Feat main script
/bin/cp /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/design.fsf design.fsf /home/paulmc/fsl/fsl-latest//bin/feat_model design mkdir .files;cp /home/paulmc/fsl/fsl-latest//doc/fsl.css .files;cp -r /home/paulmc/fsl/fsl-latest//doc/images .files/images /home/paulmc/fsl/fsl-latest//bin/fsl_sub -T 10 -l logs -N feat0_init /home/paulmc/fsl/fsl-latest//bin/feat /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/design.fsf -D /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat -I 1 -init 518546 /home/paulmc/fsl/fsl-latest//bin/fsl_sub -T 48 -l logs -N feat2_pre -j 518546 /home/paulmc/fsl/fsl-latest//bin/feat /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/design.fsf -D /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat -I 1 -prestats 518675 /home/paulmc/fsl/fsl-latest//bin/fsl_sub -T 2 -l logs -N feat3_film -j 518675 /home/paulmc/fsl/fsl-latest//bin/feat /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/design.fsf -D /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat -I 1 -stats 520464 /home/paulmc/fsl/fsl-latest//bin/fsl_sub -T 119 -l logs -N feat4_post -j 520464 /home/paulmc/fsl/fsl-latest//bin/feat /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/design.fsf -D /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat -poststats 0 520661 /home/paulmc/fsl/fsl-latest//bin/fsl_sub -T 1 -l logs -N feat5_stop -j 518675,520464,520661 /home/paulmc/fsl/fsl-latest//bin/feat /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/design.fsf -D /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat -stop
/home/paulmc/fsl/fsl-latest//bin/fslmaths /tmp/pyfeeds_k0piatu3/feat/fmri prefiltered_func_data -odt float Total original volumes = 180 /home/paulmc/fsl/fsl-latest//bin/fslroi prefiltered_func_data example_func 90 1
/home/paulmc/fsl/fsl-latest//bin/mainfeatreg -F 6.00 -d /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat -l /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/logs/feat2_pre -R /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/report_unwarp.html -r /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/report_reg.html -i /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/example_func.nii.gz -h /tmp/pyfeeds_k0piatu3/feat/structural_brain -w 6 -x 90 -s /home/paulmc/fsl/fsl-latest/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 -c T1_2_MNI152_2mm Option -F ( FEAT version parameter ) selected with argument "6.00" Option -d ( output directory ) selected with argument "/home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat" Option -l ( logfile )input with argument "/home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/logs/feat2_pre" Option -R ( html unwarping report ) selected with argument "/home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/report_unwarp.html" Option -r ( html registration report ) selected with argument "/home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/report_reg.html" Option -i ( main input ) input with argument "/home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/example_func.nii.gz" Option -h ( high-res structural image ) selected with argument "/tmp/pyfeeds_k0piatu3/feat/structural_brain" Option -w ( highres dof ) selected with argument "6" Option -x ( highres search ) selected with argument "90" Option -s ( standard image ) selected with argument "/home/paulmc/fsl/fsl-latest/data/standard/MNI152_T1_2mm_brain" Option -y ( standard dof ) selected with argument "12" Option -z ( standard search ) selected with argument "90" Option -c ( fnirt config ) selected with argument "T1_2_MNI152_2mm"
/bin/mkdir -p /home/paulmc/Projects/fsl/pyfeeds/pyfeeds-out/feat/fmri.feat/reg /home/paulmc/fsl/fsl-latest//bin/fslmaths /tmp/pyfeeds_k0piatu3/feat/structural_brain highres /home/paulmc/fsl/fsl-latest//bin/fslmaths /home/paulmc/fsl/fsl-latest/data/standard/MNI152_T1_2mm_brain standard did not find file: example_func2highres.mat. Generating transform. /home/paulmc/fsl/fsl-latest//bin/flirt -in example_func -ref highres -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear /home/paulmc/fsl/fsl-latest//bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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. /home/paulmc/fsl/fsl-latest//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 /home/paulmc/fsl/fsl-latest//bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png /bin/rm highres2standard1.png /home/paulmc/fsl/fsl-latest//bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat /home/paulmc/fsl/fsl-latest//bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear Found file: example_func2standard.mat. /home/paulmc/fsl/fsl-latest//bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//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 ; /home/paulmc/fsl/fsl-latest//bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png
