GSReg_demo
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#!/bin/tcsh -fset sdir = $PWDset stat = 0set pname = `basename $0`SETUP: set gngain = 4.0 #base nz gain factor set gnr = (1.0 2.0 1.0 2.0) #nz gain factor per group, 30 subjects per group set gbr = (1.0 1.0 2.0 2.0) #background gain factor for each group set n_grps = $#gbr set imx = `ccalc -i "$n_grps * 30 -1"` #-i以交互方式运行 set sext = .Rnd set no_corr_in_bkg = 0 #if 1 don't compute correlations in background region set regen = 0 #if 1 then recreate existing data files #if 0 then reuse when possible. Set regen to 1 when #Changing parameters under SETUP section or you'll #end up looking at previously generated data set killall = 1 #if 1 (recommended) then close then reopen all #exisiting AFNI/3dGroupInCorr when script #is rerun set all_auto_seeds = 0 #if 1 then automatically go through all seed regions #and save results. Otherwise, just stop at 3st seed set wdir = /Volumes/afni/pub/dist/edugoto PARSERET_PARSE:SKIP: #goto SHOWME2 #goto SHOWME_GRP_DIFFCREATE_LATTICE: foreach sub (`count -digits 2 0 $imx`) set ig = `ccalc -fint $sub/30+1` set sout = s$sub$sext if (-f $sout/msk+tlrc.HEAD && $regen == 0) then echo "Reusing lattice for $sout" goto NEXT_LATTICE endif rm -rf ./$sout if (! -d ${sout}) mkdir ${sout} cd ${sout} echo "Creating subject $sub" echo "10 10 1 2 10" > udm.1D echo "10 50 1 3 10" >> udm.1D echo "40 30 1 4 20" >> udm.1D 3dUndump -dimen 64 64 2 \ -dval 1 \ -ijk \ -prefix tmplt \ -overwrite \ udm.1D 3drefit -view +tlrc tmplt+orig 3dcalc -a tmplt+tlrc \ -expr '(1-step(a))+a' \ -overwrite \ -prefix msk cd - NEXT_LATTICE: endCREATE_RAND_DATA:foreach sub (`count -digits 2 0 $imx`) set ig = `ccalc -fint $sub/30+1` set sout = s$sub$sext if (-f $sout/rsort+tlrc.HEAD && $regen == 0) then echo "Reusing data for $sout" goto NEXT_DATA endif cd ${sout} echo "Creating subject $sub" 1deval -num 300 -dt 2.0 -expr 'gran(0,1)+(i-i)+0.7*z' > ARsig1.$sub.1D 1deval -num 300 -dt 2.0 -expr 'gran(0,1)+(i-i)+0.7*z' > ARsig2.$sub.1D 1deval -num 300 -dt 2.0 -expr 'gran(0,1)+(i-i)+0.7*z' > ARsig3.$sub.1D 1deval -num 300 -dt 2.0 -expr 'gran(0,1)+(i-i)+0.7*z' > ARsig4.$sub.1D #Background sharing set fn = `ccalc "$gngain * $gnr[$ig]"` #Noise gain set fb = $gbr[$ig] #Background gain 3dcalc -dt 2.0 \ -a msk+tlrc \ -b ARsig1.$sub.1D \ -c ARsig2.$sub.1D \ -d ARsig3.$sub.1D \ -e ARsig4.$sub.1D \ -expr " step(a) * (b*$fb) +\ ($fn*gran(0,1)) +\ equals(a,2) * (c ) +\ equals(a,3) * (d ) +\ equals(a,4) * (e ) "\ -overwrite \ -prefix rs 3dROIstats -quiet -mask msk+tlrc. rs+tlrc.BRIK > rall.1D 3dmaskave -quiet rs+tlrc. > gs.1D 3dmaskave -quiet -mask msk+tlrc -mrange 1 1 rs+tlrc. > r1.1D @ROI_Corr_Mat -ts rs+tlrc -roi msk+tlrc -prefix xcm.rs #Background + Some cross talk 3dcalc -dt 2.0 \ -a msk+tlrc \ -b ARsig1.$sub.1D \ -c ARsig2.$sub.1D \ -d ARsig3.$sub.1D \ -e ARsig4.$sub.1D \ -expr " step(a) * (b*$fb) +\ ($fn*gran(0,1)) +\ equals(a,2) * (c ) +\ equals(a,3) * ((d+c)/2.0) +\ equals(a,4) * (e ) "\ -overwrite \ -prefix rs_23 3dROIstats -quiet -mask msk+tlrc. rs_23+tlrc.BRIK > rall_23.1D 3dmaskave -quiet rs_23+tlrc. > gs_23.1D 3dmaskave -quiet -mask msk+tlrc -mrange 1 1 rs_23+tlrc. > r1_23.1D @ROI_Corr_Mat -ts rs_23+tlrc -roi msk+tlrc -prefix xcm.rs_23 #No background sharing 3dcalc -dt 2.0 \ -a msk+tlrc \ -b ARsig1.