[Homer-users] stim_exclude & motion_artifacts

[Janny Stapel]

Hi all,

 

I am pretty much a novice user of Homer, but I've been struggling for some
time now with a couple of questions, and I thought it's time to ask the
other users. I am running the developer's version of Homer2 in Matlab.

 

1)      For the function called 'Stim_exclude' (enStimRejection), you can
define t1 and t2. Intuitively, I thought that t1 signals the start of the
segment that I would like to throw out, and t2 the end, around the time
point I select during manual artifact rejection. However, if I select say
time points 4000 to 4010, and I set t1=-300 and t2=0, then it seems more
or less to throw out data from 4000 to 4310. I had expected it to throw
out 3700 to 4110. So my question is: in which direction (past or future)
do t1 and t2 work, and related to that: what is considered to be time
point 0? Does stim_exclude reject periods of time I select, or does it
reject periods with respect to triggers in my data?

2)      I would like to do the conversion from raw data to optical density
in one of the later steps, for instance after artifact rejection based on
the motion artifact detection algorithm. However, it seems as if I should
first run the conversion into OD, and only then I can apply motion
detection. Is that indeed the case, or am I overlooking an option?

3)      About the function Stim_exlude again: if I combine that with
motion detection on a channel level, does it indeed then only reject
periods within certain channels? Or do I then throw away time segments in
all channels?

4)      And then just to check: the motion detection algorithm: Can I see
it as a sliding window, and is the standard deviation calculated within
that window and then for each time point within the window it runs a check
whether signal is above the threshold set of the stdev? Or is the standard
deviation calculated over all the data in that channel, and are then the
time points compared to that stdev? But if so, what does t_win stand for?

 

Many thanks in advance!

Best,

Janny

 

Janny C. Stapel, MSc

Donders Insitute for Brain, Cognition and Behaviour

Radboud University Nijmegen

P.O. Box 9104, 6500 HE Nijmegen, the Netherlands

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20140206/445884fe/attachment.html