Foreach,SetLogName,UnixCommand,PfileCorrect,SpiralReconLX,Afni3dANALYZEtoAFNI,Afni3dTqual,UnixCommand,Nisthresh,UnixCommand,Nismaps,Nisoverlay,IfisSendMail,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 Set $ Browse S;T;E;I;J;P; c18;20;raw_structs;005;004;arrow; c19;20;raw_structs;005;004;arrow; c20;20;raw_structs;005;004;arrow; c21;20;raw_structs;005;004;arrow; c22;20;raw_structs;005;004;arrow; c23;20;raw_structs;005;004;arrow; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; A; 1 ; 2 ; 3 ; 4 ; 5 ; 6 ; 7 ; 8 ; 9 ; 10 ; 11 ; 12 ; 13 ; 14 ; 15 ; 16 ; 17 ; 18 ; 19 ; 20 ; 21 ; 22 ; 23 ; 24 ; 25 ; Add Variable -;A;B;C;D;F;G;H;K;L;M;N;O;Q;R;U;V;X;Y;Z Remove Variable Add rows Log filename $S/$P/$S_$P.log Browse Unix command gunzip $S/$P/Pfiles/P*.gz Browse true false false 0 false 1 true Input Dir/Pfile /anvil/proj_ccn/bwc/$S/$P/Pfiles Browse Output Dir/Pfile /anvil/proj_ccn/bwc/$S/$P/Pfiles_corr Browse Logs Dir /anvil/proj_ccn/bwc/$S/$P/logs Browse Detection strategy std dev;Mahalanobis;spike Detection parameter (std devs.) 3.0 Replacement strategy zero;average;median;std. dev. cutoff;avg of 6 neigh.;avg of 2 good neigh. 1st 2 timepoints handling off;do not correct 1st pt.;do not correct 1st 2 pts;correct 1st pt. over traj;correct 1st 2 pts over traj true 1.0 true true false false true true Verbosity off;low;medium;debug Input Dir/Pfile /anvil/proj_ccn/bwc/$S/$P/Pfiles Browse Output Dir /anvil/proj_ccn/bwc/$S/$P/func_an Browse Output format false true Output Hdr Dir /anvil/proj_ccn/bwc/$S/$P/logs Browse Pulse Sequence splx6;splx7;splx84_2;splx84_3;splxr3;splxr4;splxr5;splx8;splxr5cv;splxcnv4_1;splxvh3_1 true true true false false false true /anvil/proj_ccn/bwc/$S/$P/maps Browse true false false true Parm file /usr/ccn/pkg/spiral/bin/parm Browse Create field map off;1;2;3 Inhomogeneity correction off;1;2;3 true false false Analyze dataset(s);Analyze directory;Analyze filelist /anvil/proj_ccn/bwc/$S/$P/func_an Browse Output prefix a2a View orig;acpc;tlrc TR 1.5 ms;s;Hz false false true false /anvil/proj_ccn/bwc/$S/$P Browse z-axis origin in mm 0.0 false Orientation Axial;Saggital;Coronal Geometry (x, y, z);(x, z, y);(y, x, z);(y, z, x);(z, x, y);(z, y, x) X Right to Left;Left to Right Y Anterior to Posterior;Posterior to Anterior Z Inferior to Superior;Superior to Inferior Input Dataset /anvil/proj_ccn/bwc/$S/$P/func_an/a2a+orig.HEAD Browse false true /anvil/proj_ccn/bwc/$S/$P/logs/tqual.1D Browse true Quality Index Spearman Method;Quadrant Method false false 0 true Unix command rm $S/$P/func_an/a2a+orig.HEAD Browse false true true 0 false 1 false Input file/directory /anvil/proj_ccn/bwc/$S/$P/func_an Browse Output directory /anvil/proj_ccn/bwc/$S/$P Browse true /anvil/proj_ccn/bwc/$S/$P/logs/thresholds.txt false true false 800 Algorithm parameters (see Help) greys 2 length 5 search 0.2 cut 0.3 position 0.5 Other options false thresh_ false false Unix command /usr/local/bin/stats < /anvil/proj_ccn/bwc/$S/$P/logs/thresholds.txt Browse true false false 0 false 1 true Images file/directory /anvil/proj_ccn/bwc/$S/$P/func_an Browse Output directory /anvil/proj_ccn/bwc/$S/$P/logs Browse true mean true var Variance scale false Threshold 0 false true Functional image /anvil/proj_ccn/bwc/$S/$P/logs/var.img Browse Structural image /anvil/proj_ccn/bwc/$S/$P/func_an/func_00001.img Browse Output directory /anvil/proj_ccn/bwc/$S/$P/logs Browse Threshold 20 false true false Mail To: belangerce@msx.upmc.edu Mail From: globaldesktop Mail Subject: $S/$P part 1 done SMTP Server smtp.pitt.edu false /scratch/fissell/new_flows Browse Mail Message: End foreach loop