Hi Steve,
For information in case anyone else runs into this problem, it seems likely that there may have been an incompatibility issue between old first-level data being entered into a new second level analysis as re-running first-level post stats has solved the problem.
Thanks again for all your 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
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith
Sent: 16 May 2007 13:38
To: [log in to unmask]
Subject: Re: varcope problem
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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