$sub.1D \ -c ARsig2.$sub.1D \ -d ARsig3.$sub.1D \ -e ARsig4.$sub.1D \ -expr " equals(a,1) * (b*$fb) +\ ($fn*gran(0,1)) +\ equals(a,2) * (c) +\ equals(a,3) * (d) +\ equals(a,4) * (e) "\ -overwrite \ -prefix rsort 3dROIstats -quiet -mask msk+tlrc. rsort+tlrc.BRIK > rallort.1D 3dmaskave -quiet rsort+tlrc. > gsort.1D 3dmaskave -quiet -mask msk+tlrc -mrange 1 1 rsort+tlrc. > r1ort.1D @ROI_Corr_Mat -ts rsort+tlrc -roi msk+tlrc -prefix xcm.rsort cd $sdir NEXT_DATA:endgoto GINCORGINCOR:BANDPASS: foreach sub (`count -digits 2 0 $imx`) set ig = `ccalc -fint $sub/30+1` set sout = s$sub$sext if ( -f $sout/rs_bp_23.r1+tlrc.HEAD && $regen == 0) then echo "Reusing filtered for $sout" goto NEXT_PASS endif cd ${sout} echo "Bandpassing subject $sout ... " 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bp \ -nodetrend -notrans -quiet -input rs+tlrc 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bp.gs \ -nodetrend -notrans -quiet -input rs+tlrc -ort gs.1D 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bp.r1 \ -nodetrend -notrans -quiet -input rs+tlrc -ort r1.1D 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bport \ -overwrite -nodetrend -notrans -quiet -input rsort+tlrc 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bport.gs \ -nodetrend -notrans -quiet -input rsort+tlrc -ort gsort.1D 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bport.r1 \ -nodetrend -notrans -quiet -input rsort+tlrc -ort r1ort.1D 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bp_23 \ -overwrite -nodetrend -notrans -quiet -input rs_23+tlrc 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bp_23.gs \ -nodetrend -notrans -quiet -input rs_23+tlrc -ort gs_23.1D 3dBandpass -overwrite -blur 2.0 -band 0.01 0.10 -prefix rs_bp_23.r1 \ -nodetrend -notrans -quiet -input rs_23+tlrc -ort r1_23.1D cd $sdir NEXT_PASS: endASSEMBLE: set mopt = '' if ($no_corr_in_bkg == 1) then if (!(-f s00$sext/msk_nobkg+tlrc.HEAD) || $regen == 1) then 3dcalc -a s00$sext/msk+tlrc -expr 'a*step(a-1)' -overwrite \ -prefix s00$sext/msk_nobkg endif set mopt = "-mask s00$sext/msk_nobkg+tlrc" endif foreach ig (`count -digits 1 1 $n_grps`) if ($ig == 1) then set gflg = '' set sel = ("s[012]?$sext/rs_bp+tlrc.HEAD") else if ($ig == 2) then set gflg = 'G2.' set sel = ("s[345]?$sext/rs_bp+tlrc.HEAD") else if ($ig == 3) then set gflg = 'G3.' set sel = ("s[678]?$sext/rs_bp+tlrc.HEAD") else if ($ig == 4) then set gflg = 'G4.' set sel = ("s[9]?$sext/rs_bp+tlrc.HEAD" "s1[01]?$sext/rs_bp+tlrc.HEAD") else echo "ig = $ig is no good" goto BEND endif if ( -f ${gflg}bp_23$sext.r1.grpincorr.data && $regen == 0) then echo "Reusing GIC dataset ${gflg}bp_23$sext.*.grpincorr.data" goto NEXT_SET endif set seln = (`echo "$sel"`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bp$sext \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bp.gs/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bp$sext.gs \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bp.r1/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bp$sext.r1 \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bport/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bport$sext \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bport.gs/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bport$sext.gs \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bport.r1/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bport$sext.r1 \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bp_23/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bp_23$sext \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bp_23.gs/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bp_23$sext.gs \ $seln set seln = (`echo "$sel" | sed 's/_bp/_bp_23.r1/'`) 3dSetupGroupInCorr -overwrite $mopt -prefix ${gflg}bp_23$sext.r1 \ $seln NEXT_SET: endgoto SHOWME2SHOWME2: set vols = (bp$sext bp$sext.gs bp$sext.r1 \ bport$sext bport$sext.gs bport$sext.r1 \ bp_23$sext bp_23$sext.gs bp_23$sext.r1 ) set ccl = ( Mix$sext Mix$sext.gs Mix$sext.r1 \ Ort$sext Ort$sext.gs Ort$sext.r1 \ C23$sext C23$sext.gs C23$sext.r1) if ($killall) then @Quiet_talkers -npb_range 1 9 endif set cnt = 1 foreach cc ($ccl) set pid = `ps -a | \grep afni | \grep niml | \grep s00 | \grep "npb $cnt"` if ($status) then afni -npb $cnt -niml -yesplugouts \ -tbar $cc \ -layout layout.$cnt s00$sext/ >& /dev/null & sleep 2 plugout_drive -npb $cnt -maxwait 20 \ -com 'SET_PBAR_NUMBER A.10' \ -com 'SET_PBAR_SIGN A.-' \ -com 'SET_THRESHNEW A.0.0001 *p' \ -com 'SET_FUNC_RANGE A.3' \ -com 'SET_IJK 40 30 1' \ -quit >& /dev/null & endif set pid = `ps -a | \grep 3dGroupInCorr | \grep setA | \ \grep grpincorr.niml | \ \grep "npb $cnt"` if ($status) then echo "Plan $cc" echo " 3dGroupInCorr -npb $cnt -setA $vols[$cnt].grpincorr.niml >& /dev/null" 3dGroupInCorr -npb $cnt -setA $vols[$cnt].grpincorr.niml >& /dev/null & endif @ cnt ++ endINSTA_SETS: set seedl = () foreach loc (0 1 2 3) if ($loc < 3) then set IJK = (`1dcat s00$sext/udm.1D"[0..2]{$loc}"`) set seedloc = "Reg_`ccalc -i $loc + 2`" else set IJK = ( 10 30 1 ) #in background set seedloc = "Backg" endif set seedl = ($seedl $seedloc) set cnt = 1 foreach cc ($ccl) plugout_drive -npb $cnt \ -com "SET_IJK $IJK" \ -com 'INSTACORR SET' \ -com 'SET_THRESHNEW A.0.0001 *p' \ -com 'SET_FUNC_RANGE A.3' \ -quit plugout_drive -npb $cnt \ -com "SET_XHAIRS A.OFF" \ -com "SAVE_PNG A.axialimage $cc.$seedloc.png" \ -com "SET_XHAIRS A.MULTI" \ -quit @ cnt ++ end if ($all_auto_seeds == 0) goto INFO endASSEMBLE_IMAGES: foreach seedloc ($seedl) \rm $seedloc$sext.ppm imcat -matrix 3 3 -prefix $seedloc$sext.ppm -gap 1 -gap_col 0 0 0 \ Mix$sext.*$seedloc.png \ Ort$sext.*$seedloc.png \ C23$sext.*$seedloc.png endINFO: set l = `prompt_user -pause \"Each window shows one-sample ttest on correlations with the seed location.\n\To create a new map:\n\ Move to a seed location\n\ Right-click and select 'InstaCorr set'\n\ or\n\ Shift+ctrl+right-click (and drag if you like).\n\(To control whether or not the background region is masked, \n\ use option -mask_background 1 with $pname.)\n\\n\The windows are arranged to show 9 cases. Each row has a slightly different \n\model, and each column process the data differently.\n\Row 1: Uncorrelated regions + shared background\n\Row 2: Uncorrelated regions + No shared background\n\Row 3: Regions 2&3 correlated + shared background\n\Col 1: No Global Signal Regression\n\Col 2: Global Signal Regression\n\Col 3: Background Signal Regression\n\\n\Each of these windows is a separate afni session and communicates with a \n\separate 3dGroupInCorr program. To bring up the AFNI control window for one\n\of the images, right-click on the 'Disp' button in the lower left corner\n\of the image window. The title bars can also be used to match image window \n\to AFNI controller.