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FSL  April 2007

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Subject:

Re: FEAT malloc problems

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 13 Apr 2007 15:49:58 +0100

Content-Type:

text/plain

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text/plain (104 lines)

Try right clicking on the links and saving to file.


On 13 Apr 2007, at 15:47, Clare Kelly wrote:

> Hey Steve,
>
> Sorry for being a bit clueless, but how do I download those? I'm  
> just getting htm files??
>
> Thanks, Clare
>
> On 4/13/07, Clare Kelly <[log in to unmask]> wrote: That's  
> great, thanks a million Steve,
> Will let you know how I get on,
>
> Cheers, Clare
>
>
> On 4/13/07, Steve Smith < [log in to unmask]> wrote:Aha - the  
> current MacosX-Intel FSL download is only 32-bit, it's
> about time we released a 64-bit one too - we'll try to sort that next
> week. That will almost certainly solve your problem.
>
> In the meantime, you could try placing the following in $FSLDIR/bin
> (and make sure its executable):
> http://www.fmrib.ox.ac.uk/~steve/ftp/film_gls
> http://www.fmrib.ox.ac.uk/~steve/ftp/contrast_mgr
>
> Cheers, Steve.
>
>
>
> On 12 Apr 2007, at 19:23, Clare Kelly wrote:
>
> > Hi all,
> >
> > I am trying to run analyse a fairly large (816 timepoints) dataset.
> > I have 20 EVS, plus temporal derivatives, corresponding to several
> > classes of event regressors, two error regressors and three block
> > regressors (no temp. derivative included). I'm using 3 column
> > format EVs with the double-gamma HRF convolution. I'm also
> > orthogonalizing WRT motion.
> >
> > The processor is a Mac 2 x 2.66 GHz Dual-Core Intel Xeon, with 8GB
> > RAM (and oodles of free space). OS X Server 10.4.9
> >
> > It crashes as follows:
> >
> > /Users/Shared/fsl/bin/contrast_mgr -f design.fts stats design.con
> > contrast_mgr(2884) malloc: *** vm_allocate(size=2654208000) failed
> > (error code=3)
> > contrast_mgr(2884) malloc: *** error: can't allocate region
> > contrast_mgr(2884) malloc: *** set a breakpoint in szone_error to
> > debug
> > Uncaught exception!
> > Rendering using zmin=2.3 zmax=8
> >
> > I tried it without the prewhitening step, I've also tried removing
> > some regressors (errors) but can't really drop any more. Neither of
> > these options worked. Because of the nature of the experiment, I
> > can't analyse the data separately for each block then combine in a
> > fixed effects analysis.
> >
> > I do have a large number of contrasts (40) - does this contribute
> > to the memory problem (i.e. could be solved if I ran half the
> > contrasts in one feat and the other half in another)? Or is it
> > purely a result of the large number of timepoints and large number
> > of EVs? Perhaps I should just drop the temporal derivatives? I come
> > across this memory problem frequently with FEAT and would really
> > like to know how other people come to a solution.
> >
> > Any advice would be greatly appreciated!
> >
> > Cheers,
> > Clare
>
>
> ---------------------------------------------------------------------- 
> --
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------- 
> --
> ---
>
>


------------------------------------------------------------------------ 
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------ 
---

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