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GMan
May 16, 2019 10:25AM
Hello,

I constructed a mask containing 41 spherical ROIs . If in my analysis I am only interested in activation within these ROIs - how do I determine the cluster threshold for interpreting the results of 3dttest++ ?

I tried running 3dClustsim on the custom mask I created and got the following results: these numbers seem low to me (but I am new to fmri analysis).

CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 6.4 6.9 7.6 8.2
0.020000 4.0 4.3 4.7 5.0
0.010000 3.1 3.3 3.7 3.9
0.005000 2.5 2.7 3.0 3.2
0.002000 2.0 2.2 2.4 2.5
0.001000 1.8 1.9 2.1 2.2
0.000500 1.6 1.7 1.8 1.9
0.000200 1.4 1.5 1.6 1.7
0.000100 1.3 1.4 1.5 1.6
# 3dClustSim -mask spinal_stim_rois.nii.gz
# 1-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 12.2 13.5 15.2 16.4
0.020000 5.7 6.2 6.9 7.4
0.010000 3.9 4.3 4.8 5.1
0.005000 3.0 3.2 3.6 3.8
0.002000 2.3 2.5 2.7 2.9
0.001000 2.0 2.1 2.3 2.5
0.000500 1.7 1.9 2.0 2.2
0.000200 1.5 1.6 1.7 1.8
0.000100 1.4 1.5 1.6 1.7
# 3dClustSim -mask spinal_stim_rois.nii.gz
# 1-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 18.9 21.4 24.7 27.1
0.020000 6.8 7.5 8.5 9.2
0.010000 4.5 4.9 5.4 5.9
0.005000 3.3 3.6 3.9 4.3
0.002000 2.4 2.6 2.9 3.1
0.001000 2.0 2.2 2.4 2.5
0.000500 1.8 1.9 2.1 2.2
0.000200 1.5 1.6 1.7 1.8
0.000100 1.4 1.5 1.6 1.7
# 3dClustSim -mask spinal_stim_rois.nii.gz
# 2-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 6.4 6.9 7.7 8.3
0.020000 4.0 4.3 4.7 5.0
0.010000 3.1 3.3 3.7 3.9
0.005000 2.5 2.7 3.0 3.1
0.002000 2.0 2.2 2.4 2.5
0.001000 1.8 1.9 2.1 2.2
0.000500 1.6 1.7 1.8 1.9
0.000200 1.4 1.5 1.6 1.7
0.000100 1.3 1.4 1.5 1.6
# 3dClustSim -mask spinal_stim_rois.nii.gz
# 2-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 12.4 13.8 15.3 16.5
0.020000 5.6 6.2 6.9 7.4
0.010000 3.9 4.3 4.7 5.1
0.005000 3.0 3.3 3.6 3.8
0.002000 2.3 2.5 2.7 2.9
0.001000 2.0 2.1 2.3 2.5
0.000500 1.7 1.8 2.0 2.2
0.000200 1.5 1.6 1.7 1.8
0.000100 1.3 1.4 1.6 1.7
# 3dClustSim -mask spinal_stim_rois.nii.gz
# 2-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 19.1 21.6 25.0 27.4
0.020000 6.9 7.6 8.5 9.3
0.010000 4.5 4.9 5.4 5.9
0.005000 3.3 3.6 3.9 4.2
0.002000 2.4 2.6 2.9 3.1
0.001000 2.0 2.2 2.4 2.6
0.000500 1.8 1.9 2.1 2.2
0.000200 1.5 1.6 1.8 1.9
0.000100 1.4 1.5 1.6 1.7
# 3dClustSim -mask spinal_stim_rois.nii.gz
# bi-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 4.7 5.1 5.5 5.9
0.020000 3.3 3.6 3.9 4.1
0.010000 2.7 2.9 3.2 3.4
0.005000 2.3 2.4 2.6 2.8
0.002000 1.9 2.0 2.2 2.3
0.001000 1.7 1.8 1.9 2.1
0.000500 1.5 1.6 1.8 1.9
0.000200 1.4 1.5 1.6 1.7
0.000100 1.3 1.4 1.5 1.6
# 3dClustSim -mask spinal_stim_rois.nii.gz
# bi-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 7.1 7.7 8.5 9.1
0.020000 4.3 4.6 5.1 5.4
0.010000 3.2 3.5 3.8 4.0
0.005000 2.7 2.9 3.1 3.3
0.002000 2.1 2.3 2.5 2.6
0.001000 1.8 2.0 2.1 2.3
0.000500 1.6 1.8 1.9 2.0
0.000200 1.4 1.5 1.7 1.8
0.000100 1.3 1.4 1.5 1.6
# 3dClustSim -mask spinal_stim_rois.nii.gz
# bi-sided thresholding
# Grid: 129x153x129 1.50x1.50x1.50 mm^3 (12662 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 3 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 9.0 9.9 11.1 12.1
0.020000 4.9 5.3 5.8 6.2
0.010000 3.5 3.8 4.2 4.6
0.005000 2.8 3.0 3.3 3.6
0.002000 2.2 2.4 2.6 2.7
0.001000 1.9 2.0 2.2 2.4
0.000500 1.7 1.8 1.9 2.1
0.000200 1.5 1.6 1.7 1.8
0.000100 1.3 1.4 1.5 1.6

Thank you in advance for your guidance,

Gerome
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Subject Author Posted

Determining Cluster threshold for 3dttest ++ using ROI mask

GMan May 16, 2019 10:25AM

Re: Determining Cluster threshold for 3dttest ++ using ROI mask

gang May 16, 2019 09:26PM