[Homer-users] Oxy-Hb and DeOxy-Hb

[thuppert]

Those files are huge (480 src-det channels?).  Anyway...the structure of the
files is:

<time pts><channel number><[HbO HbR HbT]>

So the time trace for (i.e.) channel #1 for HbO2 is Avg(:,1,1) and for HbT
is Avg(:,1,3);
The channel # is referenced by the MeasurementList (i.e. the original ml
variable loaded with the file).  Its also in DOT.dataAvg.MeasList.

At the HomER interface it should let you look at the average traces for any
of the wavelengths (selected by the wavelength=? pull-down menu) or any
(all) of the Hb concentrations (by selecting to display conc and then
checking HbO,HbR, and/or HbT from the options on the pull-down menu at the
top).  If you right-click on the display window, it should let you save what
is being displayed as well (I don't let conc be saved to ASCII (only dOD) in
that version cause its 3-Dimensional, but all can be saved to *.mat files).
There is always a time-vector saved in those files as well.


*********************
Homer calculates the average response functions seperately for dOD and
dConc.  It really doesn't matter if I calculate dConc from dOD and then
average or average and then calculate conc.  They are both linear
operations, but HomER currently does the former.  Once the PCA analysis is
added dConc, then there is a potential for these two traces to differ (in
the next release).


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 Margaret
Duff
Sent: Tuesday, April 05, 2005 1:00 PM
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] Oxy-Hb and DeOxy-Hb


Hi,  I have an additional question related to this.  I have been looking
at the files Homer saves after averaging and the concentration averages
seem to have 3 parts.  In the Homer interface, it seems to only allow
you to look at wavelength 1, but my feeling is that Homer is saving
total, Oxy and DeOxy concentrations as separate files that you can read
in Matlab.  I am looking at the DOT.dataAvg.HRF.AvgC file, which has the
structure 650x480x3, with my time window for averaging being 65 seconds
long.  Can anyone confirm this is what the files are, and also which of
the 3 files stand for which concentrations?  Thanks a lot, Margaret

On Mon, 28 Mar 2005, Margaret Duff wrote:

> Hello,  Does Homer perform the separation of the deoxygenated and
> oxygenated hemoglobin from the averaged waveforms for each of the
> wavelengths of light?  Or is this conversion something that would have to
> be done outside of Homer?  Thanks, Margaret
>
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> Homer-users at nmr.mgh.harvard.edu
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