query on output of 3dClustSim

AFNI Message Board
1

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

2

Hi Ranjan,

Yes, these results are likely grossly underestimating the needed cluster sizes, as the commands do not provide information about the blur size. You should be estimating the ACF blur parameters in the data, and providing those estimates as part of the 3dClustSim command.

Search for 3dClustSim to see how it is used with the ACF parameters in AFNI_data6/FT_analysis/s12.proc.FT.align .

  • rick
3

Rick,

Thanks very much for this clarification. I had forgotten about the ACF blur parameters, thank you!

Best wishes,
Ranjan