Hi - very hard to tell what's going on from this much information I'm
afraid. There's no way you can run higher-level FEAT without having
run registration in the lower-level directories, so I'm not sure what
you mean by saying that it ran ok without normalisation....
Can you check carefully the registration summary page linked to from
the higher-level FEAT output web page - that's probably the place to
start if you're concerned about the registrations.
Cheers, Steve.
On 23 Feb 2007, at 23:31, Nicholas Wymbs wrote:
> Hi FSLers,
>
> My first pass with a group analysis was error free but the data I
> was using had yet to be
> normalized. After normalizing datasets for a group analysis, I
> received the following message
> listed below.
>
> I believe the source of the problem to be that the 'mask voxel'
> total is set to 0 but not sure why
> this is so. Also, I was able to run the same analysis when using
> data that was not yet normalized
> without a problem - could this be the product of the altered values
> in the indiviual cope images?
>
> Any advice?
>
> Thanks!
> Nicholas
>
> /Applications/fsl/fsl/bin/flame --cope=filtered_func_data --
> vc=var_filtered_func_data --
> mask=mask --ld=stats --dm=design.mat --cs=design.grp --
> tc=design.con --ols --nj=10000
> --bi=500 --se=1 --fm --zlt=100000 --zut=100000
> Log directory is: stats
> Setting up:
> No f contrasts
> nevs=1
> ntpts=16
> ngs=1
> nvoxels=309223
> Running:
> nmaskvoxels=0
> njumps = 10000
> burnin = 500
> sampleevery = 1
> nsamples = 9500
>
> Metropolis Hasting Sampling
> Number of voxels=0
> Percentage done:
>
> Saving results
>
> Log directory was: stats
>
> echo 15 > stats/dof
>
> /bin/rm -f stats/zem* stats/zols* stats/mask*
>
> /Applications/fsl/fsl/bin/smoothest -d 15 -m mask -r stats/res4d >
> stats/smoothness
> WARNING: Extreme smoothness detected in X - possibly biased global
> estimate.
> WARNING: Extreme smoothness detected in Y - possibly biased global
> estimate.
> WARNING: Extreme smoothness detected in Z - possibly biased global
> estimate.
>
> rm -f stats/res4d*
>
> /Applications/fsl/fsl/bin/avwmaths stats/zstat1 -mas mask
> thresh_zstat1
>
> echo 309223 > thresh_zstat1.vol
> zstat1: DLH=nan VOLUME=309223 RESELS=nan
>
> /Applications/fsl/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -
> t 2.3 -p 0.05 -d nan --
> volume=309223 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --
> connectivity=26 --mm --
> olmax=lmax_zstat1_std.txt > cluster_zstat1_std.txt
>
> /Applications/fsl/fsl/bin/cluster2html . cluster_zstat1 -std
>
> /Applications/fsl/fsl/bin/avwstats thresh_zstat1 -l 0.0001 -R
> 2.300080 9.533768
> Rendering using zmin=2.300080 zmax=9.533768
>
> /Applications/fsl/fsl/bin/overlay 1 0 example_func -a thresh_zstat1
> 2.300080 9.533768
> rendered_thresh_zstat1
>
> /Applications/fsl/fsl/bin/slicer rendered_thresh_zstat1 -S 2 750
> rendered_thresh_zstat1.png
>
> /bin/cp /Applications/fsl/fsl/etc/luts/ramp.gif .ramp.gif
>
> mkdir tsplot
>
> /Applications/fsl/fsl/bin/tsplot . -f filtered_func_data -o tsplot
>
> gnuplot> plot 'tsplot/tsplot_zstat1.txt' using 1 title 'data' with
> lines , 'tsplot/tsplot_zstat1.txt'
> using 2 title 'cope partial model fit' with lines , 'tsplot/
> tsplot_zstat1.txt' using 3 title 'full model fit'
> with lines
>
> ^
> line 0: Can't plot with an empty y range!
>
> convertb: MissingAnImageFilename.
>
> gnuplot> plot 'tsplot/tsplot_zstat1.txt' using 4 title 'reduced
> data' with lines , 'tsplot/
> tsplot_zstat1.txt' using 2 title 'cope partial model fit' with lines
>
> ^
> line 0: Can't plot with an empty y range!
>
> convertb: MissingAnImageFilename.
>
> gnuplot> plot 'tsplot/tsplotc_zstat1.txt' using 1 title 'data' with
> lines , 'tsplot/tsplotc_zstat1.txt'
> using 2 title 'cope partial model fit' with lines , 'tsplot/
> tsplotc_zstat1.txt' using 3 title 'full model
> fit' with lines
>
> ^
> line 0: Can't plot with an empty y range!
>
> convertb: MissingAnImageFilename.
>
> gnuplot> plot 'tsplot/tsplotc_zstat1.txt' using 4 title 'reduced
> data' with lines , 'tsplot/
> tsplotc_zstat1.txt' using 2 title 'cope partial model fit' with lines
>
> ^
> line 0: Can't plot with an empty y range!
>
> convertb: MissingAnImageFilename.
>
> Finished FEAT at Fri Feb 23 15:14:22 PST 2007
> To view the FEAT report point your web browser at
> /Users/nwymbs/Desktop/CI/CI_fMRI/subjects/test+.gfeat/cope1.feat/
> report.html
------------------------------------------------------------------------
---
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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