-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #!/bin/csh -f # mkanalysis-sess -- sets up post-processing environment for # functional analysis set VERSION = '$Id: mkanalysis-sess,v 1.3 2006/09/11 19:40:22 greve Exp $'; set scriptsdir = (); set fsd = (); set parname = (); set analysis = (); set funcstem = f; set designtype = (); set eventrelated = 0; set blocked = 0; set abblocked = 0; set retinotopy = 0; set inorm = 0; set motioncor = 0; set designtype = () set tpexclude = (); set force = 0; set runlistfile = (); set ncycles = (); set IdealTW = (); set PreStim = 0; set hanrad = 0; set fwhm = 0; set nskip = 0; set TR = (); set TER = (); set TauMax = 0; set WhitenFlag = 0; set gammafit = 0; set spmhrf = -1; set gDelta = (); set gTau = (); set gAlpha = (); set meanfit = 1; set trendfit = 1; set qtrendfit = 0; set PolyFitOrder = 1; set nyqreg = 0; set sveres = (); set svsignal = (); set nconditions = (); set timeoffset = (); set extreg = (); set nextreg = (); set extregorthog = 0; set maskstem = (); set autostimdur = 0; set stimdur = (); set PrintHelp = 0; #### If no arguments, print usage and exit #### if($#argv == 0) then goto usage_exit; exit 1; endif set n = `echo $argv | grep -e -help | wc -l` if($n != 0) then set PrintHelp = 1; goto usage_exit; exit 1; endif ##### Print out version info, if needed #### set n = `echo $argv | grep version | wc -l` if($n != 0) then echo $VERSION exit 0; endif set GSPArgs = (); set sxacfg = "analysis.cfg" # Don't require Session Arguments # set SessList = `getsesspath $argv`; if($status || $#SessList == 0) set SessList = (); goto parse_args; parse_args_return: goto check_params; check_params_return: ## File permission masking ### if(! $?MRI_UMASK ) set MRI_UMASK = `umask`; umask $MRI_UMASK; set umaskarg = "-umask $MRI_UMASK" mkdir -p $analysis ##---- Create the analysis config file ------# set sxacfg = $analysis/$sxacfg rm -f $sxacfg touch $sxacfg if($#TER == 0) set TER = $TR; if($designtype == "event-related" || $designtype == "blocked") then set Nh = `echo "($IdealTW/$TR)" | bc`; set TW = `echo "$TR*$Nh" | bc`; #if($#PreStim == 0) set PreStim = `echo "2*$TR" | bc -l`; if($gammafit) then @ nth = 1; while($nth <= $#gDelta) echo "-gammafit $gDelta[$nth] $gTau[$nth]" >> $sxacfg @ nth = $nth + 1; end if($#gAlpha != 0) echo "-gammaexp $gAlpha" >> $sxacfg endif if($spmhrf > -1) echo "-spmhrf $spmhrf" >> $sxacfg echo "-timewindow $TW" >> $sxacfg echo "-prestim $PreStim" >> $sxacfg #if(! $meanfit) then # echo "-nobaseline" >> $sxacfg #else # echo "-baseline" >> $sxacfg #endif #if($trendfit) echo "-detrend" >> $sxacfg #if($qtrendfit) echo "-qtrendfit" >> $sxacfg if($PolyFitOrder >= 0) echo "-polyfit $PolyFitOrder" >> $sxacfg if($nyqreg) echo "-nyqreg" >> $sxacfg echo "-TER $TER" >> $sxacfg if($TauMax > 0) echo "-autowhiten $TauMax" >> $sxacfg if($#timeoffset != 0) echo "-timeoffset $timeoffset" >> $sxacfg if($WhitenFlag != 0) echo "-whiten" >> $sxacfg else if($designtype == "retinotopy" || $designtype == "abblocked") then if($#ncycles) echo "-ncycles $ncycles" >> $sxacfg echo "-delay 0" >> $sxacfg endif echo "-nskip $nskip" >> $sxacfg if($hanrad != 0) then echo "-hanrad $hanrad" >> $sxacfg else echo "-fwhm $fwhm" >> $sxacfg endif if($#extreg != 0) then echo "-extreg $extreg" >> $sxacfg if($#nextreg != 0) echo "-nextreg $nextreg" >> $sxacfg if($extregorthog) echo "-extregorthog " >> $sxacfg endif if($inorm) echo "-rescale 1000" >> $sxacfg echo "" >> $sxacfg echo $sveres >> $sxacfg echo $svsignal >> $sxacfg if($autostimdur) echo "-autostimdur" >> $sxacfg if($#stimdur) echo "-stimdur $stimdur" >> $sxacfg ##---- Create the analysis info file ------# set infofile = $analysis/analysis.info rm -f $infofile touch $infofile echo "analysis $analysis" >> $infofile echo "TR $TR" >> $infofile echo "designtype $designtype" >> $infofile if($eventrelated || $blocked) then echo "nconditions $nconditions" >> $infofile endif echo "parname $parname" >> $infofile echo "fsd $fsd" >> $infofile echo "funcstem $funcstem" >> $infofile if($#runlistfile != 0) echo "runlistfile $runlistfile" >> $infofile echo "tpexclude $tpexclude" >> $infofile if($#maskstem != 0) echo "maskstem $maskstem" >> $infofile if($#SessList == 0) then echo "Completed successfully" exit 0; endif #----- Set up session-level scripts -------# echo $SessList set TRAnalysis = $TR; # Go through each session, make sure it exists, and check consistency # set n = 1; foreach sess ($SessList) set sessbase = `basename $sess`; set sifile = $sess/$fsd/seq.info if(! -e $sifile ) then echo "ERROR: cannot find $sifile" exit 1; endif # get and check the conistency of the TR # set ln = `grep TR $sifile`; if($#ln != 2) then echo "ERROR: bad format for seq.info file, $sess" exit 1; endif set tmp = $ln[2]; if($n == 1) then set TR = $tmp; else if($TR != $tmp) then echo "ERROR: $sess has inconsistent TR" exit 1; endif endif if($TR != $TRAnalysis) then echo "ERROR: TR for $sessbase = $TR, Analysis TR = $TRAnalysis" exit 1; endif # get and check the conistency of the nslices # set ln = `grep nslcs $sifile`; if($#ln != 2) then echo "ERROR: bad format for seq.info file, $sess" exit 1; endif set tmp = $ln[2]; if($n == 1) then set nslices = $tmp; else if($nslices != $tmp) then echo "ERROR: $sess has inconsistent nslices" exit 1; endif endif ## check that the runlistfile exists ## if($#runlistfile != 0) then set rlf = $sess/$fsd/$runlistfile if(! -e $rlf) then echo "ERROR: cannot find $rlf" exit 1; endif endif @ n = $n + 1; end # Loop over sessions # mkdir -p scripts set scriptsdir = $analysis/scripts mkdir -p $scriptsdir ##---- Create default motion correction script ------# set scr = scripts/run-mc-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Motion-Correction " >> $scr echo "cd .." >> $scr echo "mc-sess -method afni -toff 0 $GSPArgs $umaskarg" >> $scr echo "" >> $scr ##---- Create default inorm (no motion correction) script ------# set scr = scripts/run-inorm-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Intesity Normalization of Raw (ie, Not Motion-Corrected) Data" >> $scr echo "cd ../" >> $scr echo "inorm-sess $umaskarg $GSPArgs " >> $scr echo "" >> $scr ##---- Create default inorm (motion correction) script ------# set scr = scripts/run-inorm-mc-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Intesity Normalization of Motion-Corrected Data" >> $scr echo "cd ../" >> $scr echo "inorm-sess -motioncor $umaskarg $GSPArgs " >> $scr echo "" >> $scr if($designtype == "event-related" || $designtype == "blocked") then ##---- Create default selxavg script ------## set scr = $scriptsdir/run-selxavg-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Within-Session Averaging of Raw (ie, Not Motion-Corrected) Data" >> $scr echo "cd ../.." >> $scr echo "selxavg-sess -analysis $analysis $GSPArgs " >> $scr echo "" >> $scr ##---- Create default stxgrinder subject script ------# set scr = $scriptsdir/run-stxgrinder-subj rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Session-Level Statistical Grinding " >> $scr echo "cd ../.." >> $scr echo "stxgrinder-sess -contrast allvfix -analysis $analysis -umask 0 $GSPArgs " >> $scr echo "" >> $scr ##---- Create default tal script ------# set scr = $scriptsdir/run-func2tal-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Resampling of functional averages into Talariach Space" >> $scr echo "cd ../.." >> $scr echo "func2tal-sess -res 4 -analysis $analysis $GSPArgs -umask 0" >> $scr echo "" >> $scr ##---- Create default func2sph script ------# set scr = $scriptsdir/run-func2sph-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Resampling of functional averages into Spherical Space" >> $scr echo "cd ../.." >> $scr echo "func2sph-sess -analysis $analysis $GSPArgs -umask 0">> $scr echo "" >> $scr ##---- Create default isxavg-fe script ------# set scr = $scriptsdir/run-isxavg-fe-sess rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Intersubject Averaging (Fixed-Effects) in Talariach Space" >> $scr echo "cd ../.." >> $scr echo "isxavg-fe-sess -grpname all -analysis $analysis -resamp tal $GSPArgs -umask 0">> $scr echo "" >> $scr ##---- Create default stxgrinder group script ------# set scr = $scriptsdir/run-stxgrinder-grp rm -f $scr touch $scr chmod a+x $scr echo "#!