Thanks very much! On first-level it works fine, but on second level I
get the message I enclosed below. Any help is much appreciated.

Regards,
Benny
___

Higher-level stats

cat ../design.lcon | awk '{ print  }' > design.lcon
cat: ../design.lcon: No such file or directory
/usr/local/fsl/bin/flameo --cope=filtered_func_data
--vc=var_filtered_func_data  --mask=mask --ld=stats --dm=design.mat
--cs=design.grp --tc=design.con  --runmode=flame1
Image Exception : #22 :: ERROR: Could not open image filtered_func_data



An exception has been thrown
ERROR: Could not open image filtered_func_dataTrace: read_volume4DROI;
Design::setup; Gsmanager::setup.

Log directory is: stats
Setting up:

/bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
Post-stats
child process exited abnormally
    while executing
"if { [ catch {



for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr argin..."
    (file "/usr/local/fsl/bin/feat" line 119)


2012/9/14 Stephen Smith <[log in to unmask]>:
> Hi - it seems that on some OS's there is weird behaviour in the shell - I
> think the following should fix this.  Put the attached file into $FSLDIR/tcl
> Does this work?
> Cheers.
>
>
>
>
>
>
>
> On 14 Sep 2012, at 11:37, Franklin, Crystal G wrote:
>
> I am running it on Mac OS X 10.7.4.
>
> Crsyatl
>
> From: Stephen Smith <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Friday, September 14, 2012 10:31 AM
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: Re: [FSL] Error
>
> Hi - I can't see what might be causing this - FEAT runs fine on your
> setup/data on my computer.
> Which exact OS are you using?   What SGE setup (if any)?
> Cheers.
>
>
>
> On 14 Sep 2012, at 08:25, Franklin, Crystal G wrote:
>
> Has there been any luck determining what is the cause or solution to this
> error?
>
> Thanks,
> Crystal
>
> From: <Franklin>, ric uthscsa <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Tuesday, September 11, 2012 9:51 AM
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: Re: [FSL] Error
>
> I am still getting the same error.  I have uploaded the data.  The reference
> number is 603990.
>
> Thanks,
> Crystal
>
> From: Stephen Smith <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Tuesday, September 11, 2012 1:47 AM
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: Re: [FSL] Error
>
> Hi - did you read in an old design.fsf into the FEAT GUI and run it from
> there (or save it and run from the command-line)?   In general this should
> prepare old designs for running with new FEAT.
>
> If that doesn't help, then please upload the data (see upload link on FSL
> support page on the wiki).
>
> Cheers.
>
>
>
>
> On 10 Sep 2012, at 20:11, Franklin, Crystal G wrote:
>
> Dear FSL,
>
> I installed version 5.0  and I am trying to rerun a previous analysis that
> worked in the older version.  Now when I try running, I get the following
> error in the log:
>
> /bin/cp /tmp/feat_BEPWaM.fsf design.fsf
>
> /usr/local/fsl/bin/feat_model design
>
> mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;ln -s
> /usr/local/fsl/doc/images .files/images
>
> /usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -init
> 10568
>
> /usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat1b_reg -j 10568
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -reg
> 10648
>
> /usr/local/fsl/bin/fsl_sub -T 12 -l logs -N feat2_pre -j 10648,10568
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -prestats
> 11213
>
> /usr/local/fsl/bin/fsl_sub -T 78 -l logs -N feat3_film -j 11213
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -film
> 11548
>
> /usr/local/fsl/bin/fsl_sub -T 0 -l logs -N feat4_post -j 11548
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -poststats 0 0
> child process exited abnormally
>     while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>     switch -- [ lindex $argv $argindex ] {
>
> 	-I {
> 	    incr argin..."
>     (file "/usr/local/fsl/bin/feat" line 119)
>
> /usr/local/fsl/bin/fsl_sub -T 119 -l logs -N feat4_post -j 10648
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -poststats 1 0
> child process exited abnormally
>     while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>     switch -- [ lindex $argv $argindex ] {
>
> 	-I {
> 	    incr argin..."
>     (file "/usr/local/fsl/bin/feat" line 119)
>
> /usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 11213,11548,10648
> /usr/local/fsl/bin/feat
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -stop
>
> /usr/local/fsl/bin/mainfeatreg -d
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -l
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/logs/feat5_reg -R
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_unwarp.html -r
