[Homer-users] Short Separation in Developer's Version

[Meryem Ayse Yucel]

Hi Rachel,

If you send over one of your .nirs files, I can have a look at it.

Thanks,

Meryem



> Based on this error code, it would appear that I need to use the 1.5 cm;
> however, the SS channels do not flatten and I get the message: There are
> no
> short separation channels in this probe...performing regular
> deconvolution.
> Design matrix is VERY poorly scaled...(RCond=0.000000e+00), cannot perform
> computation
> There are no short separation channels in this probe...performing regular
> deconvolution.
> Design matrix is VERY poorly scaled...(RCond=0.000000e+00), cannot perform
> computation
>
> I am attaching a picture of my probe array after running the processing
> stream with SS. SS channels were 1 cm, all other channels were 3 cm.
>
>
>
> On Wed, Apr 29, 2015 at 3:13 PM, Rachel Mulheren <mulherrw at dukes.jmu.edu>
> wrote:
>
>> When the processing gets "stuck" on the SS, this is the following error
>> code I receive:
>>
>> Reference to non-existent field 'svs'.
>>
>> Error in EasyNIRS_ProcessOpt>pushbutton_Callback (line 268)
>> 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,3,guidata(hObject))
>>
>>
>> Error while evaluating uicontrol Callback
>>
>> Reference to non-existent field 'svs'.
>>
>> Error in EasyNIRS_ProcessOpt>pushbutton_Callback (line 268)
>> 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,3,guidata(hObject))
>>
>>
>> Error while evaluating uicontrol Callback
>>
>> Index exceeds matrix dimensions.
>>
>> Error in hmrDeconvTB_SS3rd (line 141)
>>         Ass = y(:,conc,mlSSlst(iSS));
>>
>> Error in EasyNIRS_Process (line 88)
>>         eval( fcall );
>>
>> Error in EasyNIRS>runNIRSsignalProcess (line 1022)
>> [procResult procInput err] = EasyNIRS_Process(hmr);
>>
>> Error in EasyNIRS>popupmenuNIRSsignalProcess_Callback (line 1435)
>>         runNIRSsignalProcess(iGrp,iSubj,iRun,handles);
>>
>> Error in gui_mainfcn (line 96)
>>         feval(varargin{:});
>>
>> Error in EasyNIRS (line 43)
>>     gui_mainfcn(gui_State, varargin{:});
>>
>> Error in
>>
>> @(hObject,eventdata)EasyNIRS('popupmenuNIRSsignalProcess_Callback',hObject,eventdata,guidata(hObject))
>>
>>
>> Error while evaluating uicontrol Callback
>>
>> >>
>>
>> On Wed, Apr 29, 2015 at 12:09 PM, David Boas <dboas at nmr.mgh.harvard.edu>
>> wrote:
>>
>>>  Most likely the units are mm and you need to use 15 for the
>>> rhoSD_SSThresh
>>>
>>>  The fact that the processing gets “stuck” when you use 15 probably
>>> indicates that it is busy calculating the short separation regression.
>>> Let
>>> me verify, you say it gets “stuck”, but it doesn’t crash?
>>>
>>>  What type of computer are you using? How big is your data set?
>>>
>>>
>>>
>>>  On Apr 29, 2015, at 11:49 AM, Rachel Mulheren <mulherrw at dukes.jmu.edu>
>>> wrote:
>>>
>>>    Hello,
>>>
>>>  I included 2 short separation channels (1 cm) in my probe and now that
>>> I
>>> am running the processing stream including the parameters for short
>>> separation, I get the following message: There are no short separation
>>> channels in this probe...performing regular deconvolution.
>>> Design matrix is VERY poorly scaled...(RCond=0.000000e+00), cannot
>>> perform computation
>>>
>>>  Eyeballing the HRF after running this processing stream, I am not
>>> seeing
>>> a difference with and without the short separation, so I am guessing
>>> that
>>> it was not extracted from the signal.
>>>
>>>  Suggestions for what I might be doing incorrectly?
>>>
>>>  I am using Block Avg Short Sep
>>>  trange -5 to 17
>>>  gstd 1
>>>  gms 1
>>>  rhoSD_SSThresh 1.5
>>>
>>>  I have also tried with rhoSD_SSThresh 15 (in case there was a mix-up
>>> with mm and cm), but the processing starts and gets "stuck" on the
>>> short
>>> separation.
>>>
>>>  Thanks,
>>>
>>>  Rachel
>>> _______________________________________________
>>> Homer-users mailing list
>>> Homer-users at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>>>
>>>
>>>
>>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users