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Dear AFNI users-

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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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jef
April 16, 2021 10:15AM
Thanks for your reply and sorry I missed your replies.

Here is what I was running originally
# Set path to the RX directory to save output 
rx_path=/nas/longleaf/home/jess1/whole-brain-dev-social/analysis/thresholding

# Set path to the mask used in analyses #mask is at 70% threshold grey matter mask
mask=/nas/longleaf/home/jess1/whole-brain-dev-social/thresholding/group_mask_acrosswave.7.nii

# Run 3dClustSim using the average acf outputs from the script "calculate_average_ACF.Rmd" 
#acf parameters were calculated at individual residual files, then averaged together. Note this is across 3 waves.
3dClustSim -mask ${mask} -acf 0.555380169013242 4.61362680991569 12.3309040184921 > ${rx_path}/threshold_SID.txt

and sample values. 
# 3dClustSim -mask /nas/longleaf/home/jess1/whole-brain-dev-social/thresholding/group_mask_acrosswave.7.nii -acf 0.555380169013242 4.61362680$
# bi-sided thresholding
# Grid: 91x109x91 2.00x2.00x2.00 mm^3 (172610 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3  | alpha = Prob(Cluster >= given size)
#  pthr  | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
 0.050000  1291.0 1565.2 1889.0 2153.0
 0.020000   501.2  594.0  751.8  896.7
 0.010000   281.3  343.6  433.0  491.7
 0.005000   171.1  210.4  265.7  311.5
 0.002000    97.3  120.6  153.2  186.7
 0.001000    65.4   82.0  105.9  131.3
 0.000500    45.2   57.3   74.5   92.8
 0.000200    27.8   35.9   49.2   59.6
 0.000100    19.1   25.5   35.8   43.0


Here is what I was running to see the effect of the mask. 
# Run 3dClustSim using the average acf outputs from the script "calcualte_average_ACF.Rmd"
3dClustSim -acf 0.555380169013242 4.61362680991569 12.3309040184921 > ${rx_path}/threshold_SID_nomask.txt


and sample values of p/k values. 

# 3dClustSim -acf 0.555380169013242 4.61362680991569 12.3309040184921
# bi-sided thresholding
# Grid: 64x64x32 3.50x3.50x3.50 mm^3 (131072 voxels)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3  | alpha = Prob(Cluster >= given size)
#  pthr  | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
 0.050000   463.0  537.0  624.0  708.0
 0.020000   159.8  189.1  223.2  248.6
 0.010000    86.6  101.6  123.6  141.3
 0.005000    51.9   61.6   75.2   85.7
 0.002000    29.4   35.1   43.3   50.6
 0.001000    20.3   24.1   30.2   34.8
 0.000500    14.5   17.3   21.6   25.4
 0.000200     9.6   11.6   14.3   16.7
 0.000100     7.1    8.6   10.9   12.6


Again, I'm assuming the second one is wrong, but trying to understand why it was so liberal. The first results also feel overly strict, but I trust those results more than the second version without a mask.

Thank you!!
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Subject Author Posted

inflated 3dclustsim values with no mask?

jef March 24, 2021 10:47AM

Re: inflated 3dclustsim values with no mask?

RWCox March 24, 2021 05:26PM

Re: inflated 3dclustsim values with no mask?

ptaylor March 24, 2021 06:09PM

Re: inflated 3dclustsim values with no mask?

jef April 16, 2021 10:15AM

Re: inflated 3dclustsim values with no mask?

ptaylor April 16, 2021 10:50AM

Re: inflated 3dclustsim values with no mask?

jef April 16, 2021 02:47PM

Re: inflated 3dclustsim values with no mask?

jef April 28, 2021 05:12PM

Re: inflated 3dclustsim values with no mask?

ptaylor April 28, 2021 05:56PM