I have been running 3dClustSim using the following:
3dClustSim -mask mask.nii.gz
and I get:
$ 3dClustSim -mask mask.nii.gz
++ 3dClustSim: AFNI version=AFNI_20.2.08 (Jul 31 2020) [64-bit]
++ Authored by: RW Cox and BD Ward
++ 31596 voxels in mask (45.04% of total)
++ Startup clock time = 0.1 s
++ Using 8 OpenMP threads
Simulating:0123456789.0123456789.0123456789.0123456789.0123456789.!
++ Clock time now = 23.2 s
# 3dClustSim -mask mask.nii.gz
# 1-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 7.5 8.1 9.0 9.6
0.020000 4.5 4.8 5.3 5.7
0.010000 3.4 3.7 4.0 4.3
0.005000 2.8 3.0 3.3 3.5
0.002000 2.3 2.4 2.6 2.8
0.001000 2.0 2.1 2.3 2.4
0.000500 1.7 1.9 2.0 2.2
0.000200 1.6 1.6 1.8 1.9
0.000100 1.4 1.5 1.6 1.7
# 3dClustSim -mask mask.nii.gz
# 1-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 16.5 18.1 20.1 21.8
0.020000 6.8 7.3 8.1 8.7
0.010000 4.6 4.9 5.4 5.8
0.005000 3.5 3.7 4.1 4.3
0.002000 2.6 2.8 3.1 3.3
0.001000 2.2 2.4 2.6 2.8
0.000500 1.9 2.1 2.3 2.4
0.000200 1.6 1.8 1.9 2.0
0.000100 1.5 1.6 1.7 1.8
# 3dClustSim -mask mask.nii.gz
# 1-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 28.9 32.1 36.7 40.2
0.020000 8.6 9.4 10.4 11.0
0.010000 5.3 5.7 6.4 6.9
0.005000 3.8 4.1 4.5 4.8
0.002000 2.8 3.0 3.3 3.6
0.001000 2.3 2.5 2.8 2.9
0.000500 2.0 2.1 2.4 2.5
0.000200 1.7 1.8 2.0 2.1
0.000100 1.5 1.6 1.8 1.9
# 3dClustSim -mask mask.nii.gz
# 2-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 7.5 8.1 8.9 9.4
0.020000 4.5 4.8 5.3 5.6
0.010000 3.5 3.7 4.0 4.2
0.005000 2.8 3.0 3.2 3.4
0.002000 2.3 2.4 2.6 2.8
0.001000 2.0 2.1 2.3 2.4
0.000500 1.7 1.9 2.0 2.1
0.000200 1.6 1.6 1.8 1.9
0.000100 1.4 1.5 1.6 1.7
# 3dClustSim -mask mask.nii.gz
# 2-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 16.4 18.0 20.3 22.0
0.020000 6.7 7.3 8.1 8.6
0.010000 4.6 4.9 5.4 5.7
0.005000 3.4 3.7 4.1 4.3
0.002000 2.6 2.8 3.1 3.3
0.001000 2.2 2.4 2.6 2.8
0.000500 1.9 2.0 2.2 2.3
0.000200 1.6 1.8 1.9 2.0
0.000100 1.5 1.6 1.8 1.9
# 3dClustSim -mask mask.nii.gz
# 2-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 29.1 32.4 36.4 39.8
0.020000 8.5 9.4 10.4 11.2
0.010000 5.3 5.7 6.3 6.7
0.005000 3.8 4.1 4.5 4.8
0.002000 2.8 3.0 3.3 3.6
0.001000 2.3 2.5 2.7 2.9
0.000500 2.0 2.1 2.3 2.4
0.000200 1.7 1.8 2.0 2.1
0.000100 1.5 1.6 1.8 1.9
# 3dClustSim -mask mask.nii.gz
# bi-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 5.3 5.7 6.2 6.6
0.020000 3.7 3.9 4.3 4.5
0.010000 3.0 3.2 3.5 3.7
0.005000 2.5 2.7 2.9 3.0
0.002000 2.1 2.2 2.4 2.6
0.001000 1.8 2.0 2.1 2.3
0.000500 1.7 1.8 1.9 2.0
0.000200 1.5 1.6 1.7 1.8
0.000100 1.4 1.5 1.6 1.7
# 3dClustSim -mask mask.nii.gz
# bi-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 8.6 9.3 10.2 10.9
0.020000 4.9 5.3 5.8 6.1
0.010000 3.7 4.0 4.3 4.6
0.005000 3.0 3.2 3.5 3.7
0.002000 2.4 2.5 2.8 2.9
0.001000 2.0 2.2 2.4 2.5
0.000500 1.8 1.9 2.1 2.1
0.000200 1.6 1.7 1.8 1.9
0.000100 1.5 1.6 1.7 1.8
# 3dClustSim -mask mask.nii.gz
# bi-sided thresholding
# Grid: 50x61x23 3.12x3.12x6.00 mm^3 (31596 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 11.6 12.6 14.0 15.0
0.020000 5.7 6.2 6.8 7.2
0.010000 4.1 4.4 4.8 5.2
0.005000 3.2 3.4 3.7 4.0
0.002000 2.5 2.7 2.9 3.1
0.001000 2.1 2.3 2.5 2.7
0.000500 1.9 2.0 2.1 2.3
0.000200 1.6 1.7 1.9 2.0
0.000100 1.5 1.6 1.7 1.8
So, suppose I want my threshold, under NN3, at 0.001 (as per Woo et al, Neuroimage, 2014). Then to get an alpha of 0.05, it seems to me that my cluster size should be at least 2.3 voxels for a bi-directional test. This seems very low to me, so I am wondering if I am making an error in my interpretations. Can someone please confirm/enlighten me?
Thanks again in advance for clarifications and the help, and best wishes!
Ranjan
