^3
# Measure Right-choroid-plexus, 2202.554448, mm^3
# Measure Right-Amygdala, 1483.776188, mm^3
# Measure Left-Amygdala, 1543.083787, mm^3
# Measure Right-Hippocampus, 3889.943347, mm^3
# Measure Right-Inf-Lat-Vent, 773.181432, mm^3
# Measure Left-Hippocampus, 3957.909089, mm^3
# Measure Left-choroid-plexus, 1732.272325, mm^3
# Measure Left-Inf-Lat-Vent, 374.679073, mm^3
# Measure Optic-Chiasm, 194.020527, mm^3
# Measure Right-VentralDC, 3517.897243, mm^3
# Measure Left-VentralDC, 3616.708619, mm^3
# Measure 3rd-Ventricle, 2767.856042, mm^3
# Measure Left-Accumbens-area, 582.221221, mm^3
# Measure Left-Putamen, 4786.334982, mm^3
# Measure Right-Putamen, 4722.605242, mm^3
# Measure Right-vessel, 80.863621, mm^3
# Measure Right-Accumbens-area, 461.768868, mm^3
# Measure WM-hypointensities, 20335.889722, mm^3
# Measure Left-Lateral-Ventricle, 20190.963456, mm^3
# Measure Left-vessel, 61.352892, mm^3
# Measure Right-Lateral-Ventricle, 18727.913621, mm^3
# Measure Right-Pallidum, 1703.159618, mm^3
# Measure Left-Caudate, 3777.300280, mm^3
# Measure Right-Thalamus, 5636.150208, mm^3
# Measure Left-Pallidum, 1656.295530, mm^3
# Measure Right-Caudate, 3583.231471, mm^3
# Measure Left-Thalamus, 6017.696659, mm^3
# Measure non-WM-hypointensities, 89.673417, mm^3
# Measure 5th-Ventricle, 15.867564, mm^3
# Measure Unknown, 939056.015091, mm^3
# Measure Skull, 71767.719764, mm^3
# Measure Soft_Nonbrain_Tissue, 1112717.212711, mm^3
# Measure Brain-Stem, 19396.749933, mm^3
# Measure CSF, 511873.576213, mm^3
# Measure Left-Cerebellum-Cortex, 46226.557363, mm^3
# Measure Right-Cerebellum-Cortex, 46977.164462, mm^3
# Measure 4th-Ventricle, 1932.334854, mm^3
# Measure Fluid_Inside_Eyes, 10678.846479, mm^3
# Measure Left-Cerebral-Cortex, 195097.957627, mm^3
# Measure Right-Cerebral-Cortex, 198722.232809, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.963053, mm^3
# Measure Right-Cerebellum-White-Matter, 13448.109331, mm^3
# Measure Right-Cerebral-White-Matter, 201145.753968, mm^3
# Measure Left-Cerebral-White-Matter, 199725.946038, mm^3
# Measure Right-choroid-plexus, 2196.836003, mm^3
# Measure Right-Amygdala, 1483.180736, mm^3
# Measure Left-Amygdala, 1541.752663, mm^3
# Measure Right-Hippocampus, 3885.522213, mm^3
# Measure Right-Inf-Lat-Vent, 774.735928, mm^3
# Measure Left-Hippocampus, 3954.921244, mm^3
# Measure Left-choroid-plexus, 1727.665580, mm^3
# Measure Left-Inf-Lat-Vent, 375.969644, mm^3
# Measure Optic-Chiasm, 194.100725, mm^3
# Measure Right-VentralDC, 3514.663768, mm^3
# Measure Left-VentralDC, 3624.351918, mm^3
# Measure 3rd-Ventricle, 2772.144481, mm^3
# Measure Left-Accumbens-area, 583.409147, mm^3
# Measure Left-Putamen, 4795.974528, mm^3
# Measure Right-Putamen, 4727.161970, mm^3
# Measure Right-vessel, 81.049494, mm^3
# Measure Right-Accumbens-area, 460.463919, mm^3
# Measure WM-hypointensities, 20286.439923, mm^3
# Measure Left-Lateral-Ventricle, 20198.148413, mm^3
# Measure Left-vessel, 61.483040, mm^3
# Measure Right-Lateral-Ventricle, 18752.376148, mm^3
# Measure Right-Pallidum, 1706.206364, mm^3
# Measure Left-Caudate, 3781.345908, mm^3
# Measure Right-Thalamus, 5643.708765, mm^3
# Measure Left-Pallidum, 1657.771589, mm^3
# Measure Right-Caudate, 3579.185246, mm^3
# Measure Left-Thalamus, 6021.094626, mm^3
# Measure non-WM-hypointensities, 90.822737, mm^3
# Measure 5th-Ventricle, 16.024828, mm^3
# Measure Unknown, 938636.026718, mm^3
# Measure Skull, 70342.868330, mm^3
# Measure Soft_Nonbrain_Tissue, 1117785.963774, mm^3
# Measure Brain-Stem, 19384.824975, mm^3
# Measure CSF, 510356.155842, mm^3
# Measure Left-Cerebellum-Cortex, 46239.658445, mm^3
# Measure Right-Cerebellum-Cortex, 46929.069321, mm^3
# Measure 4th-Ventricle, 1930.194182, mm^3
# Measure Fluid_Inside_Eyes, 10680.018532, mm^3
# Measure Left-Cerebral-Cortex, 194712.112215, mm^3
# Measure Right-Cerebral-Cortex, 198094.882136, mm^3
# Measure Left-Cerebellum-White-Matter, 13373.080344, mm^3
# Measure Right-Cerebellum-White-Matter, 13442.760484, mm^3
# Measure Right-Cerebral-White-Matter, 200760.683560, mm^3
# Measure Left-Cerebral-White-Matter, 199461.548374, mm^3
# Measure Right-choroid-plexus, 2201.065021, mm^3
# Measure Right-Amygdala, 1484.076878, mm^3
# Measure Left-Amygdala, 1541.862861, mm^3
# Measure Right-Hippocampus, 3890.381369, mm^3
# Measure Right-Inf-Lat-Vent, 774.235312, mm^3
# Measure Left-Hippocampus, 3959.472881, mm^3
# Measure Left-choroid-plexus, 1734.016967, mm^3
# Measure Left-Inf-Lat-Vent, 375.053731, mm^3
# Measure Optic-Chiasm, 193.852776, mm^3
# Measure Right-VentralDC, 3515.083513, mm^3
# Measure Left-VentralDC, 3621.723577, mm^3
# Measure 3rd-Ventricle, 2765.290275, mm^3
# Measure Left-Accumbens-area, 581.950463, mm^3
# Measure Left-Putamen, 4784.987066, mm^3
# Measure Right-Putamen, 4716.829853, mm^3
# Measure Right-vessel, 80.716771, mm^3
# Measure Right-Accumbens-area, 463.198638, mm^3
# Measure WM-hypointensities, 20344.477660, mm^3
# Measure Left-Lateral-Ventricle, 20206.726037, mm^3
# Measure Left-vessel, 61.270680, mm^3
# Measure Right-Lateral-Ventricle, 18733.504872, mm^3
# Measure Right-Pallidum, 1699.195763, mm^3
# Measure Left-Caudate, 3775.381385, mm^3
# Measure Right-Thalamus, 5635.202343, mm^3
# Measure Left-Pallidum, 1655.650033, mm^3
# Measure Right-Caudate, 3582.336454, mm^3
# Measure Left-Thalamus, 6010.719531, mm^3
# Measure non-WM-hypointensities, 88.957715, mm^3
# Measure 5th-Ventricle, 16.188884, mm^3
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