Progress Report / Log

Started at Mon May 18 12:28:10 EDT 2009

Feat main script


/bin/cp /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/xrun.design.tmp.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 60 -l logs -N feat2_pre   /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat -gfeatprep
11846

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 60 -l logs -N feat3a_flame -j 11846  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat -I 1 -flame1
13922

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 60 -l logs -N feat3b_flame -j 13922 -t ./.flame
14388

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 60 -l logs -N feat3c_flame -j 14388  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat -flame3
14407

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 60 -l logs -N feat4_post -j 14407  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat -poststats 0 1
14471

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 14471  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat -stop
15149

/usr/pubsw/packages/fsl/4.1.2/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 15149  /usr/pubsw/packages/fsl/4.1.2/bin/feat /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat/cope1.feat/design.fsf -D /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert.gfeat -stop

Higher-level input files preparation

/usr/pubsw/packages/fsl/4.1.2/bin/featregapply /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat

/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in example_func -out frgrot_yUGAXR -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in mask -out frgrot_qx5HJu -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in mean_func -out frgrot_PZwz5q -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_W86vqY -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_teFYEv -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/featregapply /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat

/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in example_func -out frgrot_2cGFqj -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in mask -out frgrot_KlzoIY -applyxfm -init reg/example_func2standard.mat -interp nearestneighbour -datatype char


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in mean_func -out frgrot_ssrJFr -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in stats/cope1 -out frgrot_wmnlfX -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/flirt -ref reg/standard -in stats/varcope1 -out frgrot_3D8FWF -applyxfm -init reg/example_func2standard.mat -interp trilinear -datatype float


/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg/standard bg_image

/usr/pubsw/packages/fsl/4.1.2/bin/fslmerge -t mask  /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/mask /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/mask

mkdir -p inputreg

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths ../mask -mul 2 -Tmean masksum -odt short

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths masksum -thr 2 -add masksum masksum

/usr/pubsw/packages/fsl/4.1.2/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 4 masksum_overlay

/usr/pubsw/packages/fsl/4.1.2/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths masksum -mul 0 maskunique

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths masksum -thr 1 -uthr 1 -bin -mul maskunique maskunique

/usr/pubsw/packages/fsl/4.1.2/bin/overlay 0 0 ../bg_image -a maskunique 0.9 2 maskunique_overlay

/usr/pubsw/packages/fsl/4.1.2/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png

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

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

/usr/pubsw/packages/fsl/4.1.2/bin/fslmerge -t mean_func  /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/mean_func /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/mean_func

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

/usr/pubsw/packages/fsl/4.1.2/bin/fslmerge -t cope1  /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/stats/cope1 /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/stats/cope1

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths cope1 -mas mask cope1

printf '0.9794933 ' >> design.lcon

/usr/pubsw/packages/fsl/4.1.2/bin/fslmerge -t varcope1  /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/stats/varcope1 /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/stats/varcope1

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths varcope1 -mas mask varcope1

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/stats/cope1 -mul 0 -add 83   /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/stats/FEtdof_t1

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/stats/cope1 -mul 0 -add 83   /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/stats/FEtdof_t1

/usr/pubsw/packages/fsl/4.1.2/bin/fslmerge -t tdof_t1  /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert1.feat/reg_standard/stats/FEtdof_t1 /autofs/space/crash_002/users/greve/fs-feat/fbert-feat/fbert2.feat/reg_standard/stats/FEtdof_t1

/usr/pubsw/packages/fsl/4.1.2/bin/fslmaths tdof_t1 -mas mask tdof_t1