[Homer-users] Question about averaging in HOMer

[thuppert]

This is the answer to a question about avergaing with the HOMeR program
(below).  People are reminded that if they have questions regarding HOMeR to
send them to homer-users at nmr.mgh.harvard.edu

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Question:

I have a question about calculating averages in HOMer. Here's the scenario:
We have a 330s recording, with
pre-stim = 5s and post stim = 300s. We want to calculate the average
for all 10s intervals during the session. I know  how to change the
user stim which looks like this: 0:10:300.  Does this give us the
average we want?  The graph of the average showed the same timeline as
the total which was 300s. Can you help?


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Answer:

The user stim field is used to specify stimulus timing manually.  For
example, (0:10:300) would give you a stimuli starting at 0s and then every
10sec untill 300s.  I.e.  {0,10,20,30...290,300}. The green lines should
show you where the stimuli were placed. If this is what you want (i.e 30
stimulus points as per above), then this is correct.

However if this is the case, I wouldn't recommend letting post-time be 300s.
The post-time is the time AFTER each stimulus point for which the average is
calculated.  This should (typically) be shorter then the inter-stimulus
interval (in your case 10s- I think).  When block averging, you don't want
the stimulus epoch blocks blocks to overlap in time.  In the case of your
data, let post-time be 10s.  If you want to see a longer response, then you
need to either allow more time between stimulus presentation or change to an
event-related stimulus design (i.e. see Dale, A. M. (1999). “Optimal
experimental design for event-related fMRI.” Human Brain Mapping 8:
109-114.).  Also, if you are using a blocked design, then you want to make
sure that the hemodynamic response to your stimulus is expected to recover
before the next stimulus.





Hope this helps-

Ted Huppert, M.Sc.

PhD student-Harvard Univ.
Dept of Biophysics
Photon Migration Imaging lab
Mass General Hospital/CNY

Tele: (617)726-1223
Cell: (617) 869-1205

thuppert at nmr.mgh.harvard.edu