Hi - this is a large 4D input file - I guess the resolution is pretty
high... you are either running out of RAM/SWAP, or going over the
single-process job size limit for your platform. You should first check
that you have enough swap. Have you upsampled your data?
Cheers, Steve.
On Tue, 13 Dec 2005, Mike Cohen wrote:
> Hi, FSLers. I have a very simple Feat job, but it keeps crashing and
> I'm not sure why. There are 300 epi images (concatenated into a nii.gz
> file that is 114mb) and one covariate that is entered as a custom one
> entry per volume, not convolved. What's clear from the report.log
> (pasted below) is that it can't find the sigmasquareds file, and this
> file seems not to be created. I've tried rerunning with and without
> prestats steps and registration, and always the same error. Any ideas?
> Thanks in advance..
>
>
>
> Started FEAT at Tue Dec 13 13:06:59 2005 on cohen
> FEAT output is d:/mikeData/testing/mike_dec13/normal/left2.feat
>
> /bin/cp /tmp/feat_LdSJ2c.fsf design.fsf
>
> /usr/local/fsl/bin/feat_model design
> Total original volumes = 300
>
> /usr/local/fsl/bin/avwroi
> d:/mikeData/restingNuac/testing/mike_dec13/normal/rest example_func
> 150 1
>
> /usr/local/fsl/bin/ip
> d:/mikeData/restingNuac/testing/mike_dec13/normal/rest
> filtered_func_data 10 -s 2.54777070064 -m mask -I 10000 -t 20.0 -1 |
> grep THRESHOLD | awk '{ print }' -
> 1000
>
> rm -rf prefiltered_func_data*
>
> /usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 -sp
> /usr/local/fsl/bin/susan_smooth filtered_func_data design.mat
> 1000.000000
> Log directory is: stats
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 2488.68
> sig = 8799
> Spatially smoothing auto corr estimates
> /usr/local/fsl/bin/susan_smooth stats/preSmoothVol 1
> stats/postSmoothVol 5 3D 0 1 stats/epivolume 2933 stats/usanSize
> ................
> rm -rf stats/postSmoothVol* stats/preSmoothVol* stats/usanSize*
> Completed
> Tukey M = 17
> Tukey estimates... Completed
> Completed
> Prewhitening and Computing PEs...
> Percentage done:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,
> 29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,
> 54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,
> 79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
> Saving results...
>
> /usr/local/fsl/bin/contrast_mgr stats design.con
> ** ERROR: nifti_image_read(stats/sigmasquareds): can't open header file
> ** ERROR: nifti_image_open(stats/sigmasquareds): bad header info
> Error: failed to open file stats/sigmasquareds
> Error:: FslGetDim: Null pointer passed for FSLIO
> Rendering using zmin=2.3 zmax=8
>
> mkdir tsplot
>
> /usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot
> ** ERROR: nifti_image_read(./stats/pe1): can't open header file
> ** ERROR: nifti_image_open(./stats/pe1): bad header info
> Error: failed to open file ./stats/pe1
> ERROR: Could not open image ./stats/pe1
> Image Exception : #22 :: Failed to read volume ./stats/pe1
>
> /bin/mkdir reg
>
> /usr/local/fsl/bin/flirt -ref highres -in example_func -out
> example_func2highres -omat example_func2highres.mat -cost corratio
> -dof 6 -schedule /usr/local/fsl/etc/flirtsch/sch3Dtrans_3dof -searchrx
> -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>
> /usr/local/fsl/bin/convert_xfm -matonly -inverse -omat
> highres2example_func.mat example_func2highres.mat
>
> /usr/local/fsl/bin/slicer example_func2highres highres -s 1 -x 0.35
> sla -x 0.45 slb -x 0.55 slc -x 0.65 sld -y 0.35 sle -y 0.45 slf -y
> 0.55 slg -y 0.65 slh -z 0.35 sli -z 0.45 slj -z 0.55 slk -z 0.65 sll ;
> /usr/local/fsl/bin/convert -colors 100 +append sla slb slc sld sle slf
> slg slh sli slj slk sll example_func2highres.gif ; /bin/rm -f sla slb
> slc sld sle slf slg slh sli slj slk sll
> Finished registration at Tue Dec 13 13:35:57 2005
>
> Finished FEAT at Tue Dec 13 13:35:57 2005
> To view the FEAT report point your web browser at
> d:/mikeData/testing/mike_dec13/normal/left2.feat/report.html
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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
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