>      I am using the matlab 2008b and SPM8b with the latest update. I am
> doing the VBM study using Dartel. First follow the Dartel guide to segment
> original image from both patients and controls and create the template.
> Then normalize the template_6.nii to tpm/grey.nii and generate the
> template_6_sn. After that, I use the script in John's mail in the jiscmal
> system to apply the template_6_sn to the mwrc1*.nii of all subjects. For
> group comparison, I used two-sample t test. My question is as follows:
>      1. when I use John's script, the only thing change I can see is the
> date of file has been changed. I have checked the dimension of
> the mwrc1*.nii is still the same and different from the tpm/grey.nii. I
> don't know whether it is correct that the files had been changed from
> native space to the MNI space.

If you use Check Reg, with these images shown alongside the MNI data, then you 
should (hopefully) see that they are in better alignment.  One of the 
matrices in the NIfTI headers will have changed, to reflect the new voxel 
sizes, orientation etc.

>       2. when I want to choose "FWE" or "FDR" for "p value adjustment to"
> in the result panel, it always report error as follows, (but no error when
> I choose none and imput 0.001 et al.):
>          Warning: Returning NaN for out of range arguments

I'll leave this one for the other guys.  My best guess is that you did not 
specify a "grey matter threshold" for your analysis.  You need to exclude 
voxels whos intensity is below about 0.05 from the analysis - otherwise 
estimated variances go to zero, and the estimated smoothness does bizarre 
things.

Best regards,
-John

>
> > In spm_Pcdf at 88
>
>   In spm_P_RF at 106
>   In spm_uc_RF at 37
>   In spm_uc at 39
>   In spm_getSPM at 613
>   In spm_results_ui at 274
> Warning: Returning NaN for out of range arguments
>
> > In spm_Pcdf at 88
>
>   In spm_P_RF at 106
>   In spm_uc_RF at 38
>   In spm_uc at 39
>   In spm_getSPM at 613
>   In spm_results_ui at 274
> ??? Error using ==> betainc at 42
> X must be in the interval [0,1].
> Error in ==> spm_Tcdf at 106
> F(Q) = xQxPos
> -(xQxPos*2-1).*0.5.*betainc(v(Qv)./(v(Qv)+x(Qx).^2),v(Qv)/2,1/2);
> Error in ==> spm_P_RF>spm_ECdensity at 157
>     EC(1,:) = 1 - spm_Tcdf(t,v);
> Error in ==> spm_P_RF at 59
> EC      = spm_ECdensity(STAT,Z,df);
> Error in ==> spm_uc_RF at 47
>     p       = spm_P_RF(1,0,u,df,STAT,R,n);
> Error in ==> spm_uc at 39
> u = spm_uc_RF(a,df,STAT,R,n);
> Error in ==> spm_getSPM at 613
>     u  = spm_uc(u,df,STAT,R,n,S);
> Error in ==> spm_results_ui at 274
>     [SPM,xSPM] = spm_getSPM;
> ??? Error while evaluating uicontrol Callback
>
>      Any suggestion is welcome. Thanks a lot
>
> June