/bin/csh -f " >> $scr echo "# Group-Level Statistical Grinding " >> $scr echo "cd ../.." >> $scr echo "stxgrinder-sess -contrast allvfix -analysis $analysis -umask 0 -grpname all -resamp tal" >> $scr echo "" >> $scr endif # Delete the h.dat file if it exists rm -f $analysis/h.dat echo "Completed successfully" exit 0; ############################################### ############--------------################## parse_args: set cmdline = "$argv"; while( $#argv != 0 ) set flag = $argv[1]; shift; switch($flag) case "-g": case "-s": case "-sf": case "-d": case "-df": if ( $#argv == 0) goto arg1err; set GSPArgs = ($GSPArgs $flag $argv[1]); shift; breaksw case "-cwd": set GSPArgs = ($GSPArgs -cwd); breaksw case "-clone": if ( $#argv == 0) goto arg1err; set cloneanalysis = $argv[1]; shift; if(! -e $cloneanalysis ) then echo "ERROR: $cloneanalysis does not exist" exit 1; endif set cainfo = $cloneanalysis/analysis.info set cacfg = $cloneanalysis/analysis.cfg if(! -e $cainfo ) then echo "ERROR: $cloneanalysis does have analysis.info" exit 1; endif if(! -e $cacfg ) then echo "ERROR: $cloneanalysis does have analysis.cfg" exit 1; endif set TR = `cat $cainfo | awk '{if($1 == "TR") print $2}'`; set designtype = `cat $cainfo | awk '{if($1 == "designtype") print $2}'`; set fsd = `cat $cainfo | awk '{if($1 == "fsd") print $2}'`; set funcstem = `cat $cainfo | awk '{if($1 == "funcstem") print $2}'`; set parname = `cat $cainfo | awk '{if($1 == "parname") print $2}'`; set tpexclude = `cat $cainfo | awk '{if($1 == "tpexclude") print $2}'`; set runlistfile = `cat $cainfo | awk '{if($1 == "runlistfile") print $2}'`; set nconditions = `cat $cainfo | awk '{if($1 == "nconditions") print $2}'`; set maskstem = `cat $cainfo | awk '{if($1 == "maskstem") print $2}'`; set gDelta = `cat $cacfg | awk '{if($1 == "-gammafit") print $2}'`; set gTau = `cat $cacfg | awk '{if($1 == "-gammafit") print $3}'`; set gAlpha = `cat $cacfg | awk '{if($1 == "-gammaexp") print $2}'`; if($#gDelta != 0) set gammafit = 1; set spmhrf = `cat $cacfg | awk '{if($1 == "-spmhrf") print $2}'`; if($#spmhrf == 0) set spmhrf = -1; set IdealTW = `cat $cacfg | awk '{if($1 == "-timewindow") print $2}'`; set PreStim = `cat $cacfg | awk '{if($1 == "-prestim") print $2}'`; set TER = `cat $cacfg | awk '{if($1 == "-TER") print $2}'`; set TauMax = `cat $cacfg | awk '{if($1 == "-autowhiten") print $2}'`; if($#TauMax == 0) set TauMax = 0; set WhitenFlag = `cat $cacfg | awk '{if($1 == "-whiten") print $1}'`; if($#WhitenFlag == 0) set WhitenFlag = 0; set nskip = `cat $cacfg | awk '{if($1 == "-nskip") print $2}'`; set fwhm = `cat $cacfg | awk '{if($1 == "-fwhm") print $2}'`; if($#fwhm == 0) set fwhm = 0; set extreg = `cat $cacfg | awk '{if($1 == "-extreg") print $2}'`; set nextreg = `cat $cacfg | awk '{if($1 == "-nextreg") print $2}'`; set extregorthog = `cat $cacfg | awk '{if($1 == "-extregorthog") print 1}'`; set timeoffset = `cat $cacfg | awk '{if($1 == "-timeoffset") print $2}'`; set ncycles = `cat $cacfg | awk '{if($1 == "-ncycles") print $2}'`; set trendfit = `cat $cacfg | awk '{if($1 == "-detrend") print 1}'`; set qtrendfit = `cat $cacfg | awk '{if($1 == "-qtrendfit") print 1}'`; set inorm = `cat $cacfg | awk '{if($1 == "-rescale") print 1}'`; set PolyFitOrder = `cat $cacfg | awk '{if($1 == "-polyfit") print $2}'`; set nyqreg = `cat $cacfg | awk '{if($1 == "-nyqreg") print $1}'|wc -l`; set sveres = `cat $cacfg | awk '{if($1 == "-sveres") print $1}'`; set svsignal = `cat $cacfg | awk '{if($1 == "-svsignal") print $1}'`; set tmp = `cat $cacfg | awk '{if($1 == "-autostimdur") print 1}'`; if($#tmp == 0) set autostimdur = 0; set stimdur = `cat $cacfg | awk '{if($1 == "-stimdur") print $1}'`; #goto getclone; #getclone_return: breaksw case "-sxacfg": # not