[Homer-users] hmrIntensity2OD: possible at later processing stage?

[Janny Stapel]

Dear Theresa,

 

Thanks for your answer. I tried running first the artifact rejection and
then the conversion in the ProcessStreamGUI, but it doesn't run the
conversion then, so that's where I'm a bit stuck. Indeed, checking the
settings in the Processing Stream is always a good idea, I find that quite
helpful.

 

Best,

Janny

 

From: homer-users-bounces at nmr.mgh.harvard.edu
[mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Moulton,
Theresa (NIH/CC/RMD) [F]
Sent: maandag 7 april 2014 14:51
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] hmrIntensity2OD: possible at later processing
stage?

 

Janny, 

 

>From my understanding, you can use the ProcessStreamGUI (in the Tools
menu) to very easily alter the functions you are calling, and the order in
which they are called.  Once open, click Load, then you can select either
your current processing stream or a saved one. The processing stream can
then be altered, added to or taken away from. This was covered in one of
the trainings, although I can't remember if it is one that was archived. I
would also look into the filtering/artifact rejection techniques you are
using to make sure there are no assumptions about which signal they are
being done on (intensity vs OD), or what the input to the function is
required to be. 

 

Best of luck,

Theresa

 

 

 

Theresa Sukal Moulton, DPT, PhD

Post-doctoral Fellow

Functional & Applied Biomechanics Section

Rehabilitation Medicine Department

National Institutes of Health Clinical Center

10 Center Drive, Room 1-1425

 

From: Janny Stapel [mailto:j.c.stapel at donders.ru.nl] 
Sent: Monday, April 07, 2014 6:39 AM
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] hmrIntensity2OD: possible at later processing
stage?

 

Dear all,

 

I have the impression that the conversion from raw data to optical density
(hmrIntensity2OD) cannot be done after artifact rejection, but only
before. Did I get that correctly? And is there a way to change the order?
Point is that the conversion takes the average of the whole data file, and
if the data contains partly a lot of noise (we had our nirs system record
data also during breaks and so), this noise affects the conversion
process. Therefore I'd rather first apply artifact rejection and then
convert the data to optical density. Not sure how to though?

 

Best,

Janny

 

 

Janny C. Stapel, MSc

Donders Insitute for Brain, Cognition and Behaviour

Radboud University Nijmegen

P.O. Box 9104, 6500 HE Nijmegen, the Netherlands

 

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