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Thanks Steve and Matthew, File: r3.nii.gz Ref # 627857 After the third try, this run just completed and has generated a normal filtered_func_data. Our sys admin has started looking into a possible memory problem. ted On Apr 22, 2008, at 6:46 AM, Matthew Webster wrote: > Hi, > Do you know if your input data has/had an extension removed at > some point - it looks like that could be the problem with the > missing bytes? If you upload your input data (/data/tyanagihara/ > x_ch81/s1/r3/r3)? to > > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi > > and let us know the 6-digit reference number, we would be happy to > look over your data.. > > Many Regards > > Matthew > >> 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* >> >