/home/paulmc/fsl/fsl-latest//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 /home/paulmc/fsl/fsl-latest//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 /home/paulmc/fsl/fsl-latest//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 /home/paulmc/fsl/fsl-latest//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 /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func /home/paulmc/fsl/fsl-latest//bin/bet2 mean_func mask -f 0.3 -n -m; /home/paulmc/fsl/fsl-latest//bin/immv mask_mask mask /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet /home/paulmc/fsl/fsl-latest//bin/fslstats prefiltered_func_data_bet -p 2 -p 98 -0.000000 8933.966797 /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_bet -thr 893.3966796999999 -Tmin -bin mask -odt char /home/paulmc/fsl/fsl-latest//bin/fslstats prefiltered_func_data_mcf -k mask -p 50 6846.291016 /home/paulmc/fsl/fsl-latest//bin/fslmaths mask -dilF mask /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func /home/paulmc/fsl/fsl-latest//bin/susan prefiltered_func_data_thresh 5134.718262 2.1231422505307855 3 1 1 mean_func 5134.718262 prefiltered_func_data_smooth /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_smooth -mul 1.4606448917566726 prefiltered_func_data_intnorm /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_intnorm -bptf 16.666666666666668 -1 -add tempMean prefiltered_func_data_tempfilt /home/paulmc/fsl/fsl-latest//bin/imrm tempMean /home/paulmc/fsl/fsl-latest//bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data /home/paulmc/fsl/fsl-latest//bin/fslhd -x filtered_func_data | sed 's/ dt = .*/ dt = '\''3.0'\''/g' > tmpHeader /home/paulmc/fsl/fsl-latest//bin/fslcreatehd tmpHeader filtered_func_data /bin/rm tmpHeader /home/paulmc/fsl/fsl-latest//bin/fslmaths filtered_func_data -Tmean mean_func /bin/rm -rf prefiltered_func_data*
/home/paulmc/fsl/fsl-latest//bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts Log directory is: stats 180 4 180 19328 Calculating residuals... Completed Estimating residual autocorrelation... Calculating raw AutoCorrs... Completed mode = 10128 sig = 1556 Spatially smoothing auto corr estimates ............ Completed Tukey M = 13 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 /home/paulmc/fsl/fsl-latest//bin/smoothest -d 175 -m mask -r stats/res4d > stats/smoothness
/home/paulmc/fsl/fsl-latest//bin/fslmaths stats/zstat1 -mas mask thresh_zstat1 echo 19328 > thresh_zstat1.vol zstat1: DLH=1.72682 VOLUME=19328 RESELS=2.67917 /home/paulmc/fsl/fsl-latest//bin/fslmaths stats/zstat2 -mas mask thresh_zstat2 echo 19328 > thresh_zstat2.vol zstat2: DLH=1.72682 VOLUME=19328 RESELS=2.67917 /home/paulmc/fsl/fsl-latest//bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1 echo 19328 > thresh_zfstat1.vol zfstat1: DLH=1.72682 VOLUME=19328 RESELS=2.67917 /home/paulmc/fsl/fsl-latest//bin/fsl-cluster -i thresh_zstat1 -t 2.3 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -p 0.01 -d 1.72682 --volume=19328 -c stats/cope1 > cluster_zstat1.txt /home/paulmc/fsl/fsl-latest//bin/cluster2html . cluster_zstat1 /home/paulmc/fsl/fsl-latest//bin/fsl-cluster -i thresh_zstat2 -t 2.3 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z -p 0.01 -d 1.72682 --volume=19328 -c stats/cope2 > cluster_zstat2.txt /home/paulmc/fsl/fsl-latest//bin/cluster2html . cluster_zstat2 /home/paulmc/fsl/fsl-latest//bin/fsl-cluster -i thresh_zfstat1 -t 2.3 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z -p 0.01 -d 1.72682 --volume=19328 > cluster_zfstat1.txt /home/paulmc/fsl/fsl-latest//bin/cluster2html . cluster_zfstat1 /home/paulmc/fsl/fsl-latest//bin/fsl-cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.01 -d 1.72682 --volume=19328 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt /home/paulmc/fsl/fsl-latest//bin/cluster2html . cluster_zstat1 -std /home/paulmc/fsl/fsl-latest//bin/fsl-cluster -i thresh_zstat2 -c stats/cope2 -t 2.3 -p 0.01 -d 1.72682 --volume=19328 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat2_std.txt --scalarname=Z > cluster_zstat2_std.txt /home/paulmc/fsl/fsl-latest//bin/cluster2html . cluster_zstat2 -std /home/paulmc/fsl/fsl-latest//bin/fsl-cluster -i thresh_zfstat1 -t 2.3 -p 0.01 -d 1.72682 --volume=19328 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat1_std.txt --scalarname=Z > cluster_zfstat1_std.txt /home/paulmc/fsl/fsl-latest//bin/cluster2html . cluster_zfstat1 -std /home/paulmc/fsl/fsl-latest//bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null 2.302927 16.298498 /home/paulmc/fsl/fsl-latest//bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null 2.300793 17.601126 /home/paulmc/fsl/fsl-latest//bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null 2.300243 17.410551 Rendering using zmin=2.300243 zmax=17.601126 /home/paulmc/fsl/fsl-latest//bin/overlay 1 0 example_func -a thresh_zstat1 2.300243 17.601126 rendered_thresh_zstat1 /home/paulmc/fsl/fsl-latest//bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png /bin/cp /home/paulmc/fsl/fsl-latest//etc/luts/ramp.gif .ramp.gif /home/paulmc/fsl/fsl-latest//bin/overlay 1 0 example_func -a thresh_zstat2 2.300243 17.601126 rendered_thresh_zstat2 /home/paulmc/fsl/fsl-latest//bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png /home/paulmc/fsl/fsl-latest//bin/overlay 1 0 example_func -a thresh_zfstat1 2.300243 17.601126 rendered_thresh_zfstat1 /home/paulmc/fsl/fsl-latest//bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png mkdir -p tsplot ; /home/paulmc/fsl/fsl-latest//bin/tsplot . -f filtered_func_data -o tsplot