Hi - thanks for the email. The solution is probably quite simple - sorry
for not pointing this out to the email list earlier. Almost immediately
after the latest release went out, we fixed a bug in the GLM program which
would normally only show up if people have volumes with large numbers of
voxels in - quite likely if people have slices bigger than 64*64 but
unlikely otherwise. The release of FSL was corrected for this on June 19 -
so you only just missed getting the right version! Note - this wasn't a
"silent" bug - FEAT will very obviously not finish in this case.
If other people downloaded FSL before this date and are using large images
inside FEAT they probably want to re-download FSL 1.3
Thanks, and sorry for the inconvenience, Steve.
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
On Wed, 29 Aug 2001, Greig de Zubicaray wrote:
> Hi Steve,
>
> I downloaded the new version of FSL and ran into a small problem with one of
> our er-fMRI experiments. I've reproduced the log file below. It looks like
> it might be the same bug in smoothness estimation we had with the earlier
> version due to the image being non-square (I think). Your test data suite
> ran okay. For the record, our acquisition is a 128x64 matrix, FOV is 40x20
> cm, 21 x 5mm thick slices.
>
> Regards,
>
> Greig
>
>
>
> > Started FEAT at Tuesday August 28 18:06:33 EST 2001 on behemoth
> > Total original volumes = 405
> > Deleting 5 volume(s) - BE WARNED for future analysis!
> > /export/home/greig/opt/fsl/bin/avwroi /export/home/greig/jlo_fsl/1/4D_jlo
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data 5 400
> >
> > /export/home/greig/opt/fsl/bin/avwroi
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/example_func 200 1
> >
> > /export/home/greig/opt/fsl/bin/mcflirt -in
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data -out
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data_mcf -plots
> > -refvol 200
> >
> > mv /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data_mcf.par
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par
> >
> > echo "set term pbm color ; set size 1,0.5 ; set title 'MCFLIRT estimated
> > rotations (radians)' ; plot '/export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par'
> > using 1 title 'x' with lines ,
> > '/export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par' using 2 title 'y' with lines
> > , '/export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par' using 3 title 'z' with
> > lines" | /export/home/greig/opt/fsl/bin/gnuplot >
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_rot.ppm
> >
> > /export/home/greig/opt/fsl/bin/convert
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_rot.ppm
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_rot.gif
> >
> > /bin/rm -f /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_rot.ppm
> >
> > echo "set term pbm color ; set size 1,0.5 ; set title 'MCFLIRT estimated
> > translations (mm)' ; plot '/export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par'
> > using 4 title 'x' with lines ,
> > '/export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par' using 5 title 'y' with lines
> > , '/export/home/greig/jlo_fsl/1/4D_jlo.feat/mc.par' using 6 title 'z' with
> > lines" | /export/home/greig/opt/fsl/bin/gnuplot >
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_trans.ppm
> >
> > /export/home/greig/opt/fsl/bin/convert
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_trans.ppm
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_trans.gif
> >
> > /bin/rm -f /export/home/greig/jlo_fsl/1/4D_jlo.feat/mc_trans.ppm
> >
> > /export/home/greig/opt/fsl/bin/betfunc
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data_mcf
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data_bet
> >
> > /export/home/greig/opt/fsl/bin/ip
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data_bet
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/filtered_func_data 10 -s
> > 2.12314225053 -m /export/home/greig/jlo_fsl/1/4D_jlo.feat/mask -I 10000 -t
> > 23.8095238095 -1
> > rm -rf /export/home/greig/jlo_fsl/1/4D_jlo.feat/prefiltered_func_data*
> >
> > /export/home/greig/opt/fsl/bin/film_gls -rn
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats -sa -ms 5 -sp
> > /export/home/greig/opt/fsl/bin/susan_smooth
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/filtered_func_data
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/design.mat 1330.354800
> > Log directory is: /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats
> > Loading image... Completed
> > Applying threshold to Series... Completed
> > Calculating residuals...
> > Completed
> > Estimating residual autocorrelation...
> > Calculating raw AutoCorrs... Completed
> > mode = 12197
> > sig = 1074
> > Spatially smoothing auto corr estimates
> > /export/home/greig/opt/fsl/bin/susan_smooth
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/preSmoothVol 1
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/postSmoothVol 5 3D 0 1
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/epivolume 358
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/usanSize
> > ......................................
> > rm -rf /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/postSmoothVol*
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/preSmoothVol*
> > /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/usanSize*
> > Completed
> > Tukey M = 20
> > Tukey estimates... Completed
> > Completed
> > Prewhitening and Computing PEs...
> > 0.0410953,0.0821907,0.123286,0.164381,0.205477,0.246572,0.287667,0.328763,0.36
> > 9858,0.410953,0.452049,0.493144,0.534239,0.575335,0.61643,0.657525,0.698621,0.
> > 739716,0.780811,0.821907,0.863002,0.904097,0.945193,0.986288,Completed
> > Saving results...
> > Unthresholding Series... Completed
> > Saving image... Completed
> > Thresholding Series... Completed
> > Unthresholding Series... Image error
> > cat: cannot open /export/home/greig/jlo_fsl/1/4D_jlo.feat/stats/dof
> > while executing
> > "exec cat ${FD}/stats/dof "
> > (procedure "feat4:proc" line 265)
> > invoked from within
> > "feat4:proc [ file rootname [ lindex $argv 0 ] ]"
> > (file "/export/home/greig/opt/fsl/bin/feat" line 17)
> --
> Dr Greig de Zubicaray
> Centre for Magnetic Resonance
> The University of Queensland
> Brisbane, QLD 4072
> AUSTRALIA
>
> Tel: +61 (0) 7 3365 4250 [direct]
> +61 (0) 7 3365 4100 [CMR]
> Fax: +61 (0) 7 3365 3833
>
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