Hi - it looks like the output from ip was not successful so film_gls
wasn't happy - this is most likely that you ran out of disk space or
quota?
Can you send us the result of running in the FEAT directory:
ls -l
ls -l stats
thanks :)
On Thu, 24 Apr 2003, Tugan Muftuler wrote:
> Hi,
>
> I sent an inquiry yesterday but for some reason it did not go through.
> Anyway, I am trying it again:
>
> I recently donwloaded FSL both to my Mac with OSX and RedHat 7.3 machines. I
> ran the example data set on both computers and they run without any
> problems. However, when I run an old data of mine on both machines, the one
> on Mac runs smoothly but the same data fails during FEAT analysis on the
> RedHat 7.3 machine. The 3D images are converted from a set of images ran
> under SPM. They are converted to 4D using avwmerge and merging was checked
> with slicer/display. I also checked the headers with avwhd.
>
> I checked all the header infromation, they seem fine on both machines. I
> used slicer/display to make sure that they display correctly on both
> machines. It actually does motion correction on both machines, so there
> should not be a problem with reading the images. I cannot figure out why it
> fails during the stats.
>
> It should not be an installation/configuration problem either, since it runs
> example fmri data in feeds.
>
> My redhat machine is much faster, has bigger memory and a huge hard drive.
> It takes 25-30 minutes on the Mac, so I am certainly inclined to use it on
> the linux box.
>
> So, any inputs to this matter will be greatly appreciated.
>
> Thanks,
>
> Tugan Muftuler
>
>
> Below, I have included the report.log for any clues you might catch.
> Actually, every time I run it, I get the following, which seems unusual:
>
> /home/tugan/fsl/bin/contrast_mgr stats design.con
> AvwOpen: Error while opening header!: No such file or directory
>
> *********************************
> The whole report.log:
>
> Started FEAT at Wed Apr 23 18:39:36 PDT 2003
>
> /bin/mkdir /ric_data1/users/tugan/motor/GG+++.feat
>
> /bin/cp /tmp/feat_TEeG4S.fsf design.fsf
>
> /home/tugan/fsl/bin/feat_model design
>
> Started FEAT at Wed Apr 23 18:39:36 PDT 2003 on amd2.ric.uci.edu
> Total original volumes = 88
> /home/tugan/fsl/bin/avwroi /ric_data1/users/tugan/motor/GG example_func 44 1
>
> /home/tugan/fsl/bin/betfunc /ric_data1/users/tugan/motor/GG
> prefiltered_func_data_bet
>
> /home/tugan/fsl/bin/ip prefiltered_func_data_bet filtered_func_data 10 -s
> 2.12314225053 -m mask -I 10000 -t 16.6666666667 -1 | grep THRESHOLD | awk '{
> print $2 }' -
> 1000.000000
> rm -rf prefiltered_func_data*
>
> /home/tugan/fsl/bin/film_gls -rn stats -sa -ms 5 -sp
> /home/tugan/fsl/bin/susan_smooth filtered_func_data design.mat 1000.000000
> Log directory is: stats
> Loading image...
> /home/tugan/fsl/bin/contrast_mgr stats design.con
> AvwOpen: Error while opening header!: No such file or directory
> Rendering using zmin=2.3 zmax=8
> /home/tugan/fsl/bin/tsplot . -f filtered_func_data
> Cannot open volume ./stats/pe1.hdr for reading!
> mkdir grot; mv *tsplot* grot; mv grot tsplot
> mv: cannot stat `*tsplot*': No such file or directory
> /bin/mkdir reg
>
> /bin/rm -f example_func.hdr example_func.img
>
> ln -s ../example_func.hdr example_func.hdr
>
> ln -s ../example_func.img example_func.img
>
> /bin/rm -f standard.hdr standard.img
>
> ln -s /home/tugan/fsl/etc/standard/avg152T1_brain.hdr standard.hdr
>
> ln -s /home/tugan/fsl/etc/standard/avg152T1_brain.img standard.img
>
> /home/tugan/fsl/bin/flirt -ref standard -in example_func -out
> example_func2standard -omedx example_func2standard.xfm -omat
> example_func2standard.mat -cost corratio -dof 6 -schedule
> /home/tugan/fsl/etc/flirtsch/xyztrans.sch -searchrx -90 90 -searchry -90 90
> -searchrz -90 90 -interp trilinear
>
> /home/tugan/fsl/bin/convert_xfm -matonly -inverse -omat
> standard2example_func.mat example_func2standard.mat
>
> /home/tugan/fsl/bin/slicer example_func2standard standard -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 ;
> /home/tugan/fsl/bin/convert -colors 100 +append sla slb slc sld sle slf slg
> slh sli slj slk sll example_func2standard.gif ; /bin/rm -f sla slb slc sld
> sle slf slg slh sli slj slk sll
>
> /bin/rm -f example_func2standard.hdr example_func2standard.img
>
> Finished registration at Wed Apr 23 18:46:07 PDT 2003
> Finished FEAT at Wed Apr 23 18:46:07 PDT 2003
> To view the FEAT report point your web browser at
> /ric_data1/users/tugan/motor/GG+++.feat/report.html
>
Stephen M. Smith MA DPhil CEng MIEE
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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