</pre><hr>Higher-level input files preparation<br><pre>

/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
