Foreach,UnixCommand,AirAlignlinear,AirManualReslice,AirManualReslice,AirInvert,AirCombine,Reslice,Nisnorm,AirSmooth,EndForeach false,false,false,false,false,false,false,false,false,false,false false,false,false,false,false,false,false,false,false,false,false Set $ rlJ024 Browse S;F;A;R;B;V;Z;Y;P;Q;T;E; rlJ024;air_images;structs;ref17;_strip;3.75;3.8;36;8;16;1000;3.8; rlJ005;detrended;structs;ref17;_strip;3.75;3.8;36;8;16;1000;3.8; rlJ006;detrended;structs;ref17;_strip;3.75;3.8;36;8;16;1000;3.8; rlJ007;detrended;structs;ref17;_strip;3.75;3.8;36;8;16;1000;3.8; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; A; 1 ; 2 ; 3 ; 4 ; 5 ; 6 ; 7 ; 8 ; 9 ; 10 ; 11 ; 12 ; 13 ; 14 ; 15 ; Add Variable -;H;I;J;K;L;M;N;O;U;X;G;C;D Remove Variable Add rows Unix command mkdir $A/airfiles $A/resliced $A/shrunken Browse true false false 0 false 1 true Image file(s);Image directory;Image filelist /rl/imaging/kate/$A/$S$B.img Browse Standard file /rl/imaging/kate/$A/$R$B.img Browse Air dir /rl/imaging/kate/$A/airfiles Browse Logs dir /rl/imaging/kate/$A/gtlogs/ Browse true Air file(s);Air directory;Air filelist /rl/imaging/kate Browse Image directory/file /rl/imaging/kate/$A/resliced/r$S$B Browse true r false false 1.0 false Image file(s);Image directory;Image filelist /rl/imaging/kate 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 20 Standard file partitions 1 Standard file FWHM X 4.0 Y 4.0 Z 4.0 true Mask file(s);Mask directory;Mask filelist /rl/imaging/kate Browse Reslice threshold 500 Reslice file partitions 1 Reslice file FWHM X 0.0 Y 0.0 Z 0.0 false true Sampling init/final/dec 81 1 3 Convergence threshold .01 Repeated iterations 25 Halt after n iterations 5 Alt strategy after m iterations 6 false /rl/imaging/kate Browse false /rl/imaging/kate Browse false /rl/imaging/kate/$A/airfiles/$A_to_ref.term Browse false /rl/imaging/kate Browse false /rl/imaging/kate Browse false /rl/imaging/kate Browse false Standard Threshold 20 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 /rl/imaging/kate Browse true Input file to reslice /rl/imaging/kate/$A/resliced/r$S$B Browse false /rl/imaging/kate/ Browse true Voxel size (mm) XYZ $V $V $E Dimension (voxels) XYZ 64 64 $Y true /rl/imaging/kate/$A/airfiles/r$S_64.air Browse true /rl/imaging/kate/$A/shrunken/r$S_64 Browse Intensity scale-up factor 1.0 false false false Axis shift (voxels) XYZ 0.0 0.0 0.0 Axis rotation (degrees) roll/pitch/yaw 0.0 0.0 0.0 Axis scale XYZ 1.0 1.0 1.0 false /rl/imaging/kate/kate Browse true Input file to reslice /rl/imaging/kate/$A/$S$B Browse false /rl/imaging/kate/ Browse true Voxel size (mm) XYZ $V $V $Z Dimension (voxels) XYZ 64 64 $Y true /rl/imaging/kate/$A/airfiles/$S_64.air Browse true /rl/imaging/kate/$A/shrunken/$S_64 Browse Intensity scale-up factor 1.0 false false false Input air file(s);Input air directory;Input air filelist /rl/imaging/kate/$A/airfiles/$S_64.air Browse Air directory/file /rl/imaging/kate/$A/airfiles/$S_grow.air Browse false false Input air files;Input air directory;Input air filelist /rl/imaging/kate/$A/airfiles/r$S_64.air;/rl/imaging/kate/$A/airfiles/$S$B.air;/rl/imaging/kate/$A/airfiles/$S_grow.air Browse Output air file /rl/imaging/kate/$A/airfiles/$Sto$R.air Browse false Input file/directory $F Browse Output directory func_reslice Browse Struct file/directory $A Browse Air file/directory airfiles Browse Functional slice with AC/PC $P Structural slice with AC/PC $Q true false Parallelism 1;2;3;4;5;6;7;8 List of subjects $S Subject input directory /rl/imaging/kate/ Browse Subject output directory /rl/imaging/kate/ Browse (if different from subject input directory) Subject used for std. ref. image $R Suffix for stripped structurals $B false Input file/directory /rl/imaging/kate/$S/func_reslice Browse Output directory /rl/imaging/kate/$S/func_norm Browse Threshold $T false true 3000 false false true true nrfunc_ false Input file/directory /rl/imaging/kate/$S/func_norm Browse Output directory /rl/imaging/kate/$S/func_smooth Browse Filter width in mm (x,y,z) 4.0 4.0 4.0 Parallelism 1;2;3;4;5;6;7;8 false Output filename prefix s true true false false false End foreach loop