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Subject:

Re: Possible bug in spm_orth

From:

Ryan Haynes <[log in to unmask]>

Reply-To:

Ryan Haynes <[log in to unmask]>

Date:

Wed, 13 May 2009 13:00:33 -0700

Content-Type:

text/plain

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Parts/Attachments

text/plain (114 lines)

Thanks for your response, Jan. I am aware that a parametric modulator that does not change will not explain additional variance in the data. For some of my subjects this parametric value changes and for some it does not. I could modify my scripts to omit the non-changing modulator, but technically SPM should be capable of tossing out this modulator automatically without crashing which is what the original code in spm_orth is intended to do by using the any() function. spm_orth should not work successfully for some vectors and fail on others. But, in the meantime I'll use your solution to work around the problem. 

Thanks,
Ryan


--- On Wed, 5/13/09, Jan Gläscher <[log in to unmask]> wrote:

> From: Jan Gläscher <[log in to unmask]>
> Subject: Re: [SPM] Possible bug in spm_orth
> To: "Ryan Haynes" <[log in to unmask]>
> Cc: [log in to unmask]
> Date: Wednesday, May 13, 2009, 2:08 PM
> Hi Ryan,
> 
> I came across a similar problem before and admittedly
> didn't spend as much
> time as you on figuring out a solution for spm_orth,
> because in the end it
> doesn't make sense to include a parametric modulator
> that only has the same
> value for all events, not even a single one. It doesn't
> explain any
> additional variance in the data that is not captured by the
> primary onset
> regressors. Therefore, when coding up some batch scripts I
> always check if
> my modulator has at least 2 differing values in it and if
> not, I don't
> include it in the design matrix.
> 
> Cheers,
> Jan
> 
> 
> Ryan Haynes wrote:
> > Hi,
> > 
> > I am trying to determine if an error I'm getting
> in spm_fMRI_design is coming from a possible round-off error
> in spm_orth. This bug is extremely rare as it only occurs in
> certain cases of parametric modulators and only in the
> situation in which the modulator for every event is
> identical such that the two vectors for an event are
> linearly dependent. For example, consider the following
> matrix "u" inside spm_get_ons:
> > 
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 
> > spm_orth on this matrix returns a vector of 1's
> and a vector of 7.10e-15. Mathematically this should be a
> vector of 1's and a vector of 0's of course and for
> most practical purposes 7.10e-15 is essentially 0. But, the
> problem that occurs is that if you run spm_orth on this
> matrix again you get a vector of 1's and a vector of
> 0's. This throws and error in matlab in spm_fMRI_design
> because of the following:
> > 
> > for i = 1:length(Fc)
> >   X(:,Fc(i).i) = spm_orth(X(:,Fc(i).i));
> > end
> > 
> > Matlab expects the return of spm_orth(X(:,Fc(i).i)) to
> have the same number of dimensions as X(:,Fc(i).i) which is
> doesn't since spm_orth drops vectors that contain only
> 0's. What should have happened is that spm_orth should
> have dropped the vector containing 7.10e-15 originally.
> Instead of the following code in spm_orth 
> > 
> > if any(D)
> >   x = [x D];
> > end
> > 
> > maybe this code should be used:
> > 
> > epsilon = 1e-10;
> > if ~isempty( find(D) > epsilon )
> >   x = [x D];
> > end
> > 
> > The reason this bug is rare is that it only occurs for
> certain numbers and for certain lengths of vectors. For
> example, the following vector of length 6
> > 
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 1 40
> > 
> > does not cause this error while the one of length 7
> does. Likewise, if you replace 40 with 50 in the
> 7-dimensional vector it also does not cause the error.
> Please let me know if this actually is a bug, or if not,
> please let me know what I'm doing wrong. Thanks.
> > 
> > Ryan Haynes
> > 
> 
> -- 
> Jan Gläscher, Ph.D.         Div. Humanities & Social
> Sciences
> +1 (626) 395-3898 (office)  Caltech, Broad Center, M/C
> 114-96
> +1 (626) 395-2000 (fax)     1200 E. California Blvd
> [log in to unmask]    Pasadena, CA 91125

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