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

[Perdue, Katherine]

Hi Janny,

I think that is true, that the artifact rejection can only be done after the conversion to optical density units. One thing you could do is break up your .nirs file into more than one file, and then you would have separate runs without the bad periods  that can be combined in Homer. Depending on your hardware you might be able to just export your data into several files, or you could break up your long file into a few run files using matlab.

best,
Katherine



-------------
Katherine Perdue, PhD
Research Fellow in Pediatrics
Labs of Cognitive Neuroscience
Division of Developmental Medicine
Boston Children's Hospital
Office Phone: 857-218-5214

On Apr 7, 2014, at 10:11 AM, Janny Stapel <j.c.stapel at donders.ru.nl<mailto:j.c.stapel at donders.ru.nl>> wrote:

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> [mailto:homer-users-bounces at nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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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