Feat main script
/bin/cp /tmp/feat_oACTKf.fsf design.fsf
/usr/local/fsl/bin/feat_model design
mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;cp -r /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 /Users/u4307082/Desktop/edithd/PID_nonan.feat/design.fsf -D /Users/u4307082/Desktop/edithd/PID_nonan.feat -I 1 -init
8784
/usr/local/fsl/bin/fsl_sub -T 360 -l logs -N feat2_pre -j 8784 /usr/local/fsl/bin/feat /Users/u4307082/Desktop/edithd/PID_nonan.feat/design.fsf -D /Users/u4307082/Desktop/edithd/PID_nonan.feat -I 1 -prestats
child killed: segmentation violation
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr arginde..."
(file "/usr/local/fsl/bin/feat" line 309)
FATAL ERROR ENCOUNTERED:
COMMAND:
/usr/local/fsl/bin/fsl_sub -T 360 -l logs -N feat2_pre -j 8784 /usr/local/fsl/bin/feat /Users/u4307082/Desktop/edithd/PID_nonan.feat/design.fsf -D /Users/u4307082/Desktop/edithd/PID_nonan.feat -I 1 -prestats
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE
/usr/local/fsl/bin/fslmaths /Users/u4307082/Desktop/edithd/PID_nonan prefiltered_func_data -odt float Total original volumes = 250 /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 125 1
/usr/local/fsl/bin/mainfeatreg -F 6.00 -d /Users/u4307082/Desktop/edithd/PID_nonan.feat -l /Users/u4307082/Desktop/edithd/PID_nonan.feat/logs/feat2_pre -R /Users/u4307082/Desktop/edithd/PID_nonan.feat/report_unwarp.html -r /Users/u4307082/Desktop/edithd/PID_nonan.feat/report_reg.html -i /Users/u4307082/Desktop/edithd/PID_nonan.feat/example_func.nii.gz -n 10 -h /Users/u4307082/Desktop/edithd/STRUC_brain -w BBR -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 Option -F ( FEAT version parameter ) selected with argument "6.00" Option -d ( output directory ) selected with argument "/Users/u4307082/Desktop/edithd/PID_nonan.feat" Option -l ( logfile )input with argument "/Users/u4307082/Desktop/edithd/PID_nonan.feat/logs/feat2_pre" Option -R ( html unwarping report ) selected with argument "/Users/u4307082/Desktop/edithd/PID_nonan.feat/report_unwarp.html" Option -r ( html registration report ) selected with argument "/Users/u4307082/Desktop/edithd/PID_nonan.feat/report_reg.html" Option -i ( main input ) input with argument "/Users/u4307082/Desktop/edithd/PID_nonan.feat/example_func.nii.gz" Option -n ( use nonlinear reg ) input with argument "10" Option -h ( high-res structural image ) selected with argument "/Users/u4307082/Desktop/edithd/STRUC_brain" Option -w ( highres dof ) selected with argument "BBR" Option -x ( highres search ) selected with argument "90" Option -s ( standard image ) selected with argument "/usr/local/fsl/data/standard/MNI152_T1_2mm_brain" Option -y ( standard dof ) selected with argument "12" Option -z ( standard search ) selected with argument "90"
/bin/mkdir -p /Users/u4307082/Desktop/edithd/PID_nonan.feat/reg /usr/local/fsl/bin/fslmaths /Users/u4307082/Desktop/edithd/STRUC_brain highres /usr/local/fsl/bin/fslmaths /Users/u4307082/Desktop/edithd/STRUC highres_head Checking for /Users/u4307082/Desktop/edithd/STRUC_brain2MNI152_T1_2mm_brain_warp and /Users/u4307082/Desktop/edithd/STRUC_brain2MNI152_T1_2mm_brain.mat /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm standard_head /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil standard_mask did not find file: example_func2highres.mat. Generating transform. /usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres Running FAST segmentation FLIRT pre-alignment Running BBR 1.015752 -0.054735 0.424904 0.903582 0.000000 0.032705 -0.903690 0.426936 0.000000 0.997965 0.052920 0.035567 0.000000 50.843199 212.487335 -53.874050 1.000000 /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 example_func2highres2.png /bin/rm example_func2highres1.png did not find file: highres2standard.mat. Generating transform. /usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear /usr/local/fsl/bin/fnirt --iout=highres2standard_head --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2highres_jac --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --warpres=10,10,10 /usr/local/fsl/bin/applywarp -i highres -r standard -o highres2standard -w highres2standard_warp /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 highres2standard2.png /bin/rm highres2standard1.png /usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat /usr/local/fsl/bin/convertwarp --ref=standard --premat=example_func2highres.mat --warp1=highres2standard_warp --out=example_func2standard_warp /usr/local/fsl/bin/applywarp --ref=standard --in=example_func --out=example_func2standard --warp=example_func2standard_warp /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 example_func2standard2.png
/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final
/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
-58.854519 59.754414
/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr -46.9936257 -Tmin -bin mask -odt char
/usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
0.000000
/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 44.14088925 2.12314225053 3 1 1 mean_func 44.14088925 prefiltered_func_data_smooth
FATAL ERROR ENCOUNTERED:
COMMAND:
/usr/local/fsl/bin/susan prefiltered_func_data_thresh 44.14088925 2.12314225053 3 1 1 mean_func 44.14088925 prefiltered_func_data_smooth
ERROR MESSAGE:
child killed: segmentation violation
END OF ERROR MESSAGE
child killed: segmentation violation
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr arginde..."
(file "/usr/local/fsl/bin/feat" line 309)
Error encountered while running in main feat script, halting.
child killed: segmentation violation