[Homer-users] SDgui - SD file creation

[Nagels-Coune, Laurien (Stud. FPN)]

Dear dr. Huppert,

thank you for the explanation. I am now reassured that a few mm will not matter. 

Kind regards,
Laurien Nagels-Coune
________________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu [homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Huppert, Ted [huppertt at upmc.edu]
Sent: 19 February 2015 18:00
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] SDgui - SD file creation

The SD variable in HOMER-2 is mostly used for display purposes so the
values just need to be close, but don¹t worry about getting it right to
high precision (nearest 5mm is probably fine).  HOMER2 does uses this for
the MBLL.  However, keep in mind that its also using a generic
differential path length factor (usually ~6) which in reality is just an
approximation and to really find it you would need to do modeling of light
diffusion etc (and even then is still an approximation).  Thus, being off
by a few mm in the SD layout is probably less error then this DPF
approximation anyway.  If you really want to say something about absolute
hemoglobin units, you probably need to do some modeling of the light
diffusion, need anatomical (MRI) data, etc.

With that said, I wouldn't put too much trust in the absolute values you
get for oxy- and deoxy-Hb.  Sometimes you see hemoglobin expressed as
uM*cm which is probably a more truthful unit although much harder to
interpret physiologically.
There are a lot of assumptions such as head anatomy that go into these
numbers.  You just have to be careful how you interpret the numbers.  I
feel that the T-statistics on responses (which is a normalized value so
DPF cancels at least if we can ignore cross-talk between wavelengths) is
probably a better number to be looking at to compare across regions or
subjects.



----------------
Theodore Huppert, PhD
Associate Professor
Departments of Radiology and Bioengineering
Center for Neural Basis of Cognition
University of Pittsburgh
Email: huppertt at upmc.edu
Phone: (412) 647-8459



"Insanity: doing the same thing over and over and expecting different
results"-  Einstein




On 2/18/15, 3:53 PM, "Nagels-Coune, Laurien (Stud. FPN)"
<l.nagels-coune at student.maastrichtuniversity.nl> wrote:

>Dear all,
>
>I collected some pilot data with a NIRx machine and want to use the
>NIRx2nirs matlab script by Rob Cooper to analyze my data in Homer2. I
>created an SD file in Homer2 but have a few questions concerning this
>file:
>
>I understand that I have to maintain the real-world NIRx source and
>detector numbers in the SD file but what about the optode distances? The
>X and Y axes are in cm but placing optodes in this grid feel so
>arbitrary. I found this piece of text in the Homer2 manual: " Dimensions
>are relative coordinates (i.e. to some aribitrary defined zero point).
>Although the probe dimensions can be three dimensional, display and image
>reconstructions are currently only allowed in two dimensional (i.e.
>z=constant). "
>
>I placed the optodes on the head according to the 10-20 system but I am
>not sure how to relate this to the 100 by 100 cm grid. I guess I am
>afraid that the probe geometry will influence the creation of the .nirs
>file (optode distance is incorporated in the Beer-Lambert law and will
>therefore influence my oxy and deoxy levels). Or, is the SD file only
>employed for visualization purposes?
>
>Kind regards,
>Laurien


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