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_reg.html  -i
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/example_func.nii.gz  -h
> /fmri_data/lovallo3_OFHP/EM0135/EM0135_3d_bet -w  6 -x 90 -s
> /fmri_data/lovallo3_OFHP/colinbrain/colinbrain_tlrc_2x2x2 -y 12 -z 180
> Option -d ( output directory ) selected with  argument
> "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat"
> Option -l ( logfile )input with argument
> "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/logs/feat5_reg"
> Option -R ( html unwarping report ) selected with  argument
> "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_unwarp.html"
> Option -r ( html registration report ) selected with  argument
> "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_reg.html"
> Option -i ( main input ) input with argument
> "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/example_func.nii.gz"
> Option -h ( high-res structural image ) selected with  argument
> "/fmri_data/lovallo3_OFHP/EM0135/EM0135_3d_bet"
> Option -w ( highres dof ) selected with  argument "6"
> Option -x ( highres search ) selected with  argument "90"
> Option -s ( standard image ) selected with  argument
> "/fmri_data/lovallo3_OFHP/colinbrain/colinbrain_tlrc_2x2x2"
> Option -y ( standard dof ) selected with  argument "12"
> Option -z ( standard search ) selected with  argument "180"
>
> ________________________________
> Initialisation
>
> /usr/local/fsl/bin/fslmaths /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount
> prefiltered_func_data -odt float
> Total original volumes = 120
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 60 1
>
> ________________________________
> Prestats
>
> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out
> prefiltered_func_data_mcf -mats -plots -reffile example_func -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
>
> /usr/local/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
>
> /usr/local/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
>
> /usr/local/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
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func
>
> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv
> mask_mask mask
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask
> prefiltered_func_data_bet
>
> /usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
> 0.000000 1397.647461
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 139.7647461 -Tmin
> -bin mask -odt char
>
> /usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
> 1017.465332
>
> /usr/local/fsl/bin/fslmaths mask -dilF mask
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask
> prefiltered_func_data_thresh
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
>
> /usr/local/fsl/bin/susan prefiltered_func_data_thresh 763.098999
> 2.12314225053 3 1 1 mean_func 763.098999 prefiltered_func_data_smooth
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask
> prefiltered_func_data_smooth
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 9.82834469686
> prefiltered_func_data_intnorm
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 20.0 -1
> prefiltered_func_data_tempfilt
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt
> filtered_func_data
>
> /usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
>
> /bin/rm -rf prefiltered_func_data*
>
> ________________________________
> Stats
>
> mkdir -p custom_timing_files ; /bin/cp
> /fmri_data/lovallo3_OFHP/designs/discount/discount.txt
> custom_timing_files/ev1.txt
>
> /usr/local/fsl/bin/film_gls -rn stats -sa -ms 5   filtered_func_data
> design.mat 1000.0
> Log directory is: stats
> paradigm.getDesignMatrix().Nrows()=120
> paradigm.getDesignMatrix().Ncols()=2
> sizeTS=120
> numTS=183479
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 9616.25
> sig = 1556
> Spatially smoothing auto corr estimates
> .........
> Completed
> Tukey M = 10
> 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...
> Completed
>
> /usr/local/fsl/bin/smoothest -d 118   -m mask -r stats/res4d >
> stats/smoothness
>
> ________________________________
> Post-stats
>
> /usr/local/fsl/bin/contrast_mgr  stats design.con
> child process exited abnormally
>     while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>     switch -- [ lindex $argv $argindex ] {
>
> 	-I {
> 	    incr argin..."
>     (file "/usr/local/fsl/bin/feat" line 119)
> child process exited abnormally
>     while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>     switch -- [ lindex $argv $argindex ] {
>
> 	-I {
> 	    incr argin..."
>     (file "/usr/local/fsl/bin/feat" line 119)
>
>
> Any idea what could be causing this?
>
>
> Thanks,
>
> Crystal
>
> ________________________________
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>