advertised # if ( $#argv == 0) goto arg1err; set sxacfg = $1; shift; breaksw case "-a": case "-analysis": if ( $#argv == 0) goto arg1err; set analysis = $1; shift; breaksw case "-p": case "-paradigm": if ( $#argv == 0) goto arg1err; set parname = $1; shift; breaksw case "-ssd": case "-fsd": if ( $#argv == 0) goto arg1err; set fsd = $1; shift; breaksw case "-funcstem": case "-fmcstem": if ( $#argv == 0) goto arg1err; set funcstem = $1; shift; breaksw case "-runlistfile": case "-rlf": if ( $#argv == 0) goto arg1err; set runlistfile = $1; shift; breaksw case "-norlf": set runlistfile = (); breaksw case "-nconditions": case "-nc": if ( $#argv == 0) goto arg1err; set nconditions = $argv[1]; shift; breaksw case "-tpexclude": case "-tpef": if ( $#argv == 0) goto arg1err; set tpexclude = $argv[1]; shift; breaksw case "-timewindow": case "-tw": if ( $#argv == 0) goto arg1err; set IdealTW = $argv[1]; shift; breaksw case "-timeoffset": if ( $#argv == 0) goto arg1err; set timeoffset = $argv[1]; shift; breaksw case "-prestim": case "-tprestim": case "-tps": case "-ps": if ( $#argv == 0) goto arg1err; set PreStim = $argv[1]; shift; breaksw case "-taumax": if ( $#argv == 0) goto arg1err; set TauMax = $argv[1]; shift; breaksw case "-whiten": set WhitenFlag = 1; breaksw case "-nowhiten": set WhitenFlag = 0; breaksw case "-mask": if ( $#argv < 0) goto arg1err; set maskstem = $argv[1]; shift; breaksw case "-TER": if ( $#argv == 0) goto arg1err; set TER = $argv[1]; shift; breaksw case "-TR": if ( $#argv == 0) goto arg1err; set TR = $argv[1]; shift; breaksw case "-hanrad": echo "INFO: HanRad is obsolete, though you can still use it." echo "If you really want to use HanRad, run mkanalysis-sess" echo "with -hanrad-really. Otherwise, consider using spatialsmooth-sess." echo "Do not use both." exit 1; breaksw case "-hanrad-really": if ( $#argv == 0) goto arg1err; set hanrad = $argv[1]; shift; breaksw case "-extreg": # External regressor file if ( $#argv == 0) goto arg1err; set extreg = $argv[1]; shift; breaksw case "-mcextreg": # MotionCor External regressor file set extreg = mcextreg; set nextreg = 3; breaksw case "-nextreg": # No. of External regressors to use if ( $#argv == 0) goto arg1err; set nextreg = $argv[1]; shift; breaksw case "-extregorthog": # Orthogonalize External regressors wrt Par set extregorthog = 1; breaksw case "-gammafit": if ( $#argv < 2) goto arg2err; set gDelta = ($gDelta $argv[1]); shift; set gTau = ($gTau $argv[1]); shift; set gammafit = 1; breaksw case "-gammaexp": if ( $#argv < 1) goto arg1err; set gAlpha = $argv[1]; shift; breaksw case "-nogammafit": # for use with -clone # set gDelta = (); set gTau = (); set gammafit = 0; breaksw case "-spmhrf": # for use with -clone # if ( $#argv < 1) goto arg1err; set spmhrf = $argv[1]; shift; breaksw case "-nospmhrf": set sphhrf = -1; breaksw case "-fwhm-really": if ( $#argv == 0) goto arg1err; set fwhm = $argv[1]; shift; breaksw case "-fwhm": echo "INFO: FWHM is obsolete, though you can still use it." echo "If you really want to use FWHM, run mkanalysis-sess" echo "with -fwhm-really. Otherwise, consider using spatialsmooth-sess." echo "Do not use both." exit 1; breaksw case "-nskip": if ( $#argv == 0) goto arg1err; set nskip = $argv[1]; shift; breaksw case "-ncycles": if ( $#argv == 0) goto arg1err; set ncycles = $argv[1]; shift; breaksw case "-designtype": case "-design": case "-dt": if ( $#argv == 0) goto arg1err; set designtype = $argv[1]; shift; if("$designtype" == "er") set designtype = event-related; if("$designtype" != "blocked" && "$designtype" != "abblocked" && \ "$designtype" != "event-related" && "$designtype" != "retinotopy")then echo "ERROR: design type must be one of the following:" echo " event-related, blocked, abblocked, or retinotopy" exit 1; endif breaksw case "-event-related": set eventrelated = 1; set designtype = "event-related" breaksw case "-blocked": set blocked = 1; set designtype = "blocked" breaksw case "-abblocked": set abblocked = 1; set