Progress Report / Log

Started at Mon May 18 12:21:19 EDT 2009

Feat main script


/bin/cp /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.design.fsf design.fsf

/usr/pubsw/packages/fsl/4.1.2/bin/feat_model design 

mkdir .files;cp /usr/pubsw/packages/fsl/4.1.2/doc/fsl.css .files;ln -s /usr/pubsw/packages/fsl/4.1.2/doc/images .files/images

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 8 -l logs -N feat2_pre   /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat -I 1 -prestats
9312

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 17 -l logs -N feat3_film -j 9312  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat -I 1 -film
9688

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 0 -l logs -N feat4_post -j 9688  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat -poststats 0 0
9836

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 9312  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat -I 1 -reg
10519

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 15 -l logs -N feat4_post -j 9836,10519  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat -poststats 1 0
10729

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 9312,9688,10729,10519  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat -stop
10943

Prestats

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2 prefiltered_func_data -odt float
Total original volumes = 85

/usr/pubsw/packages/fsl/4.1.2/bin/fslroi prefiltered_func_data example_func 42 1

/usr/pubsw/packages/fsl/4.1.2/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 42 -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/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func

/usr/pubsw/packages/fsl/4.1.2/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/pubsw/packages/fsl/4.1.2/bin/immv mask_mask mask

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet

/usr/pubsw/packages/fsl/4.1.2/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 605.544739 

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_bet -thr 60.5544739 -Tmin -bin mask -odt char

/usr/pubsw/packages/fsl/4.1.2/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
488.650024 

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths mask -dilF mask

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/pubsw/packages/fsl/4.1.2/bin/susan prefiltered_func_data_thresh 366.487518 2.12314225053 3 1 1 mean_func 366.487518 prefiltered_func_data_smooth

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_smooth -mul 20.4645441704 prefiltered_func_data_intnorm

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_intnorm -bptf 16.6666666667 -1 prefiltered_func_data_tempfilt

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*

Stats

/usr/pubsw/packages/fsl/4.1.2/bin/film_gls -rn stats -sa -ms 5 filtered_func_data design.mat 1000.0
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=85
paradigm.getDesignMatrix().Ncols()=2
sizeTS=85
numTS=38017
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 10636.7
sig = 623
Spatially smoothing auto corr estimates
........
Completed
Tukey M = 9
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/pubsw/packages/fsl/4.1.2/bin/smoothest -d 83   -m mask -r stats/res4d > stats/smoothness

Post-stats

/usr/pubsw/packages/fsl/4.1.2/bin/contrast_mgr  stats design.con

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1

echo 38017 > thresh_zstat1.vol
zstat1: DLH=1.48697 VOLUME=38017 RESELS=3.12215

/usr/pubsw/packages/fsl/4.1.2/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 1.48697 --volume=38017 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26  --olmax=lmax_zstat1.txt > cluster_zstat1.txt

/usr/pubsw/packages/fsl/4.1.2/bin/cluster2html . cluster_zstat1 

/usr/pubsw/packages/fsl/4.1.2/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null
2.300547 11.353125 
Rendering using zmin=2.300547 zmax=11.353125

/usr/pubsw/packages/fsl/4.1.2/bin/overlay 1 0 example_func -a thresh_zstat1 2.300547 11.353125 rendered_thresh_zstat1

/usr/pubsw/packages/fsl/4.1.2/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png

/bin/cp /usr/pubsw/packages/fsl/4.1.2/etc/luts/ramp.gif .ramp.gif

mkdir -p tsplot ; /usr/pubsw/packages/fsl/4.1.2/bin/tsplot . -f filtered_func_data -o tsplot
zstat1: DLH=1.48697 VOLUME=38017 RESELS=3.12215

/usr/pubsw/packages/fsl/4.1.2/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -d 1.48697 --volume=38017 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt > cluster_zstat1_std.txt

/usr/pubsw/packages/fsl/4.1.2/bin/cluster2html . cluster_zstat1 -std

Registration

/bin/mkdir -p reg

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain standard

/usr/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat

/usr/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/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/pubsw/packages/fsl/4.1.2/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png