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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December 02, 2019 07:57PM
Thanks Gang!
Sorry my second question wasn't clear but you basically interpreted it correctly. That's what I thought as well (it not being feasible at the event related level) but it's nice to have it confirmed.

Two final questions: I've used PROC_PY to generate my preprocessing scripts for the first analysis run-through. For the final analysis I am using 3dREMLfit to get my stats but I notice my REML command, as generated by PROC, uses the Xmat created by the previous 3dDeconvolve command as I've copied below.

3dREMLfit -matrix X.xmat.1D \
 -input "pb05.sub-S08V1A.r01.scale+tlrc.HEAD pb05.sub-S08V1A.r02.scale+tlrc.HEAD pb05.sub-S08V1A.r03.scale+tlrc.HEAD" \
 -tout -Rbuck stats.sub-S08V1A_REML -Rvar stats.sub-S08V1A_REMLvar \
 -Rerrts errts.sub-S08V1A_REML -verb $*

So I just wanted to check: 1) When I re-run new code using the
-stim_times_IM
option do I need to rerun 3dDeconvolve with the
-stim_times_IM
option, 3dREMLfit with the option, or both?

2) Even though I ultimately will be using this output for an ROI analysis, I would still use the same input files as above, correct? These are whole-brain files. I'm assuming that I rerun whole-brain deconvolution with the new options then extract the ROI betas from the new output just like a "regular" ROI analysis.

Thank you for all of your help!
Lauren
Subject Author Posted

Trial-by-Trial ROI response?

lhopkins November 24, 2019 02:40PM

Re: Trial-by-Trial ROI response?

gang November 26, 2019 09:06AM

Re: Trial-by-Trial ROI response?

lhopkins December 02, 2019 07:57PM

Re: Trial-by-Trial ROI response?

gang December 03, 2019 01:08PM