Thanks for the suggestions Steve, but unfortunately I get the same
problem. As I said, it's puzzling, since --jols works just fine. Is
there any way of getting more screen output to help in identifying the
problem? I used the --debug option, but that didn't seem to make a
difference.
Tom
----- Original Message -----
From: Steve Smith <[log in to unmask]>
Date: Friday, January 20, 2006 2:27 am
Subject: Re: [FSL] flame abort problem
To: [log in to unmask]
> Hi - you might need to add the options controlling the MCMC etc for
>
> FLAME stage 1 only:
> --nj=10000 --bi=500 --se=1 --fm --zlt=100000 --zut=100000
> or full FLAME:
> --nj=10000 --bi=500 --se=1 --fm --zlt=2.25 --zut=2.65
>
> Cheers, Steve.
>
>
> On 20 Jan 2006, at 00:07, Tom Johnstone wrote:
>
> > I'm trying to run a very simple group analysis on cope images
> that
> > I registered using the flirt command line,
> > and so I'm trying to use the flame command line. However, when I
> > run the command, after a few seconds it aborts,
> > with the simple message "Aborted". I'm running fsl-3.2 on Suse
> 9.1.
> > 3G RAM, 8G swap. The exact same analysis
> > runs just fine if I only do ols (i.e. using the --jols option).
> Any
> > advice would be greatly appreciated.
> >
> > -Tom Johnstone
> >
> > Here is the command I'm using:
> >
> > flame --copefile=copefile --vc=varcopefile --mask=mask --
> > dm=test.mat --tc=test.con --cs=test.grp --ols -v
> > --ld=group_anal_flame
> >
> > And here's the output:
> > Log directory is: group_anal_flame++
> > Setting up:
> > No f contrasts
> > nevs=1
> > ntpts=9
> > ngs=1
> > nvoxels=244117
> > Running:
> > nmaskvoxels=244117
> > njumps = 5000
> > burnin = 500
> > sampleevery = 1
> > nsamples = 4500
> >
> >
> > copefile.hdr I got using avwmerge -t on 9 registered cope images.
>
> > varcopefile.hdr I got with avwmerge -t on the
> > registered varcope images. The mask was created by binarising the
>
> > minimum of all the registered varcopes.
> >
> > Here are my mat/con/grp files:
> >
> > test.con:
> > %! VEST-Waveform File
> > /NumWaves 1
> > /NumContrasts 1
> > /PPheights 0.000000e+00
> >
> > /Matrix
> > 1.000000e+00
> >
> > test.mat:
> > %! VEST-Waveform File
> > /NumWaves 1
> > /NumPoints 9
> > /Skip 0
> > /Custom 0 /study/fMRI_tools/analysis/comp_group_glm/fsl/test
> > /PPheights 0.000000e+00
> >
> > /Matrix
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> > 1.000000e+00
> >
> >
> > test.grp:
> > %! VEST-Waveform File
> > /NumWaves 1
> > /NumPoints 9
> >
> > /Matrix
> > 1
> > 1
> > 1
> > 1
> > 1
> > 1
> > 1
> > 1
> > 1
> >
> >
> > -------------------------------------------------
> > Tom Johnstone
> > Waisman Laboratory for Functional Brain Imaging and Behavior
> > Waisman Center
> > University of Wisconsin-Madison
> > Tel. +1 608 263 2743 Fax. +1 608 265 8737
> > [log in to unmask]
>
>
> --------------------------------------------------------------------
> ----
> ------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, John Radcliffe 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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