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

[Rachel Mulheren]

Ah thank you for your help. I had previously used the executable and do not
have much Matlab experience. Does the s vector need to defined for each
file opened in Matlab? And do units have to be fixed for each file manually?

On Thu, Apr 30, 2015 at 5:17 PM, Meryem Ayse Yucel <
mayucel at nmr.mgh.harvard.edu> wrote:

> Hi Rachel,
>
> 1) Your s vector is empty. You need to fix it.
>
> 2) Your source and detector positions does not seem to be either cm or mm.
> The smallest distance calculated by homer is around 110 for your SD
> geometry, so if you type 120 for ssthreshold, it will perform short
> separation regression since it will find two SD pairs which have shorter
> distance. You need to fix your units.
>
> Hope this helps.
>
> 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
> >>>
> >>>
> >>>
> >>
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