[Homer-users] troubleshooting NIRx2nirs file conversion

[Jonas Hofstetter]

Hello all,

I´m trying to build .nirs files with the NIRx2nirs.zip matlab script (http://www.nitrc.org/projects/nirx2nirs/).
During my data collection with NIRStar I couldn´t save .nirs files for three subjects and I´m trying to use
the matlab script to create them. 

I´ve been partly successful, so far. 

I could create .nirs files for my three subjects. It´s also possible to load those .nirs files into HOMER2 (v.2.1). 
I can see all channels and triggers in the data window, and the probe window shows 
the SD-geometry (8x8 Bilateral DLPFC) that I´m using for my research project. 

However, In HOMER2 I can NOT apply Processing Streams to the resulting .nirs files and it´s not possible to 
use the stimGui to ammend triggers.
I think the errors in HOMER2 may result from the design of the .SD file which I extracted and used for the matlab script.
My general aim is to build a .SD file for a 8x8 Bilateral DLPFC Montage and merge it with the .wl1, .wl2, .hdR 
files required by the matlab script NIRxtoNirs. 
  
When building the required SD. file with AtlasViewer SDgui for the NIRx2nirs matlab script I proceeded as follows:

1) I loaded an existing .nirs file from another subject (same NIRS montage used therein) into SDgui (AtlasViewer)
   --> here I noticed that the units of my source and detector coordinates in SDgui didn´t look as tidy as
         I would have expected - those units didn´t appear in mm length untis at least.  
        (e.g. d1: x: -212891076.1223 y: 4726012621.0315 z: 583242848.047 I1: 1 I2:2 )

2) I saved the probe in SDgui as an .SD file in a common folder with .wl1 .wl2 .hdR for my subject
    for whom I wasn´t able to save a .nirs file for during data collection.

3) I applied NIRx2nirs in matlab and was able to save a .nirs file.

4) The above mentioned difficulties in HOMER2 resulted with the .nirs files. 



Does anyone have ideas how I can create a .SD-file (8x8 Bilateral DLPFC) 
that doesn´t impede the HOMER2 analysis for the .nirs file that results when running NIRx2nirs in matlab?

Attached to this email you´ll find the .SD file that I extracted and the .nirs file that resulted from running the matlab script. 


Best,

Jonas Hofstetter

B.Sc. Psychology
University of Konstanz
research assistant
Sports Psychology (Prof. Dr. Julia Schüler)

 



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