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

Wed Jul 3 14:02:59 EDT 2013

Thanks
So all is OK
best regardsAlexis

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

[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

To: 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]
On Behalf Of alexis machado

Sent: 02 July 2013 18:36

To: 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

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