[Homer-users] Homer v2.0 SD bug

[anna at blasi.com]

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
> 
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users [1]
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline [2] . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
 

Links:
------
[1] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
[2] http://www.partners.org/complianceline
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20150719/d8c32689/attachment.html