[Homer-users] channel matching in HOMER2

[Cooper, Robert]

Dear Bori, all

Looking at your data I suspect the problem is your conversion from the UCL topography data format to .nirs.

Looking at your SD.MeasList, you have:

     2     1     1     1
     2     1     1     2
     2     2     1     1
     2     2     1     2
    12     2     1     1
    12     2     1     2
     2     3     1     1
     2     3     1     2
     2     5     1     1
     2     5     1     2
    12     5     1     1
    12     5     1     2
    12     7     1     1
    12     7     1     2
    12     8     1     1
    12     8     1     2
    12    12     1     1
    12    12     1     2
     2    13     1     1
     2    13     1     2

Normally, this table is arranged such that the first half of the rows are the lower wavelength (fourth column =1) and the latter half are the second wavelength (fourth column = 2).  Although the information is the same, it is possible HOMER is assuming this arrangement and thus gets channels confused when you de-select them.  Your SD.MeasList should look like this:

     2     1     1     1
     2     2     1     1
    12     2     1     1
     2     3     1     1
     2     5     1     1
    12     5     1     1
    12     7     1     1
    12     8     1     1
    12    12     1     1
     2    13     1     1
     2     1     1     2
     2     2     1     2
    12     2     1     2
     2     3     1     2
     2     5     1     2
    12     5     1     2
    12     7     1     2
    12     8     1     2
    12    12     1     2
     2    13     1     2

Hope that works. 

Rob Cooper


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




-----Original Message-----
From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Borbala Kollod
Sent: 18 March 2013 10:44
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] channel matching in HOMER2

Thanks David, 


Unfortunately this does not work again with any of the designs that we got data of.
It would be nice to share thoughts on this problem during one of the training sessions. If anybody would be interested, attached can be found an example of a datafile that we're struggling with. 
Bori



Cognitive Development Center
Department of Cognitive Sciences
CEU
H-1051 Budapest
Hattyú u 14.
Tel.: +36 3273000/2780
>>> David Boas  03/16/13 10:33 PM >>>
Dear Bori and Austin,
I have not seen this problem before.

I have created a short tutorial on how to select different channels of data for displaying that you can view at http://www.youtube.com/watch?v=u4TXyLiPz8E

We'll get this tutorial linked form the Homer2 Tutorials web page soon.

If this doesn't help with your issues, then perhaps you can demonstrate the problem at one of our monthly homer2 online training sessions.

David



On 3/10/13 5:42 PM, austin1 wrote:
> Good Morning Borbala
>
> I don't have an answer for you but I'm having the same issue.
>
> Austin
>
>
> -----Original Message-----
>> From: Borbala Kollod
>> Sent: Mar 7, 2013 11:00 AM
>> To: homer-users at nmr.mgh.harvard.edu
>> Subject: [Homer-users] channel matching in HOMER2
>>
>> Hi there,
>>
>>
>> I'm quite new to HOMER2, I'm confused a little yet at the beginning.
>> I have problems with un-displaying and matching channels between the 
>> Probe Window and Data Window.
>> When a data file is opened in HOMER2, for some channels the 
>> un-displaying (right-click) is working, for some it does not, and in 
>> some cases right-clicking un-displays more than one channel or 
>> un-displays a channel that is labeled with a different color (eg.
>> clicking on a magenta channel on the Probe Window would un-display a 
>> green one on the Data window).
>>
>>
>> This way it is confusing to know which channel we're looking at
exactly
>> and makes especially hard to see data in those cases, when we have
deep
>> channels (4.5cm) besides normal (2cm) ones, because deep channels are
so
>> noisy compared to the normals that they obscure all normal ones.
>>
>>
>> These are infant data, and we are using NTS3 system, so data got 
>> converted into .nirs format beforehand. Also we're using the
developer
>> version of HOMER2.
>>
>>
>> Anybody has any idea for the reason of this un-match?
>> Thanks!
>> Bori Kollod
>>
>>
>> Cognitive Development Center
>> Department of Cognitive Sciences
>> CEU
>> H-1051 Budapest
>> Hattyú u 14.
>> Tel.: +36 1 88 333 45
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