-- 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 # # func2sph-sess # # with version 1.7, the old vss functions are no longer used. # Passing "-old" as an argument will invoke the old func2sphere-sess # (now called func2sphere-sess-vss). # # Original Author: Doug Greve # CVS Revision Info: # $Author: greve $ # $Date: 2008/05/13 20:43:35 $ # $Revision: 1.8.2.1 $ # # Copyright (C) 2002-2007, # The General Hospital Corporation (Boston, MA). # All rights reserved. # # Distribution, usage and copying of this software is covered under the # terms found in the License Agreement file named 'COPYING' found in the # FreeSurfer source code root directory, and duplicated here: # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense # # General inquiries: freesurfer@nmr.mgh.harvard.edu # Bug reports: analysis-bugs@nmr.mgh.harvard.edu # set VERSION = '$Id: func2sph-sess,v 1.8.2.1 2008/05/13 20:43:35 greve Exp $'; set inputargs = ($argv); set analysis = (); set ScriptOnly = 0; set umaskarg = (); set hemilist = (); set nolog = 0; set sphdir = sph set IcoOrder = 7; set ProjFrac = (); set ProjFracMin = (); set ProjFracMax = (); set ProjFracDelta = (); set Surface = "white"; set SurfaceReg = "sphere.reg" set Float2Int = (); set MapMethod = nnfr; # for surf2surf set TrgSubject = ico set Interp = "nearest"; set synth = 0; set fwhm = (); if($#argv == 0) goto usage_exit; # look for "-old" or "-vss" flag # foreach a ($argv) if("$a" == "-old" || "$a" == "-vss") then echo "INFO: running old verssion of func2sph-sess" func2sph-sess-vss $argv; exit $status; endif end # look for version string # set n = `echo $argv | grep version | wc -l` if($n != 0) then echo $VERSION exit 0; endif ## Look for nolog option ## set n = `echo $argv | grep nolog | wc -l` if($n != 0) set nolog = 1; ##### Create a log file ###### if(! $nolog) then set logdir = `pwd`/log; mkdir -p $logdir if(! -e $logdir) then echo "ERROR: could not create $logdir" exit 1; endif set LF = $logdir/func2sph-sess.log if(-e $LF) mv $LF $LF.old else echo "No log file" set LF = /dev/null endif echo "----------------------------------------------------------" echo "func2sph-sess logfile is $LF" echo "----------------------------------------------------------" echo "fucn2sph-sess log file" >> $LF echo $VERSION >> $LF pwd >> $LF echo "$0" >> $LF echo $inputargs >> $LF uname -a >> $LF date >> $LF which mri_vol2surf >> $LF set SessList = `getsesspath $argv`; if($status || $#SessList == 0) then echo "ERROR: cannot find any sessions" | tee -a $LF exit 1; endif goto parse_args; parse_args_return: goto check_params; check_params_return: ## Get functional subdirectory from the info file ## set infofile = $analysis/analysis.info if(! -e $infofile) then echo "ERROR: cannot find $infofile" exit 1; endif set fsd = `cat $infofile | awk '{if($1 == "fsd") print $2}'`; set designtype = `cat $infofile | awk '{if($1 == "designtype") print $2}'`; if($#designtype == 0) then set designtype = `cat $infofile | awk '{if($1 == "avgtype") print $2}'`; endif ####### Go through each session ###### set StartDate = `date`; set nth = 1; foreach sess ($SessList) set sessid = `basename $sess`; echo "-----------------------------------------------------" |& tee -a $LF echo "-----------------------------------------------------" |& tee -a $LF echo "Session: $sessid $nth/$#SessList" |& tee -a $LF echo $StartDate date |& tee -a $LF @ nth = $nth + 1; # Make sure the Session Dir exists (redundant) ## if(! -d $sess) then echo "ERROR: $sess does not exist" |& tee -a $LF exit 1; endif ## Go to the functional subdirectory for the session ## pushd $sess/$fsd > /dev/null df . |& tee -a $LF ## Prepare the script, if need be ## if($ScriptOnly) then if(! -d scripts) mkdir scripts set scriptfile = scripts/run-func2sph-$analysis rm -f $scriptfile touch $scriptfile echo "#!