[Homer-users] RE: about baseline

[thuppert]

The "baseline" data used by the systemic filtering in Homer should be a
seperate (no task) data file.  This gets loaded and the check box (at the
bottom left) should be checked it indicate that this is a baseline data
file.  This is the way Homer is currently written.

The reference to the systemic filtering used is:

Zhang Y, Brooks DH, Franceschini MA and Boas DA. Eigenvector-based spatial
filtering for reduction of physiological interference in diffuse optical
imaging. Journal Biomed Optics 10(1): 011014. 2005.

To answer your question, this algorithm cited does not nessacarily require
the baseline to be a seperate file.  It would be possible to create a
systemic filter from the baseline epochs contained within a "run" file (i.e.
between 2 trials).  However, this is not how Homer is currently written.

Note also, that the pure rest state file does not need to be the same length
of time as the activation runs.  A minute of data is probably fine
(respiration is ~1/6s, blood pressure/meyer waves ~1/10-1/20s and the file
just needs to be long enough to catch a few periods)  In fact, many of the
really low freq (i.e. <1/30hz) can be high-pass filtered away  (depending on
the stimulus presentation timing).   Although, the baseline file should be
high/low pass filtered the same way as the data to which the systemic filter
is applied and so the only requirement on length is that if you use a
high-pass filter, the baseline file needs to be 3 times the filter order
(i.e. if 1/30Hz HP filter, then a 90sec minimum file is required)  [Homer
issues a warning if this is not true].

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: Zhou Yuan [mailto:zhouyuan at nlpr.ia.ac.cn]
  Sent: Monday, October 17, 2005 9:31 PM
  To: Homer-users at nmr.mgh.harvard.edu
  Cc: thuppert at nmr.mgh.harvard.edu
  Subject: about baseline


  Hi,
      I noticed taht  Homer permits to remove  systemic physiology by a
systemic filtering, which uses baseline data. However, what do you mean when
you refer to baseline data?  As we know, there are pretask rest, posttask
rest, and rest between two trials during an typical experiment. These "rest"
are also referred to baseline. Of cource, a purely resting state is a
baseline. Thus, I want to know it's necessary to collect  purely resting
data or select the rest data during a task if we want to use the systemic
filtering.
      Thanks!



  Yuan Zhou, PhD Student
  Medical Imaging and Computing Group
  National Laboratory of Pattern Recognition
  Institute of Automation
  Chinese Academy of Sciences
  Tel: +86-10-6265 9278 (O)
  Fax: +86-10-6255 1993
  Add: P.O. Box 2728, Beijing, 100080, P.R.China
  Email: zhouyuan at nlpr.ia.ac.cn

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20051018/49ef7660/attachment.html