[Homer-users] Homer v2.0 SD bug

[Meryem Ayse Yucel]

Hi Anna,

Are you using group average option "require all channels pass"? Maybe that
can explain why same channels are rejected in your group analysis.

Do you want to try hmrMotionCorrectPCA_recursive instead? When you
visually inspect the channels, do you see motion artifacts are actually
detected (red shade on them)?

What are your "unreasonable" SNR thresholds?


Meryem


>
>
> Hi all,
>
> I am new to Homer2 so I was not sure wether the spatial unit request and
> the repair that apparently my files need the first time I load them in
> Homer2 was to do with something I had done wrong. Regarding the bug in
> the SD.MeasListAct that you are reporting, Katherine, I have a problem
> that seems related. When reviewing the group analysis I noticed that
> when processed as a group, all my participants have the same 3 channels
> rejected, whereas if I put them in a separate folder, there is a
> different set of channels rejected (I assume the correct set).
>
> I would like to add a couple of questions that are probably unrelated to
> this bug. I am using Matlab 2013a.
>
> - It seems like the PCA option for motion artefact correction
> (hmrMotionCorrectPCA.m) does not have any effect on our data, as it does
> not smooth or change data at all regardless of the nSV parameter
> selected. I have tried setting it to values < 1 and also integers
> greater than 1, but this does not seem to affect the data at all. After
> running the processing stream, the "Results" option from the PCA also
> errors. It shows an empty graph and the following error:
>
> Attempted to access svs(:,1); index out of bounds because
> size(svs)=[0,0].
>
> Error in hmrMotionCorrectPCA_result (line 16)
>  plot([svs(:,1) svsc(:,1)],'.');
>
> Error in EasyNIRS_ProcessOpt>pushbutton_Callback (line 245)
> eval( sprintf( '%s_result( %s );',
> procInput.procFunc.funcName{eventdata}, sargin(2:end) ) );
>
> Error in gui_mainfcn (line 96)
>  feval(varargin{:});
>
> Error in EasyNIRS_ProcessOpt (line 42)
>  gui_mainfcn(gui_State, varargin{:});
>
> Error in
> EasyNIRS_ProcessOpt>EasyNIRS_ProcessOpt_OpeningFcn/@(hObject,eventdata)EasyNIRS_ProcessOpt('pushbutton_Callback',hObject,2,guidata(hObject))
>
>
> Error while evaluating uicontrol Callback
>
> - I also tried the (enPruneChannels.m), but also regardless of the SNR
> threshold that I specify (even unreasonable ones), none of my channels
> are rejected... and I have tried it with very noisy data.
>
> Many thanks,
>
> Anna
>
> _Anna Blasi_
>
> Centre for Brain and Cognitive Development,
> Birkbeck, University of London
> London
>
> Tel: (+44) 2076316391
>
>> Hello,
>>
>> I just downloaded Homer2 v2.0 from NITRC to fix the compatibility with
>> Matlab 2014b. This version requires SD.SpatialUnit which was not
>> required with the prior version I was using (v1.5). When I started up
>> Homer2 v2.0, I got the message about the required spatial unit, and I
>> went through the windows and approved the incorporation of the spatial
>> unit field. However, it looks like there is a bug in how this
>> information is incorporated-- the SD.MeasListAct does not match between
>> the newly created .nirs file with SD.SpatialUnit and the saved .nirs.org
>> file. Specifically, it looks like all files in my directory now have the
>> same SD.MeasListAct as the first file, instead of their original values
>> that marked bad channels. I don't use the SD.MeasListVis field so I
>> don't know if that is affected as well.
>>
>> Has anyone else had issues with this?
>>
>> best,
>> Katherine
>>
>> -------------
>> Katherine Perdue, PhD
>> Research Fellow in Pediatrics
>> Labs of Cognitive Neuroscience
>> Division of Developmental Medicine
>> Boston Children's Hospital
>> Office Phone: 857-218-5214
>>
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