Thanks Gang!

This leaves a, for now, final set of questions.

1) The "currently considered acceptable threshold" I get form the Bob's power-point presentation and from these two papers:
fMRI clustering and false-positive rates.
FMRI Clustering in AFNI: False-Positive Rates Redux.
From here I gather that one should use no p-value greater than 0.002. Is there any new info/paper out there? These are from 2017.

2) We would typically use this table:

# 3dClustSim -acf .62900675 2.70203459 13.01153783 -mask /data/dsk2/iaps/group_mask/group_mask_epi_anat_gm+tlrc.
# 2-sided thresholding
# Grid: 64x76x64 3.00x3.00x3.00 mm^3 (35260 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1  | alpha = Prob(Cluster >= given size)
#  pthr  | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
 0.050000    95.2  115.8  147.0  177.0
 0.020000    39.6   48.2   62.4   76.7
 0.010000    23.5   28.5   36.1   43.1
 0.005000    15.0   18.2   22.9   26.5
 0.002000     9.1   11.0   13.8   16.3
 0.001000     6.6    7.9    9.9   11.5
 0.000500     4.9    5.9    7.4    8.5
 0.000200     3.5    4.2    5.2    6.1
 0.000100     2.7    3.3    4.1    4.8

This table do only show cluster alphas, apart from 0.05, at 0.1, 0.02 and 0.01 levels. How do I get 3dClustSim (current command can be seen at the top of the table) to produce e.g. 0.06 or 0.07 as per your suggestion?

3) "Then you can report those clusters of interest with an alpha value above but still reasonably close to 0.05. Let go of the obsession with the p-value, and don't treat the watermark of 0.05 as something carved in stone."

Yes, this sounds good and I agree! But the journals are often keen on knowing if your statistical results are multiple comparison corrected or not (annoyingly binary statement, I know). Writing a long discussion regarding thresholding in a paper can get kind of complicated and I can't really cite the AFNI message board...

Don't you think that a reviewer that is unfamiliar with AFNI and with the fact that these methods are relativley conservative compared to other softwares would be kind of sceptical to a cluster alpha over 0.05. More so than for a per voxel p-value at 0.05 that results in an alpha of 0.05.

Thanks so much for taking your time with this. We are approaching submit on one of our AFNI projects so this issue is taking its toll on us.
Thanks!



Edited 1 time(s). Last edit at 02/14/2019 04:13AM by Robin.