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*
