[Homer-users] channel matching in HOMER2
David Boas
dboas at nmr.mgh.harvard.edu
Mon Mar 18 09:25:45 EDT 2013
Bori,
Thanks for sending the NIRS file. I have recreated your problem. Rob is
probably right about why this happening. You can try changing your
MeasList for a short term fix. I will try to fix the code so that it
behaves properly independent of how you order your MeasList.
David
On 3/18/13 7:32 AM, Cooper, Robert wrote:
> 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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