\n\ \n\Press OK to close all and move to two sample results with different SNR"` if ($l == 0) goto BEND if ($killall == 0) then #Must kill when going to SHOWME_GRP_DIFF from here @Quiet_talkers -npb_range 1 9 endifSHOWME_GRP_DIFF: if ($killall) then @Quiet_talkers -npb_range 1 9 endif set cnt = 1 set g1 = ( bp$sext bp$sext.gs \ bp$sext bp$sext.gs \ bp$sext bp$sext.gs ) set ccl = ( G1-G2.+Noise.Mix.$sext G1-G2.+Noise.Mix$sext.gs \ G1-G3.+Back.Mix$sext G1-G3.+Back.Mix$sext.gs \ G1-G4.+Noise+Back.Mix$sext G1-G4.+Noise+Back.Mix$sext.gs) set lays = ( 1 2 4 5 7 8) foreach cc ($ccl) if ($cnt < 3) then set gg = G2 else if ($cnt < 5) then set gg = G3 else if ($cnt < 7) then set gg = G4 endif set pid = `ps -a | \grep afni | \grep niml | \grep s00 | \grep "npb $cnt"` if ($status) then afni -npb $cnt -niml -yesplugouts -tbar $cc \ -layout layout.$lays[$cnt] s00$sext/ \ >& /dev/null & sleep 2 plugout_drive -npb $cnt -maxwait 20 \ -com 'SET_PBAR_NUMBER A.10' \ -com 'SET_PBAR_SIGN A.-' \ -com 'SET_THRESHNEW A.0.0001 *p' \ -com 'SET_FUNC_RANGE A.3' \ -com 'SET_IJK 40 30 1' \ -quit >& /dev/null endif set pid = `ps -a | \grep 3dGroupInCorr | \grep setA | \ \grep grpincorr.niml | \ \grep "npb $cnt"` if ($status) then echo "Plan $cc" echo " 3dGroupInCorr -npb $cnt \ -setA $g1[$cnt].grpincorr.niml \ -setB $gg.$g1[$cnt].grpincorr.niml \ >& /dev/null" 3dGroupInCorr -npb $cnt \ -setA $g1[$cnt].grpincorr.niml \ -setB $gg.$g1[$cnt].grpincorr.niml \ >& /dev/null & endif set loc = 2 set IJK = (`1dcat s00$sext/udm.1D"[0..2]{$loc}"`) set seedloc = "Reg_`ccalc -i $loc + 2`" plugout_drive -npb $cnt \ -com "SET_IJK $IJK" \ -com 'INSTACORR SET' \ -com 'SET_THRESHNEW A.0.0001 *p' \ -com 'SET_FUNC_RANGE A.3' \ -quit >& /dev/null sleep 1 plugout_drive -npb $cnt \ -com 'SET_FUNC_RANGE A.3' \ -com 'SET_THRESHNEW A.0.0001 *p' \ -quit >& /dev/null if ($all_auto_seeds == 1) then set icon = 1 set con = (g1-g2 g1 g2) foreach sb ( 0 2 4 ) set sb1 = `ccalc -i $sb + 1` plugout_drive -npb $cnt \ -com "SET_SUBBRICKS A -1 $sb $sb1" \ -quit >& /dev/null plugout_drive -npb $cnt \ -com 'SET_THRESHNEW A.0.0001 *p' \ -quit >& /dev/null plugout_drive -npb $cnt \ -com "SET_XHAIRS A.OFF" \ -com "SAVE_PNG A.axialimage $cc.$con[$icon].$seedloc.png" \ -com "SET_XHAIRS A.MULTI" \ -quit >& /dev/null @ icon ++ end endif @ cnt ++ endINFO2: set l = `prompt_user -pause \"Each window shows two-sample ttest results on correlations from two groups\n\at the seed location. There are no differences between the group pairs, except\n\for levels of noise and/or shared background fluctuations.\n\To create a new map:\n\ Move to a seed location\n\ Right-click and select 'InstaCorr set'\n\ or\n\ Shift+ctrl+right-click (and drag if you like).\n\\n\The windows are arranged to show 6 cases. Each row is a contrast between two\n\ groups. The 2nd column is processed with Global Signal Regression prior to \n\the two-sample ttest.