[Homer-users] FW: MBLL Missing ln(10)

[Cooper, Robert]

Hi Alexis,

You are correct that the comments in the GetExtinction.m script state clearly the original spectra data are extinction coefficient, but Homer already does the correction in GetExtinction line 534:

        vLambdaHbOHb(:,2) = vLambdaHbOHb(:,2) * 2.303;
        vLambdaHbOHb(:,3) = vLambdaHbOHb(:,3) * 2.303;

So the function does, as I said, output absorption coefficients, which is why all the latter functions use log base e.

Regards,

Rob


From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of alexis machado
Sent: 03 July 2013 16:57
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] FW: MBLL Missing ln(10)



Hi Robert thank you for you response

This is indeed very confusing


If i look in the header of GetExtinction.m it is sais clearly that
µa = (2.303) e  x /(66,500)   or in other terms µa = ln(10).e.[X]  where [X] denotes molar concentration and e is the specific extinction coeff


Therefore i think that  GetExtinction returns the specific extinction coefficients and not the specific absorption coefficient.

Moreover it seems confirmed in [1] See Important Note



Now, If i look in the HOmer's article [2]  equation 2
ln (I/Io)=Dmua.L=(eps1.D[HbO]+eps2.D[HbR]) .L

Because It seems that HOMer use the  specific molar extinction coefficient provided in [1] in the function GetExtinction.m and calculated using a base 10 logarithm. The Biomedical optic research laboratory website states that the ln(10) scale factor should be considered for the calculation of Dmua
So , I think there is a  MISSING ln(10) scale factor in equation 2 of this article and in any articles which use the extinction coefficients provided by reference [2] instead of specific absorption coefficients.



[1] http://www.medphys.ucl.ac.uk/research/borg/research/NIR_topics/spectra/spectra.htm<http://www.medphys.ucl.ac.uk/research/borg/research/NIR_topics/spectra/spectra.htm%20:>


[2] P: HomER: a review of time-series analysis methods for near-infrared spectroscopy of the brain; Theodore J. Huppert, Solomon G. Diamond Maria A. Franceschini and David A. Boas,

best regards
Alexis







________________________________
From: robert.cooper at ucl.ac.uk<mailto:robert.cooper at ucl.ac.uk>
To: alexis.machado at hotmail.fr<mailto:alexis.machado at hotmail.fr>
Subject: RE: [Homer-users] MBLL Missing ln(10)
Date: Wed, 3 Jul 2013 14:39:13 +0000
Hi Alexis,

This is  a little confusing.  I think the explanation is the difference between specific extinction coefficient (which is defined base 10, such that I = Io*10^(-Extinction*concentration)) and specific absorption coefficient (which is defined base e, such that I = Io*exp(absorption*concentration).  I think that the homer function GetExtinctions, counter-intuitively, outputs specific absorption coefficients.  The functions hmrIntensity2OD and hmrOD2Conc are then all base e.  Homer is therefore internally consistent, although the function GetExtinctions should perhaps be renamed.

Rob



Rob J Cooper PhD.
Research Associate
Biomedical Optics Research Laboratory
Malet Place Engineering Building, Rm 3.18
University College London
Gower Street
London WC1E 6BT
T: +44 (0)20 7679 0275


From: homer-users-bounces at nmr.mgh.harvard.edu<mailto:homer-users-bounces at nmr.mgh.harvard.edu> [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of alexis machado
Sent: 02 July 2013 18:36
To: homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>
Subject: [Homer-users] MBLL Missing ln(10)

Hi
I am a PhD student in NIRS.
I have a doubt on the definition of the Modified Beer Lambert Law as used in the sofware HOMER version1. Indeed HOmer uses a natural logarithm to define the absorbance  ( also known as optical density) whereas the extinction coefficients values provided were calculated with a log base 10 definition of  the absorbance.

Let me explain much:

Let see the definition : REF  HomER: a review of time-series analysis methods for near-infrared  spectroscopy of the brain  Theodore J. Huppert  Solomon G. Diamond Maria A. Franceschini and David A. Boas you define the delta optical density or delta absorbance as

equation: 1b
DOD=-ln(I/Io)=eps_1*D[HbO] +eps_2*D[HbR] *L   % it is a natural logarithm definition

where D stands for variation from a baseline period, and OD the absorbance
where I is the detected fluence and Io the detected baseline fluence
where eps_1 is the molar extinction coeff of HbO and eps_2 the molar extinction coeff of HbR and L is the mean total optical pathlength

Because the beer lamber law states that I/Io=exp(-mua*L)  equation 1.b implies that  Dmua the absorption coeff  variation= eps_1*D[HbO] +eps_2*D[HbR]


However according to the  header explanation of the GetExtinctions.m function located in /HOMER/GeneralSubs/   the provided eps where measured using a different definition of the absorbance which is DOD=-log10(I/Io) . Indeed  they say clearly that  mua =ln(10)*( eps_1*[HbO] +eps_2*[HbR])


Therefore, I think the equation 1.b should be corrected as in REF  A review on continuous wave functional near-infrared spectroscopy and imaging instrumentation and methodology Scholkmann F, Kleiser S, Metz AJ, Zimmermann R, Mata Pavia J, Wolf U, Wolf M.
equation 1

DOD=-log10(I/Io) = eps_1*D[HbO] +eps_2*D[HbR] *L

Please correct me if i am wrong !!
best regards
Alexis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20130703/5e59cb0d/attachment.html