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SPM  March 2011

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Subject:

ns toolbox spm8 update

From:

Will McGeown <[log in to unmask]>

Reply-To:

Will McGeown <[log in to unmask]>

Date:

Thu, 10 Mar 2011 16:18:23 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (117 lines)

Dear all,
Previously I encountered a problem when running the NS toolbox with spm8.
The previous error can be found in my message at the very bottom of this posting.
A couple of people replied with the very helpful solution of switching off the FDR cluster p-value calculation using the command:
spm_get_defaults('stats.topoFDR',0);
After doing this the analyses worked fine.  Thanks for that!

I am now trying to run the same type of analyiss but now the toolbox does not work again.  I think the problem might have something to do with an update to spm8.  To try to fix this our computer technician has installed the spm8 version from the SPM website but it also appears to have been updated.

When I run an analysis using the ns toolbox the error I now get is:

SPM8: spm_results_ui (v3928)                       11:06:23 - 10/03/2011
========================================================================
	SPM computation                 :                        ...done
??? Error using ==> spm_P
Too many output arguments.

Error in ==> spm_list_nS at 275
[P Pn Em En EN] = spm_P(1,k,u,df,STAT,R,n,S);

Error in ==> spm_results_ui_nS at 33
spm_list_nS('list',SPM.xVol.VRpv,xSPM,hReg);

Error in ==> spm_ns at 8
[hReg,xSPM,SPM]=spm_results_ui_nS;

Error in ==> spm at 914
    evalin('base',xTB(i).prog);

??? Error while evaluating uicontrol Callback


I'm not sure what is wrong.
Does anyone have any suggestions of what I can do to get the ns toolbox to work with spm8 (the updated version)?
Or does anyone have an updated version of the ns toolbox?
Thanks in advance.

Will



-------------------------------------------------------------------------------------------
Dear Will and Satoru,

the NS toolbox is indeed not yet compatible with recent changes
regarding cluster-based FDR but things should be fine if you disable it by:
* editing spm_defaults.m so that defaults.stats.topoFDR  = 0;
or
* typing spm_get_defaults('stats.topoFDR',0); beforehand.

Best regards,
Guillaume.

Satoru Hayasaka wrote:
> I am not very familiar with SPM8, as I am still using SPM5.
> Nevertheless, I did look into some SPM8 functions related to the error.
> I suspect that the problem below is likely due to the cluster-based FDR
> (by Chumbley & Friston) implemented in SPM8. I guess I need to update
> the NS toolbox to accommodate this change, but first I have to think how
> I can get around it. Just as a footnote, I don't think cluster FDR
> p-values are valid for VBM since they do not account for non-uniform
> smoothness. 
> 
> -Satoru
> 
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
> On Behalf Of Will McGeown
> Sent: Monday, August 24, 2009 8:40 AM
> To: [log in to unmask]
> Subject: [SPM] ns with SPM8
> 
> Hi all,
> I have started using SPM8 and DARTEL for VBM.
> Previously I have used the non-stationarity toolbox (by Satoru Hayasaka)
> that 
> is available via a link on the SPM website.  This allows the use of
> cluster p-
> values.  I have been using SPM5.
> The ns toolbox does not seem to work with spm8 however.
> When I try I get the following error:
> 
> 
> 
> SPM8: spm_results_ui (v3081)                       10:55:41 - 24/08/2009
> ===========================================================
> =============
>         SPM computation                 :                ...initialising
>         SPM computation                 :                        ...done
>         SPM computation                 :                        ...done
> ??? Reference to non-existent field 'Ps'.
> 
> Error in ==> spm_list_nS at 122
> QPs   = varargin{3}.Ps;                                 % Needed for FDR
> 
> Error in ==> spm_results_ui_nS at 33
> spm_list_nS('list',SPM.xVol.VRpv,xSPM,hReg);
> 
> Error in ==> spm_ns at 8
> [hReg,xSPM,SPM]=spm_results_ui_nS;
> 
> Error in ==> spm at 910
>     evalin('base',xTB(i).prog);
> 
> ??? Error while evaluating uicontrol Callback.
> 
> 
> ---------------------------------------------------------------
> Has anyone converted the toolbox for use with SPM8?
> If so is there any way that they could make it available please?
> 
> Thanks in advance
> 
> Will
> 
> 

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