AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

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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JW
February 13, 2018 12:44PM
Good afternoon AFNI experts,

I am trying to make activation map using 3dmerge with pthrshold and clustsize from 3dClustsim based on 3dLME map that I already have got. The 3dclustsim result looks like the below.

# 3dClustSim -mask /Volumes/BRAINSMITH_DS/Titus/AES2016_FNT/Scripts/3dLME_Ex_Rest/3dLME_021218+tlrc -acf 0.687615103 4.503241034 16.34768621 -nodec -prefix 3dClustSim
# 2-sided thresholding
# Grid: 64x76x64 3.00x3.00x3.00 mm^3 (70663 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .10000 .05000 .02000 .01000
# ------ | ------ ------ ------ ------
0.050000 260 330 430 521
0.020000 101 125 160 190
0.010000 57 71 91 107
0.005000 36 43 56 68
0.002000 21 26 33 41
0.001000 15 18 23 27
0.000500 11 13 17 20
0.000200 7 9 12 14
0.000100 5 6 9 10

I would like to creat the map with pthr 0.01 and alpha 0.05 using 3dmerge, but failed to figure out from the AFNI -help. Could you please let me know to create the map using 3dmerge?

Best,
Jun
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3dmerge creating mask

JW February 13, 2018 12:44PM