[Homer-users] units for concentration changes in Homer

[thuppert]

Under the default settings for HomER, the pathlength  is not included in the
calculation of concentration changes.  This means that the default units are
actually [Molar*centimeters].  Only if the option to use the
partial-pathlength (and/or) partial volume factors are checked is the
pathlength included (calculated from the probe geometry).  It was done this
way since concentration is (quantitatively) inaccuraute without including
the DPF anyway.  This means that (unless these options were checked), you
need to divide the concentration changes by the pathlength.

Note that, not including these factors does not affect the oxygen saturation
(i.e. Hbo/total etc) since pathlength cancels (with the exception of
cross-talk if the factors differ for the two wavelengths)

To reference the Boas et al [2001 NeuroImage 13:76-90] paper, HomER applies
equation 4) but both "L" and "B" are being ignored unless the pathlength
info is provided.
.

For more details on DPF (etc) see:

Strangman, G, Franceschini, MA and Boas, DA. "Factors affecting the accuracy
of near-infrared spectroscopy concentration calculations for focal changes
in oxygenation parameters." NeuroImage 18: 865-879. 2003.


The "fakedata.mat" supplied is not quantitatively accurate (at least I
didn't intend it to be), I would say that a good NIRS change is more like
1-5% (dOD= 0.01-0.05) (at most!) and in concentration that's about ~8uM for
HbO2 changes (with reasonable partial volume corrections) [Boas et al.
2001].




%%%%%%%%%%%%
For the future version of HomER (to be released soon- hopefully), I'll try
to make these things more clear in the outputs.
I'm currently writing up the user's manual (technical report) to better
explain some of this.

Comming soon... (~ a month or so)




Ted Huppert, MS

PhD student-Harvard Univ.
Dept of Biophysics
Photo 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 Andrei
Medvedev
Sent: Wednesday, January 05, 2005 6:09 PM
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] units for concentration changes in Homer


This is a question to Ted Huppert.

Hi Ted,

I was wondering about the units for concentration changes calculated within
the Homer.

If my dOD signal 'response' is 0.05-0.1 (a typical value for a good NIR
response), the Homer calculates dConc as ~5E-5. For example, for the
FakeData.mat file (supplied with the Homer), dOD is ~0.1 and dConc is ~4E-5.
If this is in Moles, it looks like too high value for dConc (that is, ~40-50
mkM). Published values of dConc during finger tapping and other tasks are ~1
mkM. The same 1 mkM you can get as a dConc estimate for dOD ~5-10% from the
Beer-Lambert law (I used the formula from Boas et al, NeuroImage 2001 and
the approximate values for the extinction coefficients plotted there).

Could you please explain in what units the concentration change is
calculated in Homer?

Thank you,

Andrei.

Dr. Andrei Medvedev, Ph.D.
Assistant Professor,
Center for Functional and Molecular Imaging
Georgetown University Medical Center
3900 Reservoir Rd, NW
Preclinical Science Building LM-14
Washington, DC 20057-1488


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