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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Daniel Glen
June 23, 2009 05:04PM
The argmax type options give the time index which is related to time, of course, by a factor of a TR usually. So let's say a cue happens at a particular time index and we want to look at only a certain length of time after that cue, then we can write a 3dTstat command like this to get the time index relative to that cue :

set cue = 12
set duration = 10

@ endcue = $cue + $duration

3dTstat -argmax -prefix timetopeak_cue12 dset+orig"[${cue}..${endcue}]"

The output voxels have intensities corresponding to the relative index following the cue that has the maximum intensity. So for example if a peak occurred two sub-bricks after the cue (the third sub-brick of the piece of the dataset we are looking at), then the output will have an intensity of 2 at that voxel. If you want that in time, you can use 3dcalc to multiply the dataset by the TR value. You can use this method to look for peaks in EPI datasets or tent / spline deconvolution results, but be careful there is often a lot of noise in this data making this approach less reliable.
Subject Author Posted

time to peak activation

Brenda Benson June 22, 2009 02:23PM

Re: time to peak activation

Daniel Glen June 22, 2009 02:41PM

Re: time to peak activation

Brenda Benson June 23, 2009 04:35PM

Re: time to peak activation

Daniel Glen June 23, 2009 05:04PM