Hi - yes, this suggests either that you have a memory/swap problem on
the cluster, or maybe more likely a filesystem stability or quota
problem.
Cheers.
On 21 Apr 2008, at 22:11, Ted Yanagihara wrote:
> Recently, I've noticed this intermittent problem when I run prestats
> on our cluster. The end result is either an empty
> filtered_func_data, or the prestats just crashes and I only have
> example_func, but no filtered_func. When I run the same data on my
> local computer, everything works fine. Does this error suggest some
> kind of memory problem on our cluster?
>
> I am pasting the results of the report_log file for the prestats
> section.
>
> Thanks for your help!
>
> ted
>
>
>
> Prestats
>
> Total original volumes = 240
> Deleting 3 volume(s) - BE WARNED for future analysis!
>
> /common/fsl/bin/fslroi /data/tyanagihara/x_ch81/s1/r3/r3
> prefiltered_func_data 3 237
>
> /common/fsl/bin/fslroi prefiltered_func_data example_func 118 1
>
> /common/fsl/bin/mcflirt -in prefiltered_func_data -out
> prefiltered_func_data_mcf -mats -plots -refvol 118 -rmsrel -rmsabs
>
> /bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat
> prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms
> prefiltered_func_data_mcf_abs_mean.rms
> prefiltered_func_data_mcf_rel.rms
> prefiltered_func_data_mcf_rel_mean.rms mc
>
> /common/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t
> 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a
> x,y,z -w 640 -h 144 -o rot.png
>
> /common/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t
> 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a
> x,y,z -w 640 -h 144 -o trans.png
>
> /common/fsl/bin/fsl_tsplot -i
> prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -
> t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a
> absolute,relative -o disp.png
>
> /common/fsl/bin/slicetimer -i prefiltered_func_data_mcf --
> out=prefiltered_func_data_st -r 2 --odd
>
> /common/fsl/bin/bet prefiltered_func_data_st
> prefiltered_func_data_bet -F
> ++ WARNING: nifti_read_buffer(prefiltered_func_data_st.nii.gz):
> data bytes needed = 442368
> data bytes input = 409238
> number missing = 33130 (set to 0)
> ++ WARNING: nifti_read_buffer(prefiltered_func_data_st.nii.gz):
> data bytes needed = 442368
> data bytes input = 409238
> number missing = 33130 (set to 0)
>
> /common/fsl/bin/fslmaths prefiltered_func_data_bet -thrp 10 -Tmin -
> bin mask -odt char
>
> /common/fsl/bin/fslmaths prefiltered_func_data_bet -mas mask
> prefiltered_func_data_bet
>
> /common/fsl/bin/fslmaths mask -kernel gauss 2.12314225053 -fmean
> mask_weight -odt float
>
> /common/fsl/bin/fslmaths prefiltered_func_data_bet -kernel gauss
> 2.12314225053 -fmean -div mask_weight -mas mask filtered_func_data -
> odt float
>
> /common/fsl/bin/fslmaths filtered_func_data -ing 10000
> filtered_func_data -odt float
> ERROR:: Empty mask image
> ERROR:: Empty mask image
> ... <This error is repeated a few hundred times>
> ERROR:: Empty mask image
> ERROR:: Empty mask image
>
> /common/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
>
> /bin/rm -rf prefiltered_func_data*
>
---------------------------------------------------------------------------
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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