GlobalDesktop Created on Nov 15, 2003 Created by user fissell Created on Irix 6.5 mips platform Titles : Foreach, SetLogName, UnixCommand, PfileCorrect, SpiralReconLX, Afni3dANALYZEtoAFNI, Afni3dTqual, UnixCommand, Nisthresh, UnixCommand, Nismaps, Nisoverlay, IfisSendMail, EndForeach Foreach 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, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , fiswidgets.fisdesktop.SetLogName Log filename : $S/$P/$S_$P.log, UnixCommand Unix command : gunzip $S/$P/Pfiles/P*.gz, Options... Run using shell : is selected, Run using java : is not selected, if exit status is NOT : is not selected, 0, if exit status is : is not selected, 1, never fail : is selected, PfileCorrect Input Dir/Pfile : /anvil/proj_ccn/bwc/$S/$P/Pfiles, Output Dir/Pfile : /anvil/proj_ccn/bwc/$S/$P/Pfiles_corr, Logs Dir : /anvil/proj_ccn/bwc/$S/$P/logs, Detection strategy : spike, Detection parameter (std devs.) : 3.0, Replacement strategy : avg of 2 good neigh., 1st 2 timepoints handling : correct 1st 2 pts over traj, Exclude as motion timepoints cutoff (%) : is checked, 1.0, Real-Imaginary processing : is selected, Forward spiral : is selected, Phase-Magnitude processing : is not selected, Reverse spiral : is not selected, Do not write corrected pfile to disk : is checked, View Results : is checked, Verbosity : medium, SpiralReconLX Input Dir/Pfile : /anvil/proj_ccn/bwc/$S/$P/Pfiles, Output Dir : /anvil/proj_ccn/bwc/$S/$P/func_an, Output format : slice : is not selected, anz : is selected, Output Hdr Dir : /anvil/proj_ccn/bwc/$S/$P/logs, Pulse Sequence : splxvh3_1, 3T : is selected, 2D acq : is selected, forward : is selected, 1.5T : is not selected, 3D acq : is not selected, reverse : is not selected, Move map (1st) images to : is checked, /anvil/proj_ccn/bwc/$S/$P/maps, Run pfile consistency check : is checked, Compress pfiles : is not checked, Verbose : is not checked, View results : is checked, expert options... Parm file : /usr/ccn/pkg/spiral/bin/parm, Create field map : 3, Inhomogeneity correction : 3, Location adjustment : is checked, Override pulse sequence mismatch : is not checked, Recon 1st image only : is not checked, Afni3dANALYZEtoAFNI Analyze directory, /anvil/proj_ccn/bwc/$S/$P/func_an Output prefix : a2a, View : orig, TR : 1.5, s, Anatomical bucket : is not selected, Functional bucket : is not selected, 3d + time : is selected, Geometry parent : is not checked, /anvil/proj_ccn/bwc/$S/$P, z-axis origin in mm : 0.0, Change orientation : is not checked, Orientation : Axial, Geometry : (x, y, z), X, Right to Left, Y, Anterior to Posterior, Z, Inferior to Superior, Afni3dTqual Input Dataset : /anvil/proj_ccn/bwc/$S/$P/func_an/a2a+orig.HEAD, Print range with each quality index : is not checked, Save results : is checked, /anvil/proj_ccn/bwc/$S/$P/logs/tqual.1D, View results : is checked, Quality Index : Spearman Method, No clipping : is not selected, Clip off values below here : is not selected, JTextField : 0, Perform automatic clipping : is selected, UnixCommand Unix command : rm $S/$P/func_an/a2a+orig.HEAD, Options... Run using shell : is not selected, Run using java : is selected, if exit status is NOT : is selected, 0, if exit status is : is not selected, 1, never fail : is not selected, Nisthresh Input file/directory : /anvil/proj_ccn/bwc/$S/$P/func_an, Output directory : /anvil/proj_ccn/bwc/$S/$P, Write thresholds to file : is checked, /anvil/proj_ccn/bwc/$S/$P/logs/thresholds.txt, Compress input images when finished : is not checked, View results : is checked, Options... Force threshold to : is not checked, 800, Algorithm parameters : (see Help) : greys : 2, length : 5, search : 0.2, cut : 0.3, position : 0.5, Other options : Use output stem : is not checked, thresh_, Write thresholded images to disk : is not checked, Verbose mode : is not checked, UnixCommand Unix command : /usr/local/bin/stats < /anvil/proj_ccn/bwc/$S/$P/logs/thresholds.txt, Options... Run using shell : is selected, Run using java : is not selected, if exit status is NOT : is not selected, 0, if exit status is : is not selected, 1, never fail : is selected, Nismaps Images file/directory : /anvil/proj_ccn/bwc/$S/$P/func_an, Output directory : /anvil/proj_ccn/bwc/$S/$P/logs, Produce mean image : is checked, mean, Produce variance map : is checked, var, Variance scale : , Produce signal-to-noise map : is not checked, , Threshold : 0, View results : is not checked, Verbose mode : is checked, Nisoverlay Functional image : /anvil/proj_ccn/bwc/$S/$P/logs/var.img, Structural image : /anvil/proj_ccn/bwc/$S/$P/func_an/func_00001.img, Output directory : /anvil/proj_ccn/bwc/$S/$P/logs, Threshold : 20, Allow negative overlay values : is not checked, Save overlay montage as a jpeg file : is checked, Verbose mode : is not checked, IfisSendMail Mail To: : belangerce@msx.upmc.edu, Mail From: : globaldesktop, Mail Subject: : $S/$P part 1 done, SMTP Server : smtp.pitt.edu, Attachment: : is not checked, /scratch/fissell/new_flows Mail Message: : fiswidgets.fisdesktop.EndForeach End foreach loop :