Hi all,
I'm new to FSL and have encountered an issue.
I've been trying to run first level FEAT on scans that have undergone melodic, and had components removed.
Of the 32 i've done so far (one at a time), 14 produced normal outputs while 18 contained errors.
I have no idea why this is happening for some scans but not others (FEAT settings same for each scan).
I've included the output below; the errors seem to come in at the Post Stats stage.
Any help or advice would be greatly appreciated!
Many thanks,
Jason
Progress Report / Log
Started at Fri Jul 15 18:10:40 BST 2011
Feat main script
/bin/cp /tmp/feat_nGa6BW.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 97 -l logs -N feat2_pre -j featModelID /usr/local/fsl/bin/feat /scratch/people/jmt982/1FEATs/f8s2.feat/design.fsf -D /scratch/people/jmt982/1FEATs/f8s2.feat -I 1 -prestats
364993
/usr/local/fsl/bin/fsl_sub -T 1749 -l logs -N feat3_film -j 364993 /usr/local/fsl/bin/feat /scratch/people/jmt982/1FEATs/f8s2.feat/design.fsf -D /scratch/people/jmt982/1FEATs/f8s2.feat -I 1 -film
364994
/usr/local/fsl/bin/fsl_sub -T 27 -l logs -N feat4_post -j 364994 /usr/local/fsl/bin/feat /scratch/people/jmt982/1FEATs/f8s2.feat/design.fsf -D /scratch/people/jmt982/1FEATs/f8s2.feat -poststats 0 0
364995
/usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 364993 /usr/local/fsl/bin/feat /scratch/people/jmt982/1FEATs/f8s2.feat/design.fsf -D /scratch/people/jmt982/1FEATs/f8s2.feat -I 1 -reg
364996
/usr/local/fsl/bin/fsl_sub -T 15 -l logs -N feat4_post -j 364995,364996 /usr/local/fsl/bin/feat /scratch/people/jmt982/1FEATs/f8s2.feat/design.fsf -D /scratch/people/jmt982/1FEATs/f8s2.feat -poststats 1 0
364997
/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 364993,364994,364997,364996 /usr/local/fsl/bin/feat /scratch/people/jmt982/1FEATs/f8s2.feat/design.fsf -D /scratch/people/jmt982/1FEATs/f8s2.feat -stop
364998
Prestats
/usr/local/fsl/bin/fslmaths /scratch/people/jmt982/components_removed/f8s2_filtered prefiltered_func_data -odt float
Total original volumes = 972
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 486 1
/usr/local/fsl/bin/fslmaths prefiltered_func_data filtered_func_data
/usr/local/fsl/bin/fslmaths filtered_func_data -Tmin -bin mask -odt char
/usr/local/fsl/bin/fslstats filtered_func_data -k mask -R | awk '{ print }' -
209.263626
/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 /home/people/jmt982/EVs/1Choctaste.txt custom_timing_files/ev1.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/2Chocpic.txt custom_timing_files/ev2.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/3Choctastepic.txt custom_timing_files/ev3.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/4Strawbtaste.txt custom_timing_files/ev4.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/5Strawbpic.txt custom_timing_files/ev5.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/6Strawbtastepic.txt custom_timing_files/ev6.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/7ControlRinse.txt custom_timing_files/ev7.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/8ControlImage.txt custom_timing_files/ev8.txt
mkdir -p custom_timing_files ; /bin/cp /home/people/jmt982/EVs/9ControlRinseImage.txt custom_timing_files/ev9.txt
cp /scratch/people/jmt982/components_removed/f8s2_filtered_outliers confoundevs.txt
/usr/local/fsl/bin/feat_model design confoundevs.txt
/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 filtered_func_data design.mat 209.263626
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=972
paradigm.getDesignMatrix().Ncols()=157
sizeTS=972
numTS=60974
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 7961.37
sig = 3474
Spatially smoothing auto corr estimates
..............................
Completed
Tukey M = 31
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/smoothest -d 815 -m mask -r stats/res4d > stats/smoothness
Post-stats
/usr/local/fsl/bin/contrast_mgr stats design.con
** ERROR (nifti_image_read): failed to find header file for 'stats/corrections'
** ERROR: nifti_image_open(stats/corrections): bad header info
Error: failed to open file stats/corrections
ERROR: Could not open image stats/corrections
Image Exception : #22 :: Failed to read volume stats/corrections
An exception has been thrown
Failed to read volume stats/correctionsTrace: read_volume4DROI; ContrastMgr::Load; ContrastMgr::run.
child process exited abnormally
while executing
"exec sh -c "${FSLDIR}/bin/remove_ext $cleanedargs" "
(procedure "remove_ext" line 8)
invoked from within
"remove_ext [ lsort -dictionary [ imglob zstat*.* ] ] [ lsort -dictionary [ imglob zfstat*.* ] ] "
(procedure "feat5:proc_poststats" line 51)
invoked from within
"feat5:proc_poststats $RERUNNING $STDSPACE "
("-poststats" arm line 6)
invoked from within
"switch -- [ lindex $argv $argindex ] {
-I {
incr argindex 1
set session [ lindex $argv $argindex ]
}
-D {
incr argindex 1
set..."
("for" body line 2)
invoked from within
"for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr argindex 1
set ses..."
(file "/usr/local/fsl/bin/feat" line 77)
child process exited abnormally
while executing
"exec sh -c "${FSLDIR}/bin/remove_ext $cleanedargs" "
(procedure "remove_ext" line 8)
invoked from within
"remove_ext [ lsort -dictionary [ imglob zstat*.* ] ] [ lsort -dictionary [ imglob zfstat*.* ] ] "
(procedure "feat5:proc_poststats" line 51)
invoked from within
"feat5:proc_poststats $RERUNNING $STDSPACE "
("-poststats" arm line 6)
invoked from within
"switch -- [ lindex $argv $argindex ] {
-I {
incr argindex 1
set session [ lindex $argv $argindex ]
}
-D {
incr argindex 1
set..."
("for" body line 2)
invoked from within
"for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr argindex 1
set ses..."
(file "/usr/local/fsl/bin/feat" line 77)
Registration
/bin/mkdir -p reg
/usr/local/fsl/bin/fslmaths /scratch/people/jmt982/structural/f8/f8_t1 highres
/usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard
/usr/local/fsl/bin/flirt -ref highres -in example_func -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/local/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png
/usr/local/fsl/bin/flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; /usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; /usr/local/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png
/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
/usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/local/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png
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