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

History of AFNI updates  

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May 01, 2019 09:06AM
Hello AFNI experts,

I am using Clustsim for the first time and I would like to make sure I am using it correctly. I have also read several posts on the message board and the AFNI –help files but I have a few questions.

My current steps:
(1) Run the 3dFWHMx code on each participant
3dFWHMx -input errts.Proc_9790_April2019+tlrc.HEAD -mask mask_group+tlrc.HEAD -acf

(2)Take the average of the acf values for the participants included in the group analysis

(3) Run the 3dClustsim code
3dClustSim –acf (avg values) –mask mask+tlrc.HEAD –athr 0.05 –pthr 0.001

Follow-up questions:
(1) When I ran the 3dFWHMx code on a few of my participants, I was receiving reports of “out to radius” values ~15mm. In the examples I have seen online these values are usually ~30. Are the values below reasonable?

ID ACF values Radius
6292 0.83439 2.93607 5.85216 7.01209 15.43mm
8225 0.741657 2.8296 10.8613 7.39096 15.99mm
9164 0.800097 2.79238 7.58264 6.89804 15.28mm
9409 0.737612 2.84261 10.3543 7.39743 15.98mm
9444 0.707152 3.22763 9.68089 8.30243 17.97mm
9784 0.75646 3.04957 6.37843 7.38509 15.86mm
9790 0.881869 2.82603 6.81025 6.79469 14.91mm

(2) Do I create the –mask input for the 3dClustsim code? Is this based on all my subjects or can I use one of my participant’s masks from the afni_proc.py?

Thank you very much for your help.
Tamara
Subject Author Posted

3dClustSim

tamtam May 01, 2019 09:06AM

Re: 3dClustSim

rick reynolds May 01, 2019 01:15PM

Re: 3dClustSim

tamtam May 01, 2019 03:50PM

Re: 3dClustSim

rick reynolds May 01, 2019 10:35PM