#!/bin/tcsh #################################################################################################### ### ### ### This is a sample script to correct a 3d+time dataset using a modified RETROICOR routine. ### ### It takes as input the original 3d+time dataset, the cardiovascular and respiratory phase ### ### information based on Glover, et al. and outputs the dataset corrected on a slice by slice ### ### basis. ### ### ### ### M.A. Smith ### ### ---------------------------------------------------------------------------- ### ### 9/15/05: RMB: modified to be script to invoke with command aruments ### ### 4/10/07: RMB: modified to remove mean from physio regressors ### ### 4/27/07: RMB: modified to find baseline (t^0) BRIK automatically ### #################################################################################################### set DO_CLEANUP = 1 set DEBUG = 1 set TMP_FILE = tmp_@RETROICOR_output.txt ###### Command Line ###### echo $argv[1] echo $argv[2] echo $argv[3] echo $argv[4] echo $argv[5] if ( ${#argv} != 5 ) then echo "Wrong number of arguments specified for @RETROICOR!" echo "Usage:" echo " @RETROICOR " echo " where:" echo " = Prefix of cardiac physio file (after 1dCRphase) (e.g. card_phase_1.1D)" echo " = Prefix of respiration physio file (after 1dCRphase) (e.g. resp_phase_1.1D)" echo " = Prefix of input dataset. The dset to be corrected. " echo " = Prefix of output dataset. What you want the corrected dset to be called." echo " = Number of time points to ignore at the beginning." exit(-1) endif echo "==================================================================" echo "Thank you for running @RETROICOR." echo "Please note that outputs of intermediate programs" echo "will not appear on screen. Therefore, errors may not" echo "be immediately apparent. Outputs are stored in the file:" echo " tmp_@RETROICOR_output.txt" echo "If you run into problems, check this file for error messages first." echo "------------------------------------------------------------------" set tsname = $argv[1] # cardiovascular phase, 1D file set tsname2 = $argv[2] # respiratory phase, 1D file set Data = $argv[3] # original dataset set Filename = $argv[4] # prefix for RETROICOR corrected dataset set ignore = $argv[5] # number of timepoints to ignore #set id = $argv[6] # unique temporary id echo "------------------------------" echo "--- Reading File:" $Data echo "##################################" >>& $TMP_FILE echo "@RETROICOR script ran on: " >>& $TMP_FILE date >>& $TMP_FILE echo "----------------------------------" >>& $TMP_FILE if (-e $Data+orig.HEAD ) then set Dset_params = `3dAttribute -name TAXIS_NUMS {$Data}+orig` set NT = $Dset_params[3] @ NT1 = $NT - 1 set Dset_params2 = `3dAttribute -name DATASET_DIMENSIONS {$Data}+orig` #set NZ = $Dset_params[4] set NZ = $Dset_params2[5] if ($NZ < 1 ) then set NZ = 1 endif @ NZ2 = $NZ - 1 echo "--- NT:" $NT echo "--- NZ:" $NZ else echo "Cannot find" {$Data}"+orig.HEAD" exit(-1) endif ########### Do modified RETROICOR correction ################# set LL = "" set LL2 = "" foreach nz (`count 0 {$NZ2}`) echo "----------------------------" echo "---Processing slice: " $nz 1deval -a {$tsname}.1D'['{$nz}']' -expr 'sin(a)' > tmp_{$tsname}_sin_{$nz}.1D 1deval -a {$tsname}.1D'['{$nz}']' -expr 'cos(a)' > tmp_{$tsname}_cos_{$nz}.1D 1deval -a {$tsname}.1D'['{$nz}']' -expr 'sin(2*a)' > tmp_{$tsname}_sin2_{$nz}.1D 1deval -a {$tsname}.1D'['{$nz}']' -expr 'cos(2*a)' > tmp_{$tsname}_cos2_{$nz}.1D 1deval -a {$tsname2}.1D'['{$nz}']' -expr 'sin(a)' > tmp_{$tsname2}_sin_{$nz}.1D 1deval -a {$tsname2}.1D'['{$nz}']' -expr 'cos(a)' > tmp_{$tsname2}_cos_{$nz}.1D 1deval -a {$tsname2}.1D'['{$nz}']' -expr 'sin(2*a)' > tmp_{$tsname2}_sin2_{$nz}.1D 1deval -a {$tsname2}.1D'['{$nz}']' -expr 'cos(2*a)' > tmp_{$tsname2}_cos2_{$nz}.1D #--- Compute mean for each regressor and subtract #foreach p ($tsname $tsname2) # foreach reg (sin cos sin2 cos2) # set meanval = `1dsum tmp_{$p}_{$reg}_{$nz}.1D` # 1deval -a tmp_{$p}_{$reg}_{$nz}.1D -expr "a-$meanval" > tmp_s_{$p}_{$reg}_{$nz}.1D # end #end #echo "Cutup start..." 3dZcutup \ -keep {$nz} {$nz} \ -prefix tmp_{$Data}_{$nz} \ {$Data}+orig >>& $TMP_FILE #echo "...end" 3dDeconvolve \ -input tmp_{$Data}_{$nz}+orig \ -nfirst {$ignore} \ -bout \ -num_stimts 8 \ -stim_file 1 tmp_{$tsname}_sin_{$nz}.1D \ -stim_file 2 tmp_{$tsname}_cos_{$nz}.1D \ -stim_file 3 tmp_{$tsname}_sin2_{$nz}.1D \ -stim_file 4 tmp_{$tsname}_cos2_{$nz}.1D \ -stim_file 5 tmp_{$tsname2}_sin_{$nz}.1D \ -stim_file 6 tmp_{$tsname2}_cos_{$nz}.1D \ -stim_file 7 tmp_{$tsname2}_sin2_{$nz}.1D \ -stim_file 8 tmp_{$tsname2}_cos2_{$nz}.1D \ -tout -fout \ -errts tmp_{$Data}_corx_{$nz} \ -bucket tmp_Fit_{$Filename}_{$nz} >>& $TMP_FILE #---- Find baseline BRIK set base_indx_1 = `3dinfo tmp_Fit_{$Filename}_{$nz}+orig | grep "Pol#0_Coef" | awk '{print substr($4,2)}'` #---- check to see if this is really a number. set to null if not." set base_indx = `echo $base_indx_1 | awk '(( $1 + 0 ) == $1) {print $1}'` if ($base_indx == "" ) then echo "---Base Index was not found. Set to zero by default." set base_indx = 0 endif if ($DEBUG != 0 ) then echo "---Base Index set to: $base_indx" endif 3dcalc \ -a tmp_Fit_{$Filename}_{$nz}+orig'['$base_indx']' \ -b tmp_{$Data}_corx_{$nz}+orig \ -expr 'a+b' \ -prefix tmp_{$Filename}_{$nz} >>& $TMP_FILE set LL = "$LL tmp_{$Filename}_{$nz}+orig.BRIK" #set LL2 = "$LL tmp_Fit_{$Filename}_{$nz}+orig.BRIK" end if ( $NZ2 != 0) then 3dZcat \ -prefix {$Filename} \ $LL #3dZcat \ # -prefix Fit_{$Filename} \ # $LL2 else 3dcalc -a tmp_{$Filename}_0000+orig -expr 'a' -prefix {$Filename} endif #--- KEEP FOR NOW ---# if ($DO_CLEANUP == 1) then rm -f tmp_{$tsname}_sin_*.1D rm -f tmp_{$tsname}_cos_*.1D rm -f tmp_{$tsname}_sin2_*.1D rm -f tmp_{$tsname}_cos2_*.1D rm -f tmp_{$tsname2}_sin_*.1D rm -f tmp_{$tsname2}_cos_*.1D rm -f tmp_{$tsname2}_sin2_*.1D rm -f tmp_{$tsname2}_cos2_*.1D rm -f tmp_Fit_{$Filename}_* rm -f tmp_{$Filename}_* rm -f tmp_{$Data}_* endif