designtype = "abblocked" breaksw case "-retinotopy": case "-rtopy": case "-ret": set retinotopy = 1; set designtype = "retinotopy" breaksw case "-notrendfit": echo "ERROR: -notrendfit is no longer supported" echo " specify the polynomial order you want with -polyfit." echo " See -help." exit 1; breaksw case "-qtrendfit": echo "ERROR: -qtrendfit is no longer supported" echo " specify the polynomial order you want with -polyfit." echo " See -help." exit 1; breaksw case "-noqtrendfit": echo "ERROR: -noqtrendfit is no longer supported" echo " specify the polynomial order you want with -polyfit." echo " See -help." exit 1; breaksw case "-nomeanfit": echo "ERROR: -nomeanfit is no longer supported" echo " specify the polynomial order you want with -polyfit." echo " See -help." exit 1; breaksw case "-polyfit": case "-pf": if ( $#argv < 1) goto arg1err; set PolyFitOrder = $argv[1]; shift; breaksw case "-nyqreg": set nyqreg = -1; breaksw case "-sveres": set sveres = "-sveres"; breaksw case "-svsignal": set svsignal = "-svsignal"; breaksw case "-motioncor": set motioncor = 1; breaksw case "-force": set force = 1; breaksw case "-inorm": set inorm = 1; breaksw case "-noinorm": set inorm = 0; breaksw case "-umask": if ( $#argv == 0) goto arg1err; setenv MRI_UMASK $1; shift; breaksw case "-stimdur": if ( $#argv == 0) goto arg1err; set stimdur = $argv[1]; shift; breaksw case "-nostimdur": set stimdur = (); breaksw case "-autostimdur": set autostimdur = 1; breaksw case "-noautostimdur": set autostimdur = 0; breaksw case "-newmka": #ignore breaksw case "-debug": set verbose = 1; set echo = 1; breaksw default: echo ERROR: Flag $flag unrecognized. echo $cmdline exit 1 breaksw endsw end goto parse_args_return; ############--------------################## ############--------------################## check_params: if($#TR == 0) then echo "ERROR: must specify TR" exit 1; endif if($#fsd == 0) set fsd = bold if($#funcstem == 0) then if($motioncor) then set funcstem = fmc; else set funcstem = f; endif endif if($#designtype == 0) then echo "ERROR: must specify a design type" exit 1; endif if("$designtype" == "event-related") set eventrelated = 1; if("$designtype" == "blocked") set blocked = 1; if("$designtype" == "abblocked") set abblocked = 1; if("$designtype" == "retinotopy") set retinotopy = 1; if($#analysis == 0) then echo "ERROR: must specify an analysis name" exit 1; endif if($#parname == 0 && $abblocked) then set parname = NONE; endif if($#parname == 0) then echo "ERROR: must specify a paradigm file name" exit 1; endif if(-e $analysis && ! $force) then echo "ERROR: analysis $analysis already exists. You have three options" echo " 1. Give this analysis a different name" echo " 2. Give delete analysis $analysis and re-run mkanalysis-sess" echo " 3. Re-run mkanalysis-sess with a -force option to overwrite" exit 1; endif if(-e $analysis && $force) then echo "INFO: analysis $analysis exists, but overwrite forced by user." endif if($abblocked && $retinotopy) then echo "ERROR: cannot specify -abblocked and -retinotopy" exit 1; endif if($abblocked && ! $#ncycles && $#parname == 0) then echo "ERROR: must specify either ncycles or parname with -abblocked" exit 1; endif if($retinotopy && ! $#ncycles && $#parname == 0) then echo "ERROR: must specify either ncycles or parname with -retinotopy" exit 1; endif if($#nskip == 0) set nskip = 0; if($gammafit == 1 && $#IdealTW == 0) then set IdealTW = 40; set PreStim = 0; echo "INFO: setting Gamma time window to $IdealTW sec" endif if($spmhrf > 0 && $#IdealTW == 0) then set IdealTW = 40; set PreStim = 0; echo "INFO: setting SPM time window to $IdealTW sec" endif if("$hanrad" != "0" && "$fwhm" != "0") then echo "ERROR: cannot specify hanrad and fwhm" exit 1; endif if($eventrelated || $blocked) then if($gammafit == 0 && $#IdealTW == 0) then echo "ERROR: must set a timewindow if not fitting a gamma function" exit 1; endif if($#nconditions == 0) then echo "ERROR: must specify number of conditions" exit 1; endif endif