/bin/csh -f" >> $scriptfile echo "cd .." >> $scriptfile chmod a+x $scriptfile endif set srcreg = register.dat if(! -e $srcreg) then echo "ERROR: $srcreg does not exist, try running autoreg-sess"| tee -a $LF exit 1; endif set regsubject = `cat $srcreg | head -n 1`; set snf = ../subjectname if(! -e $snf) then echo "ERROR: cannot find subjectname file for session $sessid" exit 1; endif set subject = `cat $snf`; if($regsubject != $subject) then echo "ERROR: $sessid : subject in register.dat ($regsubject)" | tee -a $LF echo " and subjectname file ($subject) do not match" | tee -a $LF echo " Try re-running auotreg-sess." | tee -a $LF exit 1; endif if(! -e $SUBJECTS_DIR/$subject) then echo "ERROR: cannot find $subject in SUBJECTS_DIR," echo " SUBJECTS_DIR = $SUBJECTS_DIR" exit 1; endif # If retinotopy, scroll through both eccen and polar # if("$designtype" != "retinotopy") then set list = ($analysis) else set list = (eccen polar) endif foreach item ($list) foreach hemi ($hemilist) foreach h (h offset) if("$designtype" != "retinotopy") then mkdir -p $analysis/$sphdir if($h == h) then set funcstem = $analysis/h set sphstem = `pwd`/$analysis/$sphdir/h-$hemi else set funcstem = $analysis/h-offset set sphstem = `pwd`/$analysis/$sphdir/h-$hemi-offset endif else echo "---------------------------------------------" echo "$analysis/$sphdir/$item" mkdir -p $analysis/$sphdir/$item if($h == h) then set funcstem = $analysis/$item/h set sphstem = `pwd`/$analysis/$sphdir/$item/h-$hemi else set funcstem = $analysis/$item/h-offset set sphstem = `pwd`/$analysis/$sphdir/$item/h-$hemi-offset endif endif if($#Float2Int == 0) then set Float2Int = `cat $srcreg | awk '{if($1 == "round") print "round"; if($1 == "floor") print "floor"; if($1 == "tkregister") print "tkreg";}'` endif if($#Float2Int == 0) set Float2Int = tkreg; echo "Using Float2Int = $Float2Int"|& tee -a $LF #set v2s = /space/greve/1/users/greve/build/mri_vol2surf/mri_vol2surf set v2s = mri_vol2surf set fname = `stem2fname $funcstem` set cmd = (); set cmd = ($cmd $v2s --srcvol $fname --srcreg $srcreg) set cmd = ($cmd --trgsubject $TrgSubject $IcoOrderOption) set cmd = ($cmd --mapmethod $MapMethod) set cmd = ($cmd --hemi $hemi --surf $Surface --surfreg $SurfaceReg) set cmd = ($cmd --out $sphstem.$FSF_OUTPUT_FORMAT --float2int $Float2Int) set cmd = ($cmd --interp $Interp) if($#fwhm != 0) set cmd = ($cmd --fwhm $fwhm) if($synth != 0) set cmd = ($cmd --srcsynth -1) if($#ProjFrac) set cmd = ($cmd --projfrac $ProjFrac) if($#ProjFracMin) set cmd = ($cmd --projfrac-int $ProjFracMin $ProjFracMax $ProjFracDelta) echo "------------------------------------------------" |& tee -a $LF pwd |& tee -a $LF echo $cmd |& tee -a $LF echo "------------------------------------------------" |& tee -a $LF $cmd |& tee -a $LF if($status) then echo "ERROR ($sess): vol2surf failed" |& tee -a $LF exit 1; endif end # Loop over hstems # if("$designtype" == "abblocked") then # Create the sig map # bfileconvert -i $analysis/$sphdir/h-$hemi \ -o $analysis/$sphdir/avb/sig-$hemi -fp 0 -np 1 |& tee -a $LF if($status) then echo "ERROR: bfileconvert for sig map failed" |& tee -a $LF exit 1; endif cp $analysis/h.sfa $analysis/$sphdir/h-$hemi.sfa endif end # Loop over hemispheres # end # Loop over items # if("$designtype" == "retinotopy") then # Create the h-offset in sphdir # meanimg -o $analysis/$sphdir/h-offset-$hemi \ -i $analysis/$sphdir/eccen/h-$hemi-offset \ -i $analysis/$sphdir/polar/h-$hemi-offset |& tee -a $LF if($status) then echo "ERROR: meanimg failed" |& tee -a $LF exit 1; endif cp $analysis/polar/h.sfa $analysis/$sphdir/eccen/h-$hemi.sfa cp $analysis/eccen/h.sfa $analysis/$sphdir/polar/h-$hemi.sfa endif popd > /dev/null echo " " |& tee -a $LF echo " " end # Loop over sessions # echo "-----------------------------------------------------" |& tee -a $LF echo $StartDate | tee -a $LF date | tee -a $LF echo "func2sph-sess completed SUCCESSFULLY" | tee -a $LF echo " " echo " " exit 0; ############################################### ############--------------################## parse_args: set cmdline = ($argv); while( $#argv != 0 ) set flag = $argv[1]; shift; switch($flag) case "-a": case "-analysis": if ( $#argv == 0) goto arg1err; set analysis = $argv[1]; shift; breaksw case "-hemi": if ( $#argv == 0) goto arg1err; set hemi = $argv[1]; shift; if($hemi != rh && $hemi != lh) then echo "ERROR: hemi must be either lh or rh ($hemi)" exit 1; endif set hemilist = ($hemilist $hemi) breaksw case "--version": case "-version": echo $VERSION exit 0; breaksw case "-projfrac" if ( $#argv == 0) goto arg1err; set ProjFrac = $argv[1]; shift; breaksw case "-projfrac-int" if( $#argv < 3) then echo "ERROR: $flag needs 3 arguments" exit 1; endif set ProjFracMin = $argv[1]; shift; set ProjFracMax = $argv[1]; shift; set ProjFracDelta = $argv[1]; shift; breaksw case "-icoorder" if ( $#argv == 0) goto arg1err; set IcoOrder = $argv[1]; shift; breaksw case "-surfreg" if ( $#argv == 0) goto arg1err; set SurfaceReg = $argv[1]; shift; breaksw case "-float2int" if ( $#argv == 0) goto arg1err; set Float2Int = $argv[1]; shift; breaksw case "-trgsubject" if ( $#argv == 0) goto arg1err; set TrgSubject = $argv[1]; shift; breaksw case "-paintsurf": if ( $#argv == 0) goto arg1err; set Surface = $argv[1]; shift; breaksw case "-mapmethod": if ( $#argv == 0) goto arg1err; set MapMethod = $argv[1]; shift; breaksw case "-fwhm": if ( $#argv == 0) goto arg1err; set fwhm = $argv[1]; shift; breaksw case "-interp": if ( $#argv == 0) goto arg1err; set Interp = $argv[1]; shift; breaksw case "-synth": set synth = 1; breaksw case "-spacedir": case "-sphdir": if ( $#argv == 0) goto arg1err; set sphdir = $argv[1]; shift; breaksw case "-umask": if ( $#argv == 0) goto arg1err; set umaskarg = "-umask $argv[1]"; umask $argv[1]; shift; breaksw case "-nofuncvit": case "-nofuncvits": # ignored (historical) breaksw case "-verbose": set verbose = 1; breaksw case "-echo": set echo = 1; breaksw case "-debug": set verbose = 1; set echo = 1; breaksw case "-scriptonly": set ScriptOnly = 1; breaksw case "-cwd": case "-nolog": breaksw case "-g": case "-s": case "-sf": case "-df": case "-d": # ignore getsesspath arguments shift; breaksw default: echo ERROR: Flag $flag unrecognized. echo $cmdline exit 1 breaksw endsw end goto parse_args_return; ############--------------################## ############--------------################## check_params: if ($#SessList == 0) then echo "ERROR: no sessions specified"|& tee -a $LF exit 1 endif if ($#analysis == 0) then echo "ERROR: no sxa name specified"|& tee -a $LF exit 1 endif if ($#hemilist == 0) set hemilist = (lh rh); if($TrgSubject == ico) then set IcoOrderOption = (--icoorder $IcoOrder) else set IcoOrderOption = (); endif if($#ProjFrac && $#ProjFracMin) then echo "ERROR: cannot specify --projfrac and --projfrac-int" exit 1; endif goto check_params_return; ############--------------################## ############--------------################## arg1err: echo "ERROR: flag $flag requires one argument" exit 1 ############--------------################## ############--------------################## usage_exit: echo " " echo "USAGE: func2sph-sess" echo " " echo "Required Arguments:"; echo " -analysis analysisname : session-level functional analysis name" echo " " echo "Optional Arguments:"; echo " -hemi hemilist : lh, rh, or <lh rh>" echo " -surf surfacename : resample onto surfacename <white>" echo " -surfreg surfacename : use surfacename for registration <sphere.reg>" echo " -trgsubject subjectname : resample onto subject instead of ico" echo " -icoorder order : icosahedron order 0-7 <7>" echo " -mapmethod method: <nnfr> or nnf " echo " -float2int method: <tkreg>, floor, round" echo " -projfrac fraction: resample fraction of thickness into gray" echo " -projfrac-int min max delta: average along normal" echo " -spacedir : save data to spacedir (sph)" echo " -umask umask : set unix file permission mask" echo " -version : print version and exit" echo " -fwhm fwhm : smooth the volume before resampling (good with -synth) " echo " -synth : synthesize volume with white gaussian noise" echo " " echo "Session Arguments " echo " -sf sessidfile ..." echo " -df srchdirfile ..." echo " -s sessid ..." echo " -d srchdir ..." echo " " exit 1;