Hi
I suspect you did not change the brain/bg % level to 0 in the misc
tab in feat? If so, the mask will probably be empty, i.e. film never
gets to see any data.
For single time series data you'd always need to switch off film I
think - film uses patial regularisation for the estimation of
autocorrelation coefficients which won't work
Even if you set this the brain/bg threshold 0, there will be some
issues with plotting, though. The easiest to do this is to
(i) create your file (e.g. in matlab)
(ii) create design.mat and design.con in Feat (set up the stats and
save the design)
(iii) run film_gls
film_gls -rn stat -noest data design.mat 0
this creates a new directory 'stat' with results in it
(iv) run contrast_mgr to create the stats images
contrast_mgr stat design.con
I've attached an example set of files which work fine for me
hope this helps
christian
On 24 Jul 2007, at 11:31, Daniel Irlam wrote:
> On 7/24/07, Mark Woolrich <[log in to unmask]> wrote:
> Hi Dan,
>
> What is the error message that film pumps out?
>
>
> Hi Mark
>
> The report.log file shows:
>
> /usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 -sp /usr/local/fsl/
> bin/susan_smooth filtered_func_data design.mat 11453.282478
> Log directory is: stats
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
>
>
> An exception has been thrown
> Logic error:- detected by Newmat: index error: requested index = 1
>
> MatrixType = Rect # Rows = 0; # Cols = 1
> Trace: Histogram::generate; AutoCorrEstimator::spatiallySmooth.
>
> Error: FILM did not complete - it probably ran out of memory
>
> When you run with film prewhitening turned off are you sure that
> all the files are empty - check the stats/zstat files in the feat
> directory and see if the zstat files are empty.
>
> Yes I think so. This is my test:
>
> $ avwstats++ mean_func.nii.gz -V
> 1 27.000000
> $> avwstats++ stats/zstat1.nii.gz -V
> 0 0.000000
>
> It looks like there's nothing produced?
>
> many thanks
>
> Daniel
>
> --
> Daniel Irlam Ph.D
> [log in to unmask]
____
Christian F. Beckmann
University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
[log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
tel: +44 1865 222551 fax: +44 1865 222717
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