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

[Ian Wiggins]

Hi Ken

In stimGUI, do you have "Aux" signals listed in the "Add Stim Marks using Aux" section? If so, you can click the "Apply" button to convert the markers in these Aux signals into stimulus marks. You'll need to do this for each Aux signal in turn (there should be one for each condition in your experiment). Please note: You'll need to change the "Threshold" value to a number smaller than 1 in order for the markers in the Aux signals to be recognised. Remember to click the Save button at the bottom of stimGUI once you're done.

You are correct, you will need to remove the offset markers, so that only stimulus onsets are marked. For the time being, you could achieve this by manually disabling the offset markers in the main HOMER2 GUI using the "Stim Reject" facility.

I believe we have local versions of Rebecca's Hitachi_2_Homer script that (a) automatically put in the stimulus marks, and (b) automatically remove the offset markers. I'll talk to Rebecca about the possibility of issuing an update to the Hitachi_2_Homer script to reflect these changes.

Best wishes

Ian


Ian Wiggins, PhD
Research Fellow (Advanced Imaging and Translational Neuroscience)
National Institute for Health Research Nottingham Hearing Biomedical Research Unit
Ropewalk House, 113 The Ropewalk, Nottingham, NG1 5DU


From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Rando, Kenneth
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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