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 09, 2020 03:33PM
Hello great people of AFNI

I have come to find out that the stim file we have been using for rodent fMRI in 3dDeconvolve isn't an ideal shape and am needing to create a new stim file. I was told to deconvolve the "real" signal with a double gamma function and was wondering if I could do such a thing with afni. Tutorials I see all seem to create an HRF based on the onset of stimulation, but I believe with how different the HRF is with rodents, those methods won't work?

What I have is, after 3dDeconvolving with a simple boxcar onset/offset stim file, I drew an ROI in an area that show activation and calculated the percent change. This percent change is assumed to be the "real" HRF.. so I have a file called S1.1D. Is it possible to convert this into a cleaned shape that can be used as a stim file?

Furthermore, I wanted to see the effect of different stim files during 3dDeconvolve (eg, gamma and boxcar), so I thought I could set the operator as -num_stimts 2 and input the corresponding stim_files, but when I check each stim_file deconvolution in AFNI, it seems its running GLM again after the first stim file as there's less "significant" voxels than when I run 3dDeconvolve with the separate stim files individually. Is it possible to have statistics visible in one 3dDeconvolve output with various stim files?

I greatly appreciate any input and your time.
Subject Author Posted

Creating an HRF stim file for rodent GLM

kbandrew December 09, 2020 03:33PM

Re: Creating an HRF stim file for rodent GLM

gang December 10, 2020 08:22AM

Re: Creating an HRF stim file for rodent GLM

Daniel Glen December 10, 2020 11:57AM