[Homer-users] Preprocessing starting with Oxygenation

[Yucel, Meryem A.]

Hi Alex, Adam,

I am also not sure if it actually makes a difference mathematically. On the other hand, most homer functions use optical density such as motion correction algorithms (or pruning uses raw signal). So practically it is to your advantage to start with the raw signal if you prefer analyzing your data with HOMER. On a related note, Sahar Jahani is working on a conversion code for Shimadzu data (creating .nirs file, going back from oxy-deoxy to raw signal). We’ll put the instructions to homer website soon.

Meryem


From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Adam Noah
Sent: Tuesday, March 28, 2017 9:14 AM
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] Preprocessing starting with Oxygenation

You should talk to Shimadzu about the export function. This is quite standard and the ability to export to OD is actually right in the GUI, raw data export is in a matlab script that Shimadzu provides, but in looking at the code it is straightforward.  On the other hand, as you mention the conversion to oxyHB is just a linear transform, and thus I also question the need to work with raw data.  We currently use a LABNIRS as well and employ the preprocessing pipeline from NIRS-SPM.

Adam

On Mon, Mar 27, 2017 at 5:08 PM, Alexandra Boldin <aboldin at princeton.edu<mailto:aboldin at princeton.edu>> wrote:
Hi all,


We’ve been analyzing some data from a Shimadzu LABNIRS machine and are in the process of deciding on the best preprocessing pipeline. We’ve used HomER in the past (with data from Hitachi systems) and would love to continue using a similar pipeline. However, we only get oxygenation data from our system and Homer uses raw absorption data. We're able to modify the functions that we need to work with our data, but we were wondering if there's any reason not to do the filtering and other processing on data after it's converted to oxygenation? Is there a benefit to doing preprocessing on raw optical density data or should the results be the same if we start with oxygenation instead?

Thanks for your help!

- Alex

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