[Homer-users] warnings time range and tHRF

Fri Mar 17 10:54:50 EDT 2017

Hi Renata,

I can look at it, if you provide the nirs file giving the warning.

Meryem

-----Original Message-----
From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Di Lorenzo, R. (Renata)
Sent: Thursday, March 16, 2017 1:47 PM
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] warnings time range and tHRF

Hi,

thank you all for your advices.
I solved problem 1 (the last trial was not load enough) but not problem 2.
I used the same time window for all subjects (-2s 10s) and I have this WARNING for almost all of my participants. In my previous email I’ve only reported subject 2 as example.

I am not sure what you mean by frequency Meryem. I don’t have the same amount of trials per subject if that’s what you mean.

I tried different time windows and I get the warning when the upper limit of the block average is set at an higher level than 5s.
I have codes for the onset of every trial, which all last 16s, except of 2 trials that last 5s.
In addition, I have codes for sounds that are sometimes played during testing to keep babies attention to the screen, but for some babies we don’t need them so then we don’t have that code in their data.

I tried to remove the 5s-trial-codes and the sound-codes from the data by ‘dashing’ them in the main window (raw data) and also I tried to delete them from the STIM GUI window.
Unfortunately, it did’t work. I still have that Warning.

Please let me know if you need any additional information to understand the problem!

Thank you in advance for your help.

Kind regards,
Renata

> On 16 Mar 2017, at 14:58, Yucel, Meryem A. <MYUCEL at mgh.harvard.edu> wrote:
> 
> For problem 2: Is there any chance that subject 2 data has a different frequency than the rest?
> 
> Meryem
> 
> 
> 
> -----Original Message-----
> From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of David Boas
> Sent: Thursday, March 16, 2017 8:05 AM
> To: homer-users at nmr.mgh.harvard.edu
> Subject: Re: [Homer-users] warnings time range and tHRF
> 
> Problem 1 is straight-forward enough. The block average is taking a block of data around a trial onset given by the time range tHRF which usually goes from something like -2 sec before the trial onset to 10 sec or so after the trial onset. If time range tHRF around the trial onset either extends before or after your data starts, then you get this warning. It is nothing to worry about unless you want to include this trial in your analysis. The only way you can include this trial in your analysis is either to collect more data before and after the trial onset to make sure you have data for the time range tHRF, or make the time range tHRF shorter.
> 
> Problem 2 suggests that you ran subject 2 with a different time range tHRF than you ran for the other subjects. Thus, when it tries to do the group average, it is warning you that you have different tHRFs for the given subject. Solution here is to run that subject again to have the same tHRF as the other subjects.
> 
> David
> 
> 
> 
> On 3/16/17, 5:08 AM, "Di Lorenzo, R. (Renata)" <homer-users-bounces at nmr.mgh.harvard.edu on behalf of r.dilorenzo at uu.nl> wrote:
> 
>    Dear Homer users,
> 
> 
>    I hope that someone can help me understanding 2 types of warning related to the block average function.
>    1. When I run the block average for one subject (run) sometimes I get this warning message: 
>    WARNING: Trial 1 for condition 2 excluded because of time range.
>    2. When I run group analyses I get this other warning message:
>    WARNING: tHRF for subject 002 is larger than the common tHRF.
> 
>    Here some more information about the task design and analyses.
>    I use a block design with baseline of 16s and test trials of 16s (visual stimuli).
>    I use triggers for the start of the task, the end, start of baseline trials, start of experimental trials and for attentional getters (sometimes we need to play sounds to keep babies attention to the screen during baseline trials).
>    The block average function goes from -2s till 18s.
>    I haven’t applied any filter to the processing stream, which consists of Intensity2OD, enPrunechannels, OD2Conc, block average.
> 
>    I do the analyses on a Mac computer (OS X El Capitan) by using Homer v2_1 on Matlab2014b.
> 
>    Does anyone know the source of the problem and how can I fix it?
> 
>    Thank you in advance.
> 
>    Kind regards,
>    Renata
> 
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