Hi,
I was able to use surf-sess command (modified in our group) to take pictures
(rgb) of the brain; however, several days ago, I was kept getting errors (even
errors with commands that worked fine before). it keep saying tksurfer.new:
Command not found., then quit. Would you help me out?
Machine: Roma /space/roma/1/users/caplan/plaus2
Env: Standard environment
Subjects_Dir: /space/thor/1/users/west/subjects
[roma:plaus2] (nmr-std-env)
/space/roma/1/users/caplan/plaus2/scripts/surf-sess-rgb_wfile \
? -analysis plaus2_corr \
? -space sph \
? -spacedir sph20 \
? -subject west_margaret \
? -s isxavg-plaus2_corr \
? -contrast implaus_plaus_8-12sum \
? -map sig \
? -fthresh 1.3 \
? -fmid 2.0 \
? -fslope 1 \
? -df dir \
? -isxavg random \
? -avgcurv \
? -offset 0 \
? -wfile
/space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm
in16_minarea300_lh_o.w \
? -hemi lh \
? -rgbname plaus2_corr_implaus_plaus_8-12sum_300
cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory
-----------------------------------------------------------------
surf-sess logfile is /dev/null
-----------------------------------------------------------------
---------->>>>>>>>>>>....<<<<<<<<<<<<--------------------
INFO: You are about to use the NEW version of tksurfer.
INFO: If you want to use the OLD version, re-run surf-sess
INFO: with the -old flag.
---------->>>>>>>>>>>....<<<<<<<<<<<<--------------------
------------------------------------------------------
------------------------------------------------------
Session: isxavg-plaus2_corr ----
------ lh hemisphere ------
sig-0-west_margaret
west_margaret
nowsource
west_margaret
equal
wfile is
/space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm
in16_minarea300_lh_o.w
------------ tcl file -----------
set val
/space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm
in16_minarea300_lh_o.w
sclv_read_binary_values 0
set curv lh.avg_curv
read_binary_curv;
set curvflag 1;
source /usr/local/freesurfer/stable/lib/tcl/readenv.tcl
file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb
file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb
open_window
sclv_set_current_field 0
puts "Taking Snapshots..."
make_lateral_view
redraw
set rgb
/autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum
_300_lh_lat.rgb
save_rgb
rotate_brain_x 90
redraw
set rgb
/autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum
_300_lh_ven.rgb
save_rgb
make_lateral_view
rotate_brain_y 180
redraw
set rgb
/autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum
_300_lh_med.rgb
save_rgb
exit
---------------------------------
----------------------------------------------------------
/autofs/space/roma_001/users/caplan/plaus2/isxavg-plaus2_corr/bold/plaus2_corr/s
ph20-rfx/implaus_plaus_8-12sum
tksurfer.new -west_margaret lh inflated -tcl /tmp/surf-sess-22861.tcl
----------------------------------------------------------
tksurfer.new: Command not found.
Mon May 14 12:43:08 EDT 2007
I am also attaching the /surf-sess-rgb_wfile under command line.
Thanks a lot!
-Jung Min
**********************************************
Jung Min Lee
Neurology/Neuropsychology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Tel: 617-726-0303 (work)
617-780-1900 (cell)
e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
**********************************************
#!/bin/csh -f
# surf-sess
#
set VERSION = '$Id: surf-sess,v 1.1 2003/03/04 21:22:09 greve Exp $'
set FASTVER = `cat $FMRI_ANALYSIS_DIR/docs/version`;
set inputargs = ($argv);
set analysis = ();
set contrast = ();
set rtopymode = ();
set rtopy = 0;
set angleoffset = ();
set angleoffsetcode = ();
set map = sig;
set imageoffset = 0;
set grpname = ();
set space = native;
set spacedir = ();
set norgb = 0;
set rgbstem = ();
set ScriptOnly = 0;
set umaskarg = ();
set hemilist = ();
set subject = ();
set resetsubject = 0;
set srcsubject = ();
set smoothsteps = ();
set surf = ();
set SessList = ();
set isxavgmethod = ();
set nolog = 0;
set nowait = 0;
set flat = 0;
set patch = ();
set UseAvgCurv = 0;
set code = (); # a way to uniquely id a paint, issued by paint-sess
set usenew = ".new";
set usertcl = ();
set Medial = 1;
set Lateral = 1;
set Ventral = 1;
set rgbwd = `pwd`;
## tksurfer variables ###
setenv fthresh 2.0
setenv fslope 0.1
setenv fmid 5.0
if($#argv == 0) then
goto usage_exit;
exit 1;
endif
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) then
set nolog = 1;
endif
##### 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/surf-sess.log
if(-w $LF) then
mv -f $LF $LF.old
else
set LF = /dev/null
endif
else
set LF = /dev/null
endif
echo "-----------------------------------------------------------------"
echo "surf-sess logfile is $LF"
echo "-----------------------------------------------------------------"
echo "surf-sess log file" >> $LF
echo $VERSION >> $LF
echo "FAST Version $FASTVER" >> $LF
id >> $LF
pwd >> $LF
echo "$0" >> $LF
echo $inputargs >> $LF
uname -a >> $LF
date >> $LF
which tksurfer >> $LF
goto parse_args;
parse_args_return:
set SessList = `getsesspath $inputargs`;
if($status) then
echo "$SessList" |& tee -a $LF
exit 1;
endif
goto check_params;
check_params_return:
if($#usenew != 0) then
echo " "
echo " "
echo " "
echo "---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- "
echo "INFO: You are about to use the NEW version of tksurfer."
