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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Nicholas Balderston
March 07, 2018 04:07PM
Hi everyone,

I think I have a potential solution to this, which is to use 3dLME, which can export the residuals, for the group level analysis. Afterward, I use 3dFWHMx to estimate the smoothness of the data, and 3dclustsim to run the monte carlo simulations. Here are example commands that I am using for my data. I understand that this is potentially a somewhat new approach, and that there are differences between 3dLME and 3dMVM, so feedback is appreciated.

3dLME 
3dLME \
-prefix ${resdir}/3dLME.${cond}.${load}.${dur}.${beam}.healthy_subs.${subnum}_subs \
-jobs ${jobs} \
-model "cond*load" \
-ranEff '~1' \
-SS_type 3 \
-resid ${resdir}/3dLME.${cond}.${load}.${dur}.${beam}.resid.healthy_subs.${subnum}_subs \
-dataTable \
#data table goes here

3dFWHMx 
3dFWHMx \
-detrend \
-input 3dLME.thr.r.${dur}.resid.healthy_subs.${subnum}_subs+orig \
| tee 3dLME.${dur}.blur_estimate.acf.${subnum}_subs.1d

3dClustSim 
3dClustSim \
-mask 3dLME.thr.r.${dur}.resid.healthy_subs.${subnum}_subs+orig \
-dxyz 2 2 2 \
-acf $acf \
-MEGA \
-both \
-prefix 3dLME.${dur}.3dclustsim.acf.${subnum}_subs

best,
-nick
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Subject Author Posted

3dclustsim with MEG data

Nicholas Balderston May 19, 2016 01:32PM

Re: 3dclustsim with MEG data

Nicholas Balderston March 07, 2018 04:07PM

Re: 3dclustsim with MEG data

gang March 08, 2018 01:21PM