[Homer-users] averaging and LPF

[thuppert]

Shaun-

 1)  That sounds right for the stim averaging.  Pretime of -5 (negative)
means that blocks start 5 seconds before the green lines and extend
"Post-time" afterward.  That sounds right for the block timing for your
experiment.  Blocks that extend beyond the data set (i.e. if you had a stim
10 seconds from the end of data collection and asked to include more then
10s of post-time), these get ignored in averaging.

2)  To my knowledge, I don't know if anyone has done cardiac gating.
Certainly, people do that for fMRI.  There are other options for removing
cardiac, for example:

Eigen-vector filtering.  (i.e. Zhang et al.  2005. "Eigenvector-based
spatial filtering for reduction of physiological interference in diffuse
optical imaging". Journal of        Biomedical Optics 10(1))

Linear regresssion with auxillaries (i.e. pulse Oximeter).

Adaptive filtering/autoregressive

Kalman filtering:  (i.e. Prince et al.  2003.  "Time-series estimation of
biological factors in optical diffusion tomography" Phys. Med. Biol. 48
(2003) 1491–1504)

 (The first two options are either in HomER currently or in the next release
that I keep promising).


___________________________________________
With respect to the next release of HomER:  We will have a poster on this at
this years Human Brain Mapping in Toronto.  The next version (with a bunch
of fixes and which no longer requires Matlab to run) will come out about
that time as well.


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







  -----Original Message-----
  From: homer-users-bounces at nmr.mgh.harvard.edu
[mailto:homer-users-bounces at nmr.mgh.harvard.edu]On Behalf Of Shaun Ali
  Sent: Monday, May 02, 2005 5:03 PM
  To: homer-users at nmr.mgh.harvard.edu
  Subject: [Homer-users] averaging and LPF


  Hi Ted,

  I've got a question regarding averaging and stim bars.  I've been placing
the stim bars at the beginning of each stimuli and then doing the averaging
as follows:

  _15s_|--5s---__15s__
  rest   |stim    rest

  15 second rest, 5 second stimulus time and then a 15s rest.  I set my
averaging bars at the stim start time and then my pretime at ~5s and post
time of 15s.  Is this the way I'm supposed to be doing it or am I averaging
about the wrong point?

  I'm also wondering if gating to the heartbeat has been done and if it's
feasible as opposed to just recording data and using the LPF?  Thanks!

  Shaun



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