\n\Row 1: G1 vs. G2, G2 has twice the noise as G1\n\Row 2: G1 vs. G3, G3 has twice the background fluctuations as G1\n\Row 3: G1 vs. G4, G4 has twice the background fluctuations and noise as G1\n\Col 1: No Global Signal Regression\n\Col 2: Global Signal Regression\n\\n\Press OK to close all and end demo. Cancel to keep everything up."` if ($l == 0) goto BEND @Quiet_talkers -npb_range 1 9 goto ENDPARSE: set Narg = $# set cnt = 1 while ($cnt <= $Narg) if ( "$argv[$cnt]" == "-echo") then set echo goto NEXT endif if ( ("$argv[$cnt]" == "-h" || "$argv[$cnt]" == "-help") ) then goto HELP endif if ("$argv[$cnt]" == "-recreate") then set regen = 1 goto NEXT endif if ("$argv[$cnt]" == "-webit") then if (-f ./$pname) then echo "" echo "Enter c if you want to copy ./$pname to: $wdir" echo "" set jnk = $< if ($jnk == 'c' || $jnk == 'C') then cp -p ./$pname $wdir if ($status) then echo "Failed to copy ./$pname to: $wdir" goto BEND endif goto END endif else echo "" echo "$pname is not in the current directory." echo "This option should be run from the directory." echo "where $pname resides." echo "Perhaps: `which $pname` " echo "" goto BEND endif goto NEXT endif if ("$argv[$cnt]" == "-mask_background") then set regen = 1 @ cnt ++ if ($cnt > $Narg) then echo "Need 0 or 1 after -mask_background" goto BEND endif set no_corr_in_bkg = `printf %d $argv[$cnt]` goto NEXT endif if ("$argv[$cnt]" == "-noise_gain") then set regen = 1 @ cnt ++ if ($cnt > $Narg) then echo "Need a value after -noise_gain" goto BEND endif set gngain = `printf %f $argv[$cnt]` goto NEXT endif if (1) then echo "Error: Option or parameter '$argv[$cnt]' not understood" goto END endif NEXT:@ cnt ++end goto RET_PARSEHELP: echo "" echo "Usage: $pname " echo "A script to illustrate the effects of Global Signal Regression" echo "on a toy model of a brain made." echo "The group correlation maps are generated interactively with" echo "AFNI's 3dGroupInCorr" echo "The script takes time to setup the first time it is run to generate the" echo "data. Once the data are created the script launches AFNI and " echo "3dGroupInCorr sessions for interactive amusement." echo "" echo "You can change default parameters by directly editing the section" echo "SETUP in the beginning of the script, or by using the options below" echo "" echo "Options:" echo " -mask_background MSK: MSK=0 => Do include background region in " echo " corelation computations. " echo " MSK=1 => Do not include background." echo " Default is $no_corr_in_bkg" echo " -noise_gain GN: Noise gain factor common to all groups." echo " Default GN is $gngain" echo "" echo " -recreate: Recreate simulated data. Default is to reuse" echo " whatever is available, unless you use options" echo " -mask_background or -noise_gain on the command line" echo "" echo " -help: This message" echo " -webit: Put copy of this script on afni website" echo " This option only works from Ziad's computer." echo "" echo "Questions, comments should be addressed to:" echo " saadz@mail.nih.gov" echo "This script can be obtained from:" echo " http://afni.nimh.nih.gov/pub/dist/edu/@GSReg_demo" echo "and requires AFNI versions compiled after July 07/2011" echo "If you have AFNI installed already, you can update with" echo " @update_binaries -defaults" echo "" goto END BEND: echo "$pname : Error, or User Interruption" set stat = 1 goto END END: exit $stat 0 0
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