Foreach,SetLogName,UnixCommand,UnixCommand,AirResize,AirManualReslice,AirInvert,AirCombine,AirResize,AirInvert,AirAlignlinear,AirAlignwarp,AirManualReslice,AirResize,AirCombine,AirCombinewarp,AirCombinewarp,AirReslicewarp,AirReslicewarp,AirReslice,EndForeach false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false,false Set $ Browse S;Z;C;B;P;T;O;D; PD01;36;25;3;42;1;-11;corr_images; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; A; 1 ; 2 ; 3 ; 4 ; 5 ; 6 ; 7 ; 8 ; 9 ; 10 ; 11 ; 12 ; 13 ; 14 ; 15 ; Add Variable -;A;E;F;G;H;I;J;K;L;M;N;Q;R;U;V;X;Y Remove Variable Add rows Log filename $S/$S_xreg.log Browse Unix command /usr/ccn/pkg/kristi_scripts/makemni.pl -s 1.5 -a $C -z $Z -p $B -o warpfiles Browse true false false 0 true 1 false Unix command mkdir warpfiles reslice_warp Browse false true false 0 false 1 true Input file/directory /pilot/park/$S/$D/func_00002.hdr Browse Output file/directory /pilot/park/warpfiles/$S_func_rz Browse New matrix dim (voxels) XYZ 64 64 $P Origin shift (voxels) XYZ 0 0 $O true true Set new alignment graphically Axis shift (voxels) XYZ 0.0 0.0 0.0 Axis rotation (degrees) roll/pitch/yaw 0.0 0.0 0.0 Axis scale XYZ 1.0 1.0 1.0 false /pilot/park Browse true Input file to reslice /pilot/park/MNI_final.img Browse true /pilot/park/warpfiles/$S_func_rz Browse false Voxel size (mm) XYZ 0.0 0.0 0.0 Dimension (voxels) XYZ 0 0 0 true /pilot/park/warpfiles/$S_shrink1 Browse false /pilot/park Browse Intensity scale-up factor 1.0 false false true Input air file(s);Input air directory;Input air filelist /pilot/park/warpfiles/$S_shrink1.air Browse Air directory/file /pilot/park/warpfiles/$S_grow1.air Browse false true Input air files;Input air directory;Input air filelist /pilot/park/warpfiles/$S_grow1.air;/pilot/park/warpfiles/$S_func_rz.air Browse Output air file /pilot/park/warpfiles/$S_func2struct.air Browse true Input file/directory /pilot/park/structs/$S_strip.img Browse Output file/directory /pilot/park/structs/$S_strip_pad.img Browse New matrix dim (voxels) XYZ 256 256 $P Origin shift (voxels) XYZ 0 0 -$B true true Set new alignment graphically Input air file(s);Input air directory;Input air filelist /pilot/park/structs/$S_strip_pad.air Browse Air directory/file /pilot/park/warpfiles/inv_$S_strip_pad.air Browse false true Image file(s);Image directory;Image filelist /pilot/park/structs/$S_strip_pad.img Browse Standard file /pilot/park/MNI_final.img Browse Air dir /pilot/park/warpfiles/r1$S_strip_pad.air Browse Logs dir /pilot/park/logs/ Browse true Air file(s);Air directory;Air filelist /pilot/park Browse Image directory/file /pilot/park/reslice_warp Browse true r1 true false 1.0 false Image file(s);Image directory;Image filelist /pilot/park Browse Nearest neighbor;Trilinear;Windowed sinc in XY plane;Windowed sinc in XZ plane;Windowed sinc in YZ plane;3-D windowed sinc;3-D windowed scanline sinc;3-D unwindowed scanline sinc;3-D scanline chirp-z;Scanline chirp-z in XY plane with half-window width (voxels) XYZ true false false false false false New matrix dim(voxels) Voxel size(mm) Origin shift(voxels) false Model 3-d Rigid Body (6);3-d Global Rescale (7);3-d Traditional (9);3-d Affine (12);3-d Perspective (15);2-d Rigid Body (23);2-d Global Rescale (24);2-d Affine/Fixed Det (25);2-d Affine (26) Cost Std dev of ratio image;Least squares;Least sq w/ intensity scaling Standard file mask Browse Standard threshold $T Standard file partitions 256 Standard file FWHM X 2.0 Y 2.0 Z 2.0 true Mask file(s);Mask directory;Mask filelist /pilot/park Browse Reslice threshold 500 Reslice file partitions 1 Reslice file FWHM X 0.0 Y 0.0 Z 0.0 false false Sampling init/final/dec 81 1 3 Convergence threshold .001 Repeated iterations 50 Halt after n iterations 5 Alt strategy after m iterations 6 false /pilot/park Browse false /pilot/park Browse true /pilot/park/warpfiles/$S_to_ref.term Browse false /pilot/park Browse false /pilot/park Browse false /pilot/park Browse false Standard Threshold $T false Image file(s);Image directory;Image filelist /pilot/park/structs/$S_strip_pad.img Browse Standard file /pilot/park/MNI_final.img Browse Warp file dir /pilot/park/warpfiles Browse Logs dir /pilot/park/logs Browse true Warp file(s);Warp directory;Warp filelist /pilot/park Browse Image directory/file /pilot/park/reslice_warp Browse true r true false 1.0 false Image file(s);Image directory;Image filelist /pilot/park Browse Nearest neighbor;Trilinear;Windowed sinc in XY plane;Windowed sinc in XZ plane;Windowed sinc in YZ plane;3-D windowed sinc with half-window width (voxels) XYZ false Model 3-d 1st Order Linear (1);3-d 2nd Order Nonlinear (2);3-d 3rd Order Nonlinear (3);3-d 4th Order Nonlinear (4);3-d 5th Order Nonlinear (5);2-d 1st Order Linear (21);2-d 2nd Order Nonlinear (22);2-d 3rd Order Nonlinear (23);2-d 4th Order Nonlinear (24);2-d 5th Order Nonlinear (25) Final model none;3-d 1st Order Linear (1);3-d 2nd Order Nonlinear (2);3-d 3rd Order Nonlinear (3);3-d 4th Order Nonlinear (4);3-d 5th Order Nonlinear (5);2-d 1st Order Linear (21);2-d 2nd Order Nonlinear (22);2-d 3rd Order Nonlinear (23);2-d 4th Order Nonlinear (24);2-d 5th Order Nonlinear (25) Standard file mask Browse Standard threshold $T Standard file FWHM X 0.0 Y 0.0 Z 0.0 true Reslice file mask Browse Reslice threshold $T Reslice file FWHM X 0.0 Y 0.0 Z 0.0 true Sampling init/final/dec 81 1 3 Convergence threshold .0001 Repeated iterations 80 Halt after n iterations 5 Alt strategy after m iterations 6 true /pilot/park/warpfiles/$S_to_ref.term Browse false /home/clark/mostcurrentscripts/guis Browse false /home/clark/mostcurrentscripts/guis Browse false /home/clark/mostcurrentscripts/guis Browse false false Standard Threshold $T false Axis shift (voxels) XYZ 0.0 0.0 0.0 Axis rotation (degrees) roll/pitch/yaw 0.0 0.0 0.0 Axis scale XYZ 1.0 1.0 1.0 false /pilot/park Browse true Input file to reslice /pilot/park/reslice_warp/r$S_strip_pad.img Browse true /pilot/park/warpfiles/$S_func_rz.img Browse false Voxel size (mm) XYZ 0.0 0.0 0.0 Dimension (voxels) XYZ 0 0 0 true /pilot/park/warpfiles/$S_shrink2.air Browse false /pilot/park Browse Intensity scale-up factor 1.0 false false true Input file/directory /pilot/park/warpfiles/$S_func_rz.img Browse Output file/directory /pilot/park/warpfiles/$S_func_unrz.img Browse New matrix dim (voxels) XYZ 64 64 $Z Origin shift (voxels) XYZ 0 0 $B true true Set new alignment graphically Input air files;Input air directory;Input air filelist /pilot/park/warpfiles/$S_func_unrz.air;/pilot/park/warpfiles/$S_shrink2.air Browse Output air file /pilot/park/warpfiles/$S_rstruct2func Browse false Air file /pilot/park/warpfiles/$S_rstruct2func.air Browse Warp file /pilot/park/warpfiles/r$S_strip_pad.warp Browse Air file /pilot/park/warpfiles/$S_func2struct.air Browse Warp file /pilot/park/warpfiles/$S_to_MNI_func.warp Browse true Air file /pilot/park/warpfiles/mystruct2MNIatlas.air Browse Warp file /pilot/park/warpfiles/r$S_strip_pad.warp Browse Air file /pilot/park/warpfiles/$S_func2struct.air Browse Warp file /pilot/park/warpfiles/$S_func2MNIatlas.warp Browse false Warp file(s);Warp directory;Warp filelist /pilot/park/warpfiles/$S_to_MNI_func.warp Browse Image directory/file /pilot/park/$S/func_reslicew Browse true r false false 1.0 true Image file(s);Image directory;Image filelist /pilot/park/$S/$D Browse Nearest neighbor;Trilinear;Windowed sinc in XY plane;Windowed sinc in XZ plane;Windowed sinc in YZ plane;3-D windowed sinc with half-window width (voxels) XYZ Warp file(s);Warp directory;Warp filelist /pilot/park/warpfiles/$S_func2MNIatlas.warp Browse Image directory/file /pilot/park/reslice_warp/r$S_atlas Browse false r true false 1.0 true Image file(s);Image directory;Image filelist /pilot/park/PD01/corr_images/func_00002.img Browse Nearest neighbor;Trilinear;Windowed sinc in XY plane;Windowed sinc in XZ plane;Windowed sinc in YZ plane;3-D windowed sinc with half-window width (voxels) XYZ Air file(s);Air directory;Air filelist /pilot/park/warpfiles/inv_$S_strip_pad.air Browse Image directory/file /pilot/park/reslice_warp/r$S_strip.img Browse false r true false 1.0 true Image file(s);Image directory;Image filelist /pilot/park/reslice_warp/r$S_strip_pad.img Browse Nearest neighbor;Trilinear;Windowed sinc in XY plane;Windowed sinc in XZ plane;Windowed sinc in YZ plane;3-D windowed sinc;3-D windowed scanline sinc;3-D unwindowed scanline sinc;3-D scanline chirp-z;Scanline chirp-z in XY plane with half-window width (voxels) XYZ true false false false false false New matrix dim(voxels) Voxel size(mm) Origin shift(voxels) End foreach loop