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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February 17, 2016 09:55AM
Hi Peter,

Thanks for your response! I am not sure I understand your suggestion, though. I thought in 3dDeconvolve the "-stim_times" option allows you to set the times of the stimuli, not the times at which the volume are acquired. In my case, I want to change the times at which volumes are acquired. So in your example, if I understand correctly, "-nodata 290 2" tells us that there will be 290 volumes acquired in 2 seconds each, and they are assumed to be acquired back-to-back, meaning that the volumes are acquired at times 2n for n in {1,2,3,...} (in seconds), correct?

However, in my case, volumes would be acquired at times 7n+3 and 7n+5 for n in {1,2,3,...}. The stimuli occur at times 7n (in seconds). So to put the stimulus times into 3dDeconvolve I would do something like:

3dDeconvolve -nodata {something} -num_stimts 1 -stim_times '1D: 0 7 14 21 28 etc.' "GAM" etc etc.

But how do I tell 3dDeconvolve what the volume acquisition times are?

I have the feeling I'm missing something here, though! Thanks for your help
Floris
Subject Author Posted

3dDeconvolve with irregular volume acquisition times (sparse sampling)

florisvanvugt February 16, 2016 10:59AM

Re: 3dDeconvolve with irregular volume acquisition times (sparse sampling)

Peter Molfese February 16, 2016 12:31PM

Re: 3dDeconvolve with irregular volume acquisition times (sparse sampling)

florisvanvugt February 17, 2016 09:55AM

Re: 3dDeconvolve with irregular volume acquisition times (sparse sampling)

jkeidel February 17, 2016 10:42AM

Re: 3dDeconvolve with irregular volume acquisition times (sparse sampling)

rick reynolds February 17, 2016 11:16AM