/bin/mkdir -p reg

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/fslmaths /corral-repl/utexas/poldracklab/openfmri/shared2//ds052/sub010/anatomy/inplane001_brain initial_highres

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/fslmaths /corral-repl/utexas/poldracklab/openfmri/shared2//ds052/sub010/anatomy/highres001_brain highres

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/fslmaths /work/01329/poldrack/software_lonestar/fsl/data/standard/MNI152_T1_2mm_brain standard

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/flirt -ref initial_highres -in example_func -out example_func2initial_highres -omat example_func2initial_highres.mat -cost corratio -dof 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear  

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -inverse -omat initial_highres2example_func.mat example_func2initial_highres.mat

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer example_func2initial_highres initial_highres -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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_func2initial_highres1.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer initial_highres example_func2initial_highres -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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_func2initial_highres2.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/pngappend example_func2initial_highres1.png - example_func2initial_highres2.png example_func2initial_highres.png; /bin/rm -f sl?.png

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/flirt -ref highres -in initial_highres -out initial_highres2highres -omat initial_highres2highres.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear  

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -inverse -omat highres2initial_highres.mat initial_highres2highres.mat

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer initial_highres2highres highres -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 initial_highres2highres1.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer highres initial_highres2highres -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 initial_highres2highres2.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/pngappend initial_highres2highres1.png - initial_highres2highres2.png initial_highres2highres.png; /bin/rm -f sl?.png

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -omat example_func2highres.mat -concat initial_highres2highres.mat example_func2initial_highres.mat

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/flirt -ref highres -in example_func -out example_func2highres -applyxfm -init example_func2highres.mat -interp trilinear

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer example_func2highres highres -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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_func2highres1.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer highres example_func2highres -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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_func2highres2.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear  

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer highres2standard 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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 highres2standard1.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/slicer standard highres2standard -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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 highres2standard2.png ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear

/corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat

/corral-repl/utexas/poldracklab/software_lonestar/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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 ; /corral-repl/utexas/poldracklab/software_lonestar/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 ; /corral-repl/utexas/poldracklab/software_lonestar/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png