In reference to toolboxes, for me, just having them in the SPM5 toolbox
directory does not necessarily load them into the path. However, once
invoked from the SPM GUI drop-down toolbox menu selector, then SPM does seem
to put the selected toolbox's path on top and leave it there until the
MATLAB session is over.
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of d gitelman
Sent: Sunday, June 01, 2008 5:35 PM
To: [log in to unmask]
Subject: Re: [SPM] SPM 5 VBM: FWE/FDR errors
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
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.
> -----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.
> 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
> 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?
> 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