if($TauMax > 0 && $WhitenFlag) then echo "ERROR: cannot use both -taumax and -whiten" echo $TauMax exit 1; endif goto check_params_return; ############--------------################## ############--------------################## arg1err: echo "ERROR: flag $flag requires one argument" exit 1 ############--------------################## ############--------------################## arg2err: echo "ERROR: flag $flag requires two arguments" exit 1 ############--------------################## ############--------------################## usage_exit: echo "" echo "USAGE: mkanalysis-sess (and mkanalysis-sess.new)" echo "" echo "Required Arguments" echo " -analysis analysisname : name of session-level functional analysis"; echo " -TR TR : TR value in seconds" echo " -paradigm parname : name of paradigm file" echo " -designtype type : type of design. Legal values are: event-related," echo " blocked, abblocked, retinotopy" echo "" echo "Optional Arguments" echo " -fsd FSD : functional subdirectory" echo " -funcstem stem : stem of functional data (default = f or fmc)" echo " -motioncor : use motion corrected data (see mc-sess) " echo " -runlistfile filename : file with list of runs to include in analysis" echo " -inorm : intensity normalize data (see inorm-sess)" echo " -fwhm FWHM : Full-Width/Half-Max for in-plane smoothing (mm)" echo " -nskip N : skip the first N time points in each run" echo " -tpef filename : time-point exclude file name" echo " -polyfit N : fit trend with polynomial of order N" echo " -extreg extregstem : external regressor" echo " -mcextreg : use motion parameters as external regressors" echo "" echo "Event-Related and Blocked Arguments " echo " -nconditions Nc : number of conditions (excluding fixation)" echo " -timewindow TW : event time window (sec)" echo " -prestim PS : event prestimulus window (sec)" echo " -TER TER : temporal estimation resolution (sec)" echo " -gammafit gfDelta gfTau : assume IRF is a gamma function" echo " -gammaexp gfAlpha : gamma exponent (default is 2) " echo " -taumax TauMax : maximum lag for noise autocor and whitening (sec)" echo " -mask maskid : use masks/maskid to compute autocor and whitening" echo " -timeoffset toffset : time offset (sec) to add to each paradigm file" echo "" echo "Retinotopy and AB Blocked Arguments (Required)" echo " -ncycles N : number of cycles in each run" echo "" echo "Other Optional Arguments" echo " -umask umask : set unix file permission mask" echo " -version : print version and exit" echo " -help : my analysis has fallen, and it can't get up!" echo "" echo "See also mkanalysis-sess.old" echo "" if( ! $PrintHelp) exit 1; echo $VERSION cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }' exit 1; #---- Everything below here is printed out as part of help -----# BEGINHELP This program creates an 'analysis'. An analysis is a concept within the FS-FAST processing stream framework. The analysis is meant to be a placeholder for all the within-session processing options (eg, motion correction, spatial smoothing, event-type definition, etc). As such, the parameters apply to ALL sessions (ie, it does not need to be run separately for each session), and does not depend upon the data in any one session. This program should be run from your FS-FAST Study Directory. This program only configures the analysis; it does not analyze the data (see selxavg-sess or sfa-sess). ARGUMENTS AND FLAGS: -analysis analysisname (Shortcut: -a) This is the name given to the analysis. A folder called analysisname will be created in the Study Directory. Two files (analysis.info and analysis.cfg) will be created in this directory. The analysis parameters will be stored in these files. Contrast matrices (created by mkcontrast-sess) will also be stored in this directory. When the session data are analyzed with selxavg-sess or sfa-sess data, a folder called analysisname will be created in the functional subdirectory (FSD), and the results of the analysis will be placed there. -TR