[Homer-users] Losing stimulus marks in ETG to .nirs conversion

[Cooper, Robert]

Hi Ken,


If your s-vector is all zeros, it is likely that your conversion script (from Hitachi to .nirs) is failing. I recommend you check through that script, find the point where the stimulus marks are extracted from the .csv and see if you can determine why they are not successfully being assigned to the s-vector.


Regarding off-set marks: yes, you do want to remove them. Homer2 treats every value of 1 in the s vector as the onset of a stimulus. The length of the stimulus is dictated in Homer2 by the t-range variables in the block average or deconvolution functions.


Hope this helps,


Rob Cooper



Rob J Cooper PhD.
Research Associate
Biomedical Optics Research Laboratory
Malet Place Engineering Building, Rm 3.18
University College London
Gower Street
London WC1E 6BT
T: [X] +44 (0)20 7679 0275





________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu <homer-users-bounces at nmr.mgh.harvard.edu> on behalf of Rando, Kenneth <kenneth.rando at yale.edu>
Sent: 28 July 2014 20:05
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] Losing stimulus marks in ETG to .nirs conversion

Hello Homer2 Users,

I am attempting to create my first analysis of patients and controls using Homer2. We collect data using the Hitachi ETG-4000. I converted the measurement (MES) file to a .nirs file using Hitachi_2_Homer_single_v2.m as we only use one 3x5 optode array. When I look at stimGUI inder tools, I see no blue lines marking the stimuli. I examined the .nirs file in Matlab and compared it to the .csv measurement file. The stimulus marks in the .csv file ar not reproduced in the .nirs file. The s variable is all zeros.  Any suggestions would be appreciated.

I have one more question related to the stimulus marks. The ETG-4000 marks the beginning and end of a stimulus presentation. However, a series of postings ending February 12, 2013 says "your stimulus vector s should have 1's at the onset, not throughout." Do I want to remove the offset mark? Note that to rule out the possibility that my problem results from the file containing both an onset and offset mark, I tried converting the data and creating an analysis with the offset mark removed. The .nirs file still contains only zeros.

Thanks very much.

Ken




Kenneth Rando
Research Assistant 2
203-974-7731

Yale OCD Research Clinic
Yale University School of Medicine
Connecticut Mental Health Center
34 Park Street, Room W309
New Haven, CT 06519


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