Feat main script
/bin/cp /tmp/feat_oFdWnj.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 20 -l logs -N feat2_pre -j featModelID /usr/local/fsl/bin/feat /Users/chris/demo/event/eventfmri.feat/design.fsf -D /Users/chris/demo/event/eventfmri.feat -I 1 -prestats 36450 /usr/local/fsl/bin/fsl_sub -T 120 -l logs -N feat3_film -j 36450 /usr/local/fsl/bin/feat /Users/chris/demo/event/eventfmri.feat/design.fsf -D /Users/chris/demo/event/eventfmri.feat -I 1 -film 36872 /usr/local/fsl/bin/fsl_sub -T 3 -l logs -N feat4_post -j 36872 /usr/local/fsl/bin/feat /Users/chris/demo/event/eventfmri.feat/design.fsf -D /Users/chris/demo/event/eventfmri.feat -poststats 0 0 37046 /usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 36450 /usr/local/fsl/bin/feat /Users/chris/demo/event/eventfmri.feat/design.fsf -D /Users/chris/demo/event/eventfmri.feat -I 1 -reg 37913 /usr/local/fsl/bin/fsl_sub -T 15 -l logs -N feat4_post -j 37046,37913 /usr/local/fsl/bin/feat /Users/chris/demo/event/eventfmri.feat/design.fsf -D /Users/chris/demo/event/eventfmri.feat -poststats 1 0 38121 /usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 36450,36872,38121,37913 /usr/local/fsl/bin/feat /Users/chris/demo/event/eventfmri.feat/design.fsf -D /Users/chris/demo/event/eventfmri.feat -stop
/usr/local/fsl/bin/fslmaths /Users/chris/demo/event/eventfmri prefiltered_func_data -odt float Total original volumes = 200 Deleting 1 volume(s) - BE WARNED for future analysis! /usr/local/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 1 199 /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 99 1 /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 99 -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 1182.150269 /usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 118.2150269 -Tmin -bin mask -odt char /usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50 876.384705 /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 657.28852875 3.39702760085 3 1 1 mean_func 657.28852875 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 11.4105140619 prefiltered_func_data_intnorm /usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 16.6666666667 -1 prefiltered_func_data_tempfilt /usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data /usr/local/fsl/bin/fslhd -x filtered_func_data | sed 's/ dt = .*/ dt = '3.0'/g' > grot cat grot | /usr/local/fsl/bin/fslcreatehd - filtered_func_data /bin/rm grot /usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func /bin/rm -rf prefiltered_func_data*
mkdir -p custom_timing_files ; /bin/cp /Users/chris/demo/event/onsetL_1dummy.txt custom_timing_files/ev1.txt mkdir -p custom_timing_files ; /bin/cp /Users/chris/demo/event/onsetR_1dummy.txt custom_timing_files/ev2.txt mkdir -p custom_timing_files ; /bin/cp /Users/chris/demo/event/onsetU_1dummy.txt custom_timing_files/ev3.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()=199 paradigm.getDesignMatrix().Ncols()=6 sizeTS=199 numTS=64713 Calculating residuals... Completed Estimating residual autocorrelation... Calculating raw AutoCorrs... Completed mode = 10213.8 sig = 863 Spatially smoothing auto corr estimates ............. Completed Tukey M = 14 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 193 -m mask -r stats/res4d > stats/smoothness
/usr/local/fsl/bin/contrast_mgr stats design.con /usr/local/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1 echo 64713 > thresh_zstat1.vol zstat1: DLH=0.0779672 VOLUME=64713 RESELS=59.3195 /usr/local/fsl/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2 echo 64713 > thresh_zstat2.vol zstat2: DLH=0.0779672 VOLUME=64713 RESELS=59.3195 /usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.0779672 --volume=64713 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt > cluster_zstat1.txt /usr/local/fsl/bin/cluster2html . cluster_zstat1 /usr/local/fsl/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 2.3 -p 0.05 -d 0.0779672 --volume=64713 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt > cluster_zstat2.txt /usr/local/fsl/bin/cluster2html . cluster_zstat2 /usr/local/fsl/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null 2.300474 6.344453 /usr/local/fsl/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null 2.301164 8.059585 Rendering using zmin=2.300474 zmax=8.059585 /usr/local/fsl/bin/overlay 1 0 example_func -a thresh_zstat1 2.300474 8.059585 rendered_thresh_zstat1 /usr/local/fsl/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png /bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif /usr/local/fsl/bin/overlay 1 0 example_func -a thresh_zstat2 2.300474 8.059585 rendered_thresh_zstat2 /usr/local/fsl/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png mkdir -p tsplot ; /usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot zstat1: DLH=0.0779672 VOLUME=64713 RESELS=59.3195 zstat2: DLH=0.0779672 VOLUME=64713 RESELS=59.3195 /usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -d 0.0779672 --volume=64713 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt > cluster_zstat1_std.txt /usr/local/fsl/bin/cluster2html . cluster_zstat1 -std /usr/local/fsl/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 2.3 -d 0.0779672 --volume=64713 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat2_std.txt > cluster_zstat2_std.txt /usr/local/fsl/bin/cluster2html . cluster_zstat2 -std
/bin/mkdir -p reg /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard /usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -omat example_func2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -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