Determining Cluster threshold for 3dttest ++ using ROI mask

Gerome_Manson · May 16, 2019, 2:25pm

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

Gang · May 17, 2019, 1:26am

I constructed a mask containing 41 spherical ROIs . If in my analysis I am only
interested in activation within these ROIs

If you want to focus your analysis on those 41 regions, a more reasonable approach is to perform region-based analysis:

https://afni.nimh.nih.gov/afni/community/board/read.php?1,157054,157054#msg-157054

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

If you’re using those isolated 41 ROIs as a mask to determine the minimum cluster size, that would be inappropriate because intrinsically it would not be able to form large clusters. And it’s no surprise you got those small numbers. A mask should be contiguous and ideally should be conceptually determined before, not after, the experiment.