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Subject:

Re: Ask help from wei

From:

Stephen Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 26 Jan 2004 05:27:09 +0000

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (194 lines)

Hi - looks like there's either a problem with the input Analyze file image
or the design matrix - if you send us directly a tarfile of the complete
(unfinished)  FEAT output directory we can have a look.

Cheers.


On Wed, 21 Jan 2004, Wei Qiu wrote:

> Hi all,
>
> I went through the login file, It says:
> ****************************************
> vwOpen: Error while opening header!: No such file or directory
> Rendering using zmin=2.3 zmax=8
> ***************************************
>
> Is any people can tell me which headfile it could be?
>
> Thanks!
>
> wei
>
> Started FEAT at Tue Jan 20 12:35:00 EST 2004 on kids
>
> /bin/cp /tmp/feat_WITwRM.fsf design.fsf
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/feat_model design
> Total original volumes = 1478
> Deleting 2 volume(s) - BE WARNED for future analysis!
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/avwroi
> /space/kids/11/users/Kuo_gingiJan162004/bold/023/fmri
> prefiltered_func_data 2 1476
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/avwroi
> prefiltered_func_data example_func 738 1
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/betfunc
> prefiltered_func_data prefiltered_func_data_bet
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/ip
> prefiltered_func_data_bet filtered_func_data 10 -s 4.24628450106 -m mask
> -I 10000 -t 10.0 -1 | grep THRESHOLD | awk '{ print  }' -
> 1000.000000
>
> rm -rf prefiltered_func_data*
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/film_gls -rn
> stats -sa -ms 5 -sp
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/susan_smooth
> filtered_func_data design.mat 1000.000000
> Log directory is: stats
> Loading image... Completed
> Applying threshold to Series... Completed
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 9449.12
> sig = 3952
> Spatially smoothing auto corr estimates
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/susan_smooth
> stats/preSmoothVol 1 stats/postSmoothVol 5 3D 0 1 stats/epivolume 1317
> stats/usanSize
> .....................................
> rm -rf stats/postSmoothVol* stats/preSmoothVol* stats/usanSize*
> Completed
> Tukey M = 38
> 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...
> Unthresholding Series... Completed
> Saving image... Completed
> Thresholding Series... Completed
> Unthresholding Series...
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/contrast_mgr
> stats design.con
> AvwOpen: Error while opening header!: No such file or directory
> Rendering using zmin=2.3 zmax=8
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/tsplot . -f
> filtered_func_data
> Cannot open volume ./stats/pe1.hdr for reading!
>
> mkdir tsplot
>
> /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 highres.hdr highres.img
>
> ln -s /space/kids/11/users/Kuo_gingiJan162004/Struc/005/Stru_brain.hdr
> highres.hdr
>
> ln -s /space/kids/11/users/Kuo_gingiJan162004/Struc/005/Stru_brain.img
> highres.img
>
> /bin/rm -f standard.hdr standard.img
>
> ln -s
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/etc/standard/avg152T1_brain.hdr
> standard.hdr
>
> ln -s
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/etc/standard/avg152T1_brain.img
> standard.img
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/flirt -ref
> highres -in example_func -out example_func2highres -omedx
> example_func2highres.xfm -omat example_func2highres.mat -cost corratio
> -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp
> trilinear
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/convert_xfm
> -matonly -inverse -omat highres2example_func.mat example_func2highres.mat
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/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 ;
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/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
>
> /bin/rm -f example_func2highres.hdr example_func2highres.img
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/flirt -ref
> standard -in highres -out highres2standard -omedx highres2standard.xfm
> -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90
> -searchry -90 90 -searchrz -90 90 -interp trilinear
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/convert_xfm
> -matonly -inverse -omat standard2highres.mat highres2standard.mat
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/slicer
> highres2standard 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 ;
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/convert -colors
> 100 +append sla slb slc sld sle slf slg slh sli slj slk sll
> highres2standard.gif ; /bin/rm -f sla slb slc sld sle slf slg slh sli slj
> slk sll
>
> /bin/rm -f highres2standard.hdr highres2standard.img
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/convert_xfm -ref
> standard -in example_func -omedx example_func2standard.xfm -omat
> example_func2standard.mat -concat highres2standard.mat -middlevol highres
> example_func2highres.mat
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/flirt -ref
> standard -in example_func -out example_func2standard -applyxfm -init
> example_func2standard.mat -interp trilinear
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/bin/convert_xfm
> -matonly -inverse -omat standard2example_func.mat
> example_func2standard.mat
>
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/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 ;
> /autofs/space/lyon_006/pubsw/Linux2/packages/fsl/3.1/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 Jan 21 00:36:18 EST 2004
>
> Finished FEAT at Wed Jan 21 00:36:18 EST 2004
> To view the FEAT report point your web browser at
> /autofs/space/kids_011/users/Kuo_gingiJan162004/bold/023/no_motion_correction.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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