Dear Bruno,
Perhaps it would be possible to work with a different 2nd level design.
If you have eg one factor with L levels, and tell SPM to allow for
correlated errors, then SPM has L(L+1)/2 different variance components
to estimate (it has to set up an individual covariance basis function
for each, which is what spm_get_vc is doing).
This part of SPM has not been optimised for large models as we did not
envisage it being widely used.
Your quick work around options are:
1. Do lots of simple two-level models by taking differential contrasts
at the first level and one-sample t-tests at the second.
Or
2. Tell SPM that that there is no correlation between levels - ie
independence.
Out of interest - how many levels are there in your factor(s) ?
There may be a third option - reduce the number of levels and still
allow for dependence.
Best,
Will.
Bruno L. Giordano wrote:
> Hello,
>
> I am trying to estimate a rather large (and perhaps crazy) 2nd level
> model, with around 5000 contrast images.
>
> I should have managed to free up enough RAM in my XP 32bit system (RAM
> defrag + 3 Gb Windows boot switch + startup in -nojvm mode): I do no get
> the memory error when the factorial design specification starts.
>
> However, the computation appears to hang: after 10 hours of full-load
> CPU the Matlab process appears to have read or written nothing more than
> what it did at the beginning of the factorial design specification
> phase. Is it possible to estimate roughly how much time this phase would
> take, AKA, at which point should I start suspecting a problem with the
> computations, if any? I am finding, for instance, that the sort
> rows/columns loop in spm_get_vs alone takes around 190 minutes.
>
> Thanks,
>
> Bruno
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Bruno L. Giordano, PhD
> Postdoctoral Research Fellow
> CIRMMT - Schulich School of Music
> 555 Sherbrooke Street West
> Montréal, QC H3A1E3
> Canada
> +1 514 398 4535, Ext. 00900 (voice)
> +1 514 398 2962 (fax)
> http://www.music.mcgill.ca/~bruno
>
>
--
William D. Penny
Wellcome Trust Centre for Neuroimaging
University College London
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