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SPM  June 2008

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Subject:

Re: SPM 5 VBM: FWE/FDR errors

From:

Darren G <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Sun, 1 Jun 2008 22:51:41 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (145 lines)

It isn't precisely clear to me what you are doing. 

After you click the FWE or FDR or None buttons you need to enter a voxel threshold between 0 and 1. 

If any voxels survive the voxel threshold you will be asked to enter a cluster size threshold. This 
number must be >0 and an integer. 

The message below looks like you tried to enter a number outside of the [0 1] interval for the
question about the voxel threshold. Otherwise I'm not sure why you are getting the error, and I
would follow Tom's suggestions.

Darren

-------------------------------
On Sun, 01 Jun 2008 10:07:38 pm CDT Megan Walsh wrote:

Thanks for your response.  I will definitely look into this.

To clarify what I was doing.  I wanted to use FWE correction for multiple
comparisons.  When this didn't work (with the error previously sent) I
attempted a cluster level threshold.  I just want an FWE of 0.05. Is that
clear?  So am I doing the right thing?

Thanks,

Meg

On Sun, Jun 1, 2008 at 5:34 PM, d gitelman <[log in to unmask]>
wrote:

> Megan
>
> Are you trying to do cluster-wise thresholding in VBM using a probability
> threshold? This is available in Christian Gaser's VBM toolbox, but is not
> available in SPM, which only allows the specification of a number of voxels
> for thresholding clusters. You will have to get the toolbox in order to do
> the probability type of cluster thresholding
> http://dbm.neuro.uni-jena.de/vbm/>
> Remember that once a toolbox is placed in the toolbox directory it is
> always
> loaded into the spm path. This can give unexpected results with toolboxes
> such as the VBM toolbox which uses some functions with the same names as
> those in SPM.
>
> Darren
>
> > -----Original Message-----
> > From: SPM (Statistical Parametric Mapping)
> > [mailto:[log in to unmask]] On Behalf Of Thomas Nichols
> > Sent: Sunday, June 01, 2008 4:28 PM
> > To: [log in to unmask]
> > Subject: Re: [SPM] SPM 5 VBM: FWE/FDR errors
> >
> > Dear Megan,
> >
> > This sounds very strange, as FWE and FDR calculations are
> > quite different.
> >
> > Can you clarify exactly what you enter ('0.05' ?) and in
> > response to exactly which question?
> >
> > Also not that you say 'cluster = 100', but that's just an
> > arbitrary number (all clusters smaller than 100 are omitted)
> > and not a specific FWE-level threshold.  FWE cluster
> > inferences are read off of the table for any uncorrected
> > threshold you give SPM.
> >
> > -Tom
> >
> >
> >
> > On Fri, May 30, 2008 at 2:56 PM, Megan Walsh <[log in to unmask]> wrote:
> >
> >
> >       Hey fellow SPM-ers-
> >
> >       I am currently doing a multiple regression analysis on
> > some VBM data.  I understand that cluster-wise thresholding
> > is certainly not ideal for multiple comparison corrections.
> > To correct for multiple comparisons I wanted to specify my
> > FWE as p<0.05.  When I specify this I get the following error message:
> >
> >       ??? 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 602
> >        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
> >
> >       The same idea goes for the FDR correction.  However, if
> > I cluster threshold it works fine (cluster=100).
> >       Can anyone help me figure out how to either a) fix the
> > problem, or b) an alternative manner in which I can correct
> > for multiple comparisons?
> >
> >       Thanks,
> >       Meg
> >
> >       --
> >       Megan Kay Walsh
> >       Graduate Student
> >       Johns Hopkins University
> >       Psychological & Brain Sciences
> >       204 Ames Hall
> >       3400 N. Charles St.
> >       Baltimore, MD 21218
> >
> >
> >
> >
> > --
> > ____________________________________________
> > Thomas Nichols, PhD
> > Director, Modelling & Genetics
> > GlaxoSmithKline Clinical Imaging Centre
> >
> > Senior Research Fellow
> > Oxford University FMRIB Centre
> >
>



-- 
Megan Kay Walsh
Graduate Student
Johns Hopkins University
Psychological & Brain Sciences
204 Ames Hall
3400 N. Charles St.
Baltimore, MD 21218
===========End of original message text===========

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