Hmmm... I don't know if this problems comes from mixing old first-
level analyses with new second-level maybe (or even if you're doing
that).
If that doesn't sound like a clue then you might need to upload
the .gfeat directory for us to play with.
Cheers, Steve.
On 16 May 2007, at 11:40, Donna Lloyd wrote:
> 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>
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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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