[Homer-users] Baseline for concentration plots

[Huppert, Ted]

Mark-

The calculation of optical density (from which concentration is derived) is

dOD = - log( I / mean( I) );

Where "I" is the intensity data (e.g. The raw or filtered data your system measures between a src-det pair).  Thus, dOD is mean zero over the whole file.  Concentration is also mean zero.  This means the average of all the data (baseline, task, any artifacts, etc) so when there is a lot of drift at the start of the file it may not start at zero as appears at the start of your data, which I imagine may be because the first few points are a really large artifact and then the low-pass filter smeared it over a larger time window.  But, the average over the whole experiment is zero.


-Ted


----------------
Theodore Huppert, PhD
Assistant Professor
Departments of Radiology and Bioengineering
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

From: Mark William Boyer <mwboyer at mit.edu<mailto:mwboyer at mit.edu>>
Reply-To: "homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>" <homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>>
Date: Thursday, October 3, 2013 2:45 PM
To: "homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>" <homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>>
Cc: Erin Treacy Solovey <erinsol at mit.edu<mailto:erinsol at mit.edu>>, "afergan at gmail.com<mailto:afergan at gmail.com>" <afergan at gmail.com<mailto:afergan at gmail.com>>
Subject: [Homer-users] Baseline for concentration plots

Hello,

I am fairly new to HOMER and was hoping to better understand how the y-scale and 'zero' is set for the concentration plots.  Specifically, I understand the meaning of the y-axis scales for the raw signal and OD plots, but I wanted to know exactly what the concentration scale indicates and how the zero value is set.

I've attached a diagram that hopefully provides some context to the question.  I could not find a definite answer in the documentation, so any insights into this would be much appreciated.

Thank you,

Mark Boyer
Humans and Automation Lab
Aero-Astro Dept, MIT