echo "INFO: If you want to use the OLD version, re-run surf-sess"
echo "INFO: with the -old flag."
echo "---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- "
echo " "
echo " "
echo " "
sleep 2;
else
echo " "
echo " "
echo " "
echo "---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- "
echo "INFO: You are about to use the OLD version of tksurfer."
echo "INFO: If you want to use the NEW version, re-run surf-sess"
echo "INFO: WITHOUT the -old flag."
echo "---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- "
echo " "
echo " "
echo " "
sleep 1;
endif
## Prepare the script, if need be ##
if($ScriptOnly) then
mkdir -p scripts
set scriptfile = scripts/run-surf-$analysis-$contrast
echo "Script File is $scriptfile" |tee -a $LF
rm -f $scriptfile
touch $scriptfile
echo "#\!/bin/csh -f" >> $scriptfile
echo "cd .." >> $scriptfile
chmod a+x $scriptfile
endif
foreach sess ($SessList)
set sessid = `basename $sess`;
echo "------------------------------------------------------"|tee -a $LF
echo "------------------------------------------------------"|tee -a $LF
echo "Session: $sessid ----"|tee -a $LF
## Loop through each hemi (if needed) ##
foreach hemi ($hemilist)
echo "------ $hemi hemisphere ------" |& tee -a $LF
set sessinfo = $sess/session.info
set IsGroup = `grep GroupAverage $sessinfo | wc -l`;
if(! $IsGroup) then
#---- It is an individual average ----#
set regfile = $sess/$fsd/register.dat
if(! -e $regfile) then
echo "ERROR: cannot find $regfile"|tee -a $LF
exit 1;
endif
set srcsubject = `head -n 1 $regfile`;
if($#subject == 0) then
set subject = $srcsubject;
set resetsubject = 1;
set Stat = $map-$imageoffset
else
set Stat = $map-$imageoffset-$subject
endif
if($space == native) then
set spacesubdir = ();
else
set spacesubdir = $spacedir;
endif
else
#---- It is a group average ----#
set srcsubject = $subject;
if($isxavgmethod == "fixed") then
set spacesubdir = $spacedir-ffx
else
set spacesubdir = $spacedir-rfx
endif
set Stat = $map-$imageoffset-$subject
endif
if(! $rtopy ) then
set Stat = $Stat$code
echo $Stat
else
set Stat = map;
endif
## Construct the path to the map ##
## contrast will = () for rtopy ##
set mapdir = $sess/$fsd/$analysis/$spacesubdir/$contrast
if(! -d $mapdir) then
echo "ERROR: $mapdir does not exist" |& tee -a $LF
exit 1;
endif
set StatDir = $mapdir;
set name = $subject;
if(! $rtopy ) then
echo $subject
echo nowsource
echo $srcsubject
if($srcsubject == $subject) then
echo equal
set wfile = $StatDir/$Stat-$hemi.w
else
set wfile = $StatDir/$Stat-$subject-$hemi.w
endif
set wfile = $wfilename
if(! -e $wfile ) then
echo "ERROR: cannot find $wfile"|tee -a $LF
exit 1;
endif
echo "wfile is $wfile" |tee -a $LF
else
if("$rtopymode" == polar || "$rtopymode" == eccen) then
set wfile1 = $StatDir/$rtopymode/map-real-$hemi.w
set wfile2 = $StatDir/$rtopymode/map-imag-$hemi.w
foreach wfile ($wfile1 $wfile2)
if(! -e $wfile) then
echo "ERROR: cannot find $wfile"
exit 1;
endif
end
endif
endif
set surffile = $SUBJECTS_DIