Feat main script
/bin/cp /data/project/studyforrest_ppa/sub-20/run-3_1st_audio-ppa-grp.fsf design.fsf /usr/share/fsl/5.0/bin/feat_model design Warning: at least one EV is (close to) a linear combination of the others. You probably need to alter your design. (Design matrix is rank deficient - ratio of min:max eigenvalues in SVD of matrix is 5.73733e-18) Contrasts involving these combinations will be set to zero. mkdir .files;cp /usr/share/fsl/5.0/doc/fsl.css .files;cp -r /usr/share/fsl/5.0/doc/images .files/images /usr/share/fsl/5.0/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat -I 1 -init 1813 /usr/share/fsl/5.0/bin/fsl_sub -T 111 -l logs -N feat2_pre -j 1813 /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat -I 1 -prestats 2923 /usr/share/fsl/5.0/bin/fsl_sub -T 247 -l logs -N feat3_film -j 2923 /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat -I 1 -stats 17297 /usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j 17297 /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat -poststats 0 14492 /usr/share/fsl/5.0/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 2923,17297,14492 /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-20/run-3_audio-ppa-grp.feat -stop 2330
/usr/share/fsl/5.0/bin/fslmaths /data/project/studyforrest_ppa/inputs/studyforrest-data-aligned/sub-20/in_bold3Tp2/sub-20_task-aomovie_run-3_bold prefiltered_func_data -odt float Total original volumes = 438 /usr/share/fsl/5.0/bin/fslroi prefiltered_func_data example_func 219 1
/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -Tmean mean_func /usr/share/fsl/5.0/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/share/fsl/5.0/bin/immv mask_mask mask /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_bet /usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_bet -p 2 -p 98 0.000000 727.000000 /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_bet -thr 72.7 -Tmin -bin mask -odt char /usr/share/fsl/5.0/bin/fslstats prefiltered_func_data -k mask -p 50 485.000000 /usr/share/fsl/5.0/bin/fslmaths mask -dilF mask /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_thresh /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func /usr/share/fsl/5.0/bin/susan prefiltered_func_data_thresh 363.75 1.6985138004246285 3 1 1 mean_func 363.75 prefiltered_func_data_smooth /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mul 20.61855670103093 prefiltered_func_data_intnorm /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -bptf 37.5 -1 -add tempMean prefiltered_func_data_tempfilt /usr/share/fsl/5.0/bin/imrm tempMean /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data /usr/share/fsl/5.0/bin/fslmaths filtered_func_data -Tmean mean_func /bin/rm -rf prefiltered_func_data*
mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/body.txt custom_timing_files/ev1.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/bpart.txt custom_timing_files/ev2.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/fahead.txt custom_timing_files/ev3.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/furn.txt custom_timing_files/ev4.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/geo.txt custom_timing_files/ev5.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/groom.txt custom_timing_files/ev6.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/obj.txt custom_timing_files/ev7.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/se_new.txt custom_timing_files/ev8.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/se_old.txt custom_timing_files/ev9.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/sex_f.txt custom_timing_files/ev10.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/sex_m.txt custom_timing_files/ev11.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/vse_new.txt custom_timing_files/ev12.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/vse_old.txt custom_timing_files/ev13.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/vlo_ch.txt custom_timing_files/ev14.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/vpe_new.txt custom_timing_files/ev15.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/fg_ad_lrdiff.txt custom_timing_files/ev17.txt mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-20/onsets/aomovie/run-3/fg_ad_rms.txt custom_timing_files/ev18.txt paste -d ' ' /data/project/studyforrest_ppa/inputs/phase1/sub020/BOLD/task001_run003/bold_dico_moco.txt > confoundevs.txt /usr/share/fsl/5.0/bin/feat_model design confoundevs.txt Warning: at least one EV is (close to) a linear combination of the others. You probably need to alter your design. (Design matrix is rank deficient - ratio of min:max eigenvalues in SVD of matrix is 6.19318e-18) Contrasts involving these combinations will be set to zero. /usr/share/fsl/5.0/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con Log directory is: stats paradigm.getDesignMatrix().Nrows()=438 paradigm.getDesignMatrix().Ncols()=42 sizeTS=438 numTS=63811 Calculating residuals... Completed Estimating residual autocorrelation... Calculating raw AutoCorrs... Completed mode = 10175.8 sig = 2396 Spatially smoothing auto corr estimates ................... Completed Tukey M = 20 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/share/fsl/5.0/bin/smoothest -d 396 -m mask -r stats/res4d > stats/smoothness
/usr/share/fsl/5.0/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1 echo 63811 > thresh_zstat1.vol zstat1: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2 echo 63811 > thresh_zstat2.vol zstat2: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3 echo 63811 > thresh_zstat3.vol zstat3: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat4 -mas mask thresh_zstat4 echo 63811 > thresh_zstat4.vol zstat4: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat5 -mas mask thresh_zstat5 echo 63811 > thresh_zstat5.vol zstat5: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat6 -mas mask thresh_zstat6 echo 63811 > thresh_zstat6.vol zstat6: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat7 -mas mask thresh_zstat7 echo 63811 > thresh_zstat7.vol zstat7: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat8 -mas mask thresh_zstat8 echo 63811 > thresh_zstat8.vol zstat8: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat9 -mas mask thresh_zstat9 echo 63811 > thresh_zstat9.vol zstat9: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat10 -mas mask thresh_zstat10 echo 63811 > thresh_zstat10.vol zstat10: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat11 -mas mask thresh_zstat11 echo 63811 > thresh_zstat11.vol zstat11: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat12 -mas mask thresh_zstat12 echo 63811 > thresh_zstat12.vol zstat12: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/fslmaths stats/zstat13 -mas mask thresh_zstat13 echo 63811 > thresh_zstat13.vol zstat13: DLH=0.286124 VOLUME=63811 RESELS=16.1462 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat1 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z > cluster_zstat2.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat2 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat3 -c stats/cope3 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z > cluster_zstat3.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat3 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat4 -c stats/cope4 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26 --olmax=lmax_zstat4.txt --scalarname=Z > cluster_zstat4.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat4 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat5 -c stats/cope5 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26 --olmax=lmax_zstat5.txt --scalarname=Z > cluster_zstat5.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat5 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat6 -c stats/cope6 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26 --olmax=lmax_zstat6.txt --scalarname=Z > cluster_zstat6.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat6 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat7 -c stats/cope7 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat7 -o cluster_mask_zstat7 --connectivity=26 --olmax=lmax_zstat7.txt --scalarname=Z > cluster_zstat7.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat7 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat8 -c stats/cope8 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat8 -o cluster_mask_zstat8 --connectivity=26 --olmax=lmax_zstat8.txt --scalarname=Z > cluster_zstat8.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat8 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat9 -c stats/cope9 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat9 -o cluster_mask_zstat9 --connectivity=26 --olmax=lmax_zstat9.txt --scalarname=Z > cluster_zstat9.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat9 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat10 -c stats/cope10 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat10 -o cluster_mask_zstat10 --connectivity=26 --olmax=lmax_zstat10.txt --scalarname=Z > cluster_zstat10.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat10 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat11 -c stats/cope11 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat11 -o cluster_mask_zstat11 --connectivity=26 --olmax=lmax_zstat11.txt --scalarname=Z > cluster_zstat11.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat11 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat12 -c stats/cope12 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat12 -o cluster_mask_zstat12 --connectivity=26 --olmax=lmax_zstat12.txt --scalarname=Z > cluster_zstat12.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat12 /usr/share/fsl/5.0/bin/cluster -i thresh_zstat13 -c stats/cope13 -t 3.4 -p 0.05 -d 0.286124 --volume=63811 --othresh=thresh_zstat13 -o cluster_mask_zstat13 --connectivity=26 --olmax=lmax_zstat13.txt --scalarname=Z > cluster_zstat13.txt /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat13 /usr/share/fsl/5.0/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null 3.474420 4.416855 /usr/share/fsl/5.0/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null 3.400314 5.460175 /usr/share/fsl/5.0/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat4 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat5 -l 0.0001 -R 2>/dev/null 3.403006 5.082434 /usr/share/fsl/5.0/bin/fslstats thresh_zstat6 -l 0.0001 -R 2>/dev/null 3.408556 4.404272 /usr/share/fsl/5.0/bin/fslstats thresh_zstat7 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat8 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat9 -l 0.0001 -R 2>/dev/null 3.403376 4.254945 /usr/share/fsl/5.0/bin/fslstats thresh_zstat10 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat11 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat12 -l 0.0001 -R 2>/dev/null 0.000000 0.000000 /usr/share/fsl/5.0/bin/fslstats thresh_zstat13 -l 0.0001 -R 2>/dev/null 3.475024 4.786578 Rendering using zmin=3.400314 zmax=5.460175 /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat1 3.400314 5.460175 rendered_thresh_zstat1 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png /bin/cp /usr/share/fsl/5.0/etc/luts/ramp.gif .ramp.gif /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat2 3.400314 5.460175 rendered_thresh_zstat2 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat3 3.400314 5.460175 rendered_thresh_zstat3 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat3 -A 750 rendered_thresh_zstat3.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat4 3.400314 5.460175 rendered_thresh_zstat4 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat4 -A 750 rendered_thresh_zstat4.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat5 3.400314 5.460175 rendered_thresh_zstat5 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat5 -A 750 rendered_thresh_zstat5.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat6 3.400314 5.460175 rendered_thresh_zstat6 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat6 -A 750 rendered_thresh_zstat6.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat7 3.400314 5.460175 rendered_thresh_zstat7 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat7 -A 750 rendered_thresh_zstat7.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat8 3.400314 5.460175 rendered_thresh_zstat8 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat8 -A 750 rendered_thresh_zstat8.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat9 3.400314 5.460175 rendered_thresh_zstat9 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat9 -A 750 rendered_thresh_zstat9.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat10 3.400314 5.460175 rendered_thresh_zstat10 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat10 -A 750 rendered_thresh_zstat10.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat11 3.400314 5.460175 rendered_thresh_zstat11 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat11 -A 750 rendered_thresh_zstat11.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat12 3.400314 5.460175 rendered_thresh_zstat12 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat12 -A 750 rendered_thresh_zstat12.png /usr/share/fsl/5.0/bin/overlay 1 0 example_func -a thresh_zstat13 3.400314 5.460175 rendered_thresh_zstat13 /usr/share/fsl/5.0/bin/slicer rendered_thresh_zstat13 -A 750 rendered_thresh_zstat13.png mkdir -p tsplot ; /usr/share/fsl/5.0/bin/tsplot . -f filtered_func_data -o tsplot