TR This is the TR in seconds. It will be checked against the TR in each session when selxavg-sess is run. See also -TER. -paradigm parname (Shortcut: -p) This is the name of the paradigm file as found in each functional run directory. For blocked and event-related designs, the paradigm file defines which event type was presented when. For periodic designs (retinotopy and AB blocked), it defines the phase and period of stimulation for each run. The name of the paradigm file must be the same across runs and sessions, though its contents can change. If event types are redefined (eg, post-hoc event sorting), then a new paradigm file (with a different name) should be created followed by creating a new analysis. For event and blocked designs, time=0 is relative to the time of acquisition of the first stored image. -designtype type (Shortcut: -dt) This specifies the type of design for which the analysis is being created. Legal values are event-related, blocked, abblocked, and retinotopy. Event-related and blocked must be analyzed with selxavg-sess. abblocked and retinotopy must be analyzed with sfa-sess. abblocked is a block design in which only two conditions (or one condition and one null condition) are presented in a periodic fashion. Ie, each condition is presented for for the same duration in an alternating fashion. -fsd FSD Functional subdirectory (FSD). This is the folder under the sessions directory in which the runs of raw functional data will be found (default is bold). -funcstem stem This is the bshort/bfloat stem of the functional volume to process. This volume must exist in each functional run. By default, the stem is f. If the -motioncor flag is included, then the stem fmc is used (this is the default output of mc-sess). -motioncor (see -funcstem stem). -runlistfile filename (Shortcut: -rlf) This is a file that should exist in each FSD that lists the runs to be processed in that session. The name must be the same across sessions but the contents of each file can vary. If an RLF is not specified, all runs found in the FSD will be processed. -inorm Perform intensity normalization. This requires that inorm-sess be run on the volume specified by -funcstem (or whatever it defaults to). Intensity normalization will force the grand within-tissue mean of the functional data to be 1000 for each run. -fwhm Full-Width-Half-Max This functionality is somewhat obsolete. Consider using spatialsmooth-sess for 3D smoothing. -fwhm Specifies that within-plane (ie, 2D) spatial smoothing using a Hanning kernel should be performed. The Full-Width-Half-Max (FWHM) indicates the extent of the smoothing and is specified in mm. -nskip N Skip the first N time points in each functional run. It may be necessary to eliminate the first 4 or 5 time points in a functional run because the sample has not reached magnetic equilibrium. This is usually not necessary if the sample was scanned with discarded acquisitions (DISTACQS or DDAs). Note: the nskip does not affect the definition of time=0 in the paradigm file (see -paradigm). This functionality can also be implemented using a time-point exclude file (see -tpef). -tpef filename This is the name of a time point exclude file (TPEF). The TPEF stores a list of times (in seconds) of time points to exclude from the analysis. The TPEF must be found in the run directory with the functional data to which it applies. Like paradigm files, the TPEFs must have the same name across subjects and runs though their contents can differ. Unlike paradigm files, it is not necessary to have a TPEF in each run; if no TPEF is found, no time points are excluded. -polyfit N Drift removal. Fit and remove polynomial of order N. Default is 1 (ie, 0=mean, 1=linear, and 2=quadradic). -nconditions Nc (Shortcut: -nc) (For blocked and event-related designs). This is the number of conditions as found in the paradigm files. When selxavg-sess runs, it checks the number of conditions found the paradigm files against Nc and returns