[Homer-users] FW: MBLL Missing ln(10)
David Boas
dboas at nmr.mgh.harvard.edu
Thu Jul 4 09:52:29 EDT 2013
Alexis
I really appreciate you checking this and getting to the bottom of it. I will make the changes to GetExtinction.m to clear up this confusion.
Thx
David
Sent from my iPhone
On Jul 3, 2013, at 9:02 PM, alexis machado <alexis.machado at hotmail.fr> wrote:
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> Thanks
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> So all is OK
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> best regards
> Alexis
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> Hi Alexis,
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> 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:
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> vLambdaHbOHb(:,2) = vLambdaHbOHb(:,2) * 2.303;
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> vLambdaHbOHb(:,3) = vLambdaHbOHb(:,3) * 2.303;
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> So the function does, as I said, output absorption coefficients, which is why all the latter functions use log base e.
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> Regards,
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> Rob
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> 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)
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> Hi Robert thank you for you response
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> This is indeed very confusing
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> If i look in the header of GetExtinction.m it is sais clearly that
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> 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
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> Therefore i think that GetExtinction returns the specific extinction coefficients and not the specific absorption coefficient.
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> Moreover it seems confirmed in [1] See Important Note
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> Now, If i look in the HOmer's article [2] equation 2
> ln (I/Io)=Dmua.L=(eps1.D[HbO]+eps2.D[HbR]) .L
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> 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.
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> [1] http://www.medphys.ucl.ac.uk/research/borg/research/NIR_topics/spectra/spectra.htm
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> [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,
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> best regards
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> Alexis
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> 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
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> Hi Alexis,
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> 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.
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> Rob
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> Rob J Cooper PhD.
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> Research Associate
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> Biomedical Optics Research Laboratory
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> Malet Place Engineering Building, Rm 3.18
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> University College London
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> Gower Street
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> London WC1E 6BT
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> T: +44 (0)20 7679 0275
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> 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.
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> Let me explain much:
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> 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
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> equation: 1b
> DOD=-ln(I/Io)=eps_1*D[HbO] +eps_2*D[HbR] *L % it is a natural logarithm definition
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> 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
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> 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]
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> 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])
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> 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
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> DOD=-log10(I/Io) = eps_1*D[HbO] +eps_2*D[HbR] *L
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> Please correct me if i am wrong !!
> best regards
> Alexis
>
>
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