Hi Steve,
Thanks for the suggestions. When I ran the varcope a couple of the volumes were noticeably brighter than the rest (over the whole brain, not just CSF). The -Tmean and -Tstd images looked OK; bit brighter at the borders maybe.
I've checked each individual's varcope1. There are a couple I could subjectively say look to have higher intensities at the borders than the rest.
Is this information useful? FWIW, I previously analysed this data with an older of version of FSL, although I only ran Flame 1, and it worked OK.
Cheers, Donna
Dr. Donna Lloyd
Lecturer in Psychology
School of Psychological Sciences
The University of Manchester
Oxford Road
Manchester M13 9PL
U.K.
Tel: +44 (0) 161 275 2573
Fax: +44 (0) 161 275 2685/2588
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith
Sent: 15 May 2007 17:31
To: [log in to unmask]
Subject: Re: varcope problem
Hi Donna,
Could you find the varcope1 and run it as a movie loop in FSLView,
also try things like
avwmaths++ varcope1 -Tmean grot1
avwmaths++ varcope1 -Tstd grot2
and view the grots too.... does that show any problems with the
varcope file?
Cheers.
On 15 May 2007, at 16:49, Donna Lloyd wrote:
> Hi,
>
> I'm trying to run a higher-level Flame 1+2 analysis on some old
> data (fslerrorreport attached). All goes well until it gets to this
> point:
>
> /usr/local/fsl/bin/avwmaths varcope1 -mas mask varcope1
>
> and then it stops. There's no error message, I've checked the
> varcope images and they look OK to me and I've tried a few datasets
> and it stops at the same point on all of them!
>
> Hope you can see where the problem lies. Thanks as always for any
> help,
>
> Donna
>
> Dr. Donna Lloyd
> Lecturer in Psychology
> School of Psychological Sciences
> The University of Manchester
> Oxford Road
> Manchester M13 9PL
> U.K.
> Tel: +44 (0) 161 275 2573
> Fax: +44 (0) 161 275 2685/2588
>
> <fsl_p615lx.gz>
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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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