an error if they differ. -timewindow TimeWindow (Shortcut: -tw) (For blocked and event-related designs). If no shape to the hemodynamic response is to be assumed (ie, -gammafit is not used), then this is the amount of time needed to capture the entire event and response, including a prestimulus window. Here, for blocked designs, the event refers to the entire block. If a shape to the hemodynamic response will be assumed (ie, -gammafit is used), then the time window should be long enough to capture the gamma function. In this case, there is no penalty for a long time window. If no time window is selected with -gammafit, an appropriate one will be selected automatically. -extreg extregstem Use external regressors when doing estimation. The external regressors should be stored in the bfloat "volume" with stem extregstem. There should actually be only one file there (extregstem_000.bfloat). It should have one row, and the number of columns should be equal to the number of external regressors. The number of frames must be equal to the number time points. There should be an external regressor file in each run directory. By default, all the regressors will be used, but this can be changed with -nextreg. See also -mcextreg. -nextreg N Use only N external regressors. See -extreg. -mcextreg Use motion parameters as external regressors. This is the same as setting "-extreg mcextreg -nextreg 3". mcextreg is created when running mc-sess by orthognalizing the motion parameters. Only the top three components are used (unless changed with -nextreg). Note: this feature was incorporated into mc-sess on 7/1/02. If motion correction was run before this date, it will need to be re-run in order to create the mcextreg file. -prestim PreStimTimeWindow (Shortcut: -ps) (For blocked and event-related designs). Start averaging PreStimTimeWindow seconds before the onset of the stimulus. This only applies to analyses in which the no shape to the hemodynamic response is to be assumed (ie, -gammafit is not used). -gammafit gfDelta gfTau (For blocked and event-related designs). Assume that the hemodynamic response takes the shape of a gamma function. gfDelta is the hemodynamic delay (ie, the time until the onset of the response), and gfTau is the dispersion, which controls the rise and fall times. Both are specified in seconds. gfAlpha is the exponent for the gamma function (see -gammaexp); for BOLD, alpha=2. The gamma function takes the form: f(t) = ((t-delta)/tau)^alpha * exp(-(t-delta)/tau) -gammaexp gfAlpha Exponent for the gamma function. Default is 2, which tends to fit the BOLD hemodynamic response better. -taumax TauMax (For blocked and event-related designs). This instructs selxavg-sess to estimate and correct for global autocorrelation in the noise. It will assume that the autocorrelation function is zero beyond a delay of TauMax seconds. -mask maskid This only applies when using -taumax. This is a mask (as found in bold/masks) that is used to limit the voxels used in the computation of the whitening fillter. Usually, one would run mkbrainmask-sess to create masks/brain, and then specify brain as maskid. -TER TemporalEstimationResolution (For event-related designs). The TER is the Temporal Estimation Resolution. This is the resolution to which the hemodynamic response will be estimated (in seconds). It must be an integer divisor of the TR. The stimulus schedule (ie, paradigm file) must have been created with with the given TER in mind. -timeoffset toffset (For blocked and event-related designs). The time to add to the times listed in each paradigm file. This is only useful if, for some reason, each paradigm file if off by the same amount. This may happen if there was a systematic delay between the beginning of the stimulus stream and the beginning of scanning. -ncycles N (For retinotopy and AB blocked designs). For designs in which the stimuli are presented periodically, this is the number of cycles of stimulation presented in each run.