There is some stochasticity in these calculations, so they will be likely to vary a litttle bit across runs. 3dClustSim calcs are also generally intended to be run in more spherical, whole-brain masklike masks, as well. Having a mask that is composed of set of linear-ish structures with complicated boundaries can affect some of convergence, I would guess. I mention this because from your filenames, I think you are running this in a gray matter only mask, which will be relatively filamentary rather than blobby/spherical-ish.
That being said, I generated a practice GM-only mask on the same dimensions of template you are using, using the GM mask from the MNI152 template resampled onto the 91x109x91, 2mm iso MNI_avg152T1+tlrc brain (see attached image):
3dresample -prefix TMP_RES.nii.gz -master MNI_avg152T1+tlrc. -input MNI152_2009_template_SSW.nii.gz'[4]' -rmode NN
This gave me a GM mask that is approximately the same size as yours:
3dROIstats -nomeanout -quiet -nzvoxels -mask TMP_RES.nii.gz TMP_RES.nii.gz
… shows that this mask is 178964 voxels, and yours was 160,742 (just a 10% diff). NB: this might not be the best mask for your template specifically- I did grab this one from a different MNI152 just for testing purposes, so you should verify that whatever you are using is a good GM map. The MNI_avg152T1+tlrc. template itself is relatively low-resolution and low-contrast, so distinct GM-WM boundaries are difficult to tell, anyways.
Then I ran 3 runs of your 3dClustSim command, using the same ACF parameters (note that I let the whole output tables be produced, rather than just one pvalue and one FWE value):
3dClustSim -mask TMP_RES.nii.gz -acf 0.5128 3.8451 11.3839 -nodec -prefix TMP_RES_CLUST
3dClustSim -mask TMP_RES.nii.gz -acf 0.5128 3.8451 11.3839 -nodec -prefix TMP_RES_CLUST2
3dClustSim -mask TMP_RES.nii.gz -acf 0.5128 3.8451 11.3839 -nodec -prefix TMP_RES_CLUST3
… and the pthr=0.001 with alpha=0.05 are quite similar in all cases: 46, 46, 47. The full output tables are below, just for reference.
So, I am not seeing a huge amount of variability. Would you mind posting an image of your GM mask, perhaps that might help show some relative difference? The GM one used here doesn’t have a lot of sharp structure, it should be noted. It is possible that with a mask that has a complicated structure and boundary, more iterations would be necessary for convergence. The default is 10000 iterations, and you could try increasing it: “-iter 20000” or “-iter 30000”, perhaps. Those would be my main suggestions (checking the GM mask for complicatedness, as a reason why convergence might be more complicated, and then increasing the number of iterations to see if that suggests better converge.)
–pt
# 3dClustSim -mask TMP_RES.nii.gz -acf 0.5128 3.8451 11.3839 -nodec -prefix TMP_RES_CLUST
# bi-sided thresholding
# Grid: 91x109x91 2.00x2.00x2.00 mm^3 (178964 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 757 910 1135 1325
0.020000 294 362 452 539
0.010000 165 202 256 296
0.005000 100 121 154 185
0.002000 56 68 88 103
0.001000 38 46 61 71
0.000500 26 32 42 50
0.000200 16 21 27 33
0.000100 11 15 20 24
# 3dClustSim -mask TMP_RES.nii.gz -acf 0.5128 3.8451 11.3839 -nodec -prefix TMP_RES_CLUST
# bi-sided thresholding
# Grid: 91x109x91 2.00x2.00x2.00 mm^3 (178964 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 757 910 1135 1325
0.020000 294 362 452 539
0.010000 165 202 256 296
0.005000 100 121 154 185
0.002000 56 68 88 103
0.001000 38 46 61 71
0.000500 26 32 42 50
0.000200 16 21 27 33
0.000100 11 15 20 24
# 3dClustSim -mask TMP_RES.nii.gz -acf 0.5128 3.8451 11.3839 -nodec -prefix TMP_RES_CLUST3
# bi-sided thresholding
# Grid: 91x109x91 2.00x2.00x2.00 mm^3 (178964 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 2 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 763 922 1140 1300
0.020000 291 355 449 513
0.010000 166 201 248 290
0.005000 100 123 156 182
0.002000 56 70 89 104
0.001000 38 47 61 71
0.000500 26 33 43 50
0.000200 16 21 28 34
0.000100 11 15 20 25
