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
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