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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Bob Cox
November 25, 2016 01:28PM
The "usual" way to use 3dDeconvolve is to provide a timing file that gives the start times for each stimulus (which are not required to be on the TR timing grid) -- this file is specified using the -stim_times option.

For the HRF, you choose a model function to define the shape of the response for the stimulus. There are many options for that.

The "best" way to run 3dDeconvolve (or its daughter program, 3dREMLfit) is to use the AFNI super script afni_proc.py -- whose help is here. This script takes as input the anatomical and EPI datasets, plus the timing files, and will run the entire analysis for you: aligning the anatomical and EPI datasets together and to MNI/Talairach space, running the GLM analysis, and writing out some simple diagnostic reports about the data.
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Subject Author Posted

doing GLM with 3dDeconvolve what kind of stim_files to input?

Liu Mengxing November 25, 2016 08:45AM

Re: doing GLM with 3dDeconvolve what kind of stim_files to input?

Bob Cox November 25, 2016 01:28PM

Re: doing GLM with 3dDeconvolve what kind of stim_files to input?

Liu Mengxing November 25, 2016 06:56PM

Re: doing GLM with 3dDeconvolve what kind of stim_files to input?

Bob Cox November 26, 2016 09:51AM

Re: doing GLM with 3dDeconvolve what kind of stim_files to input?

Liu Mengxing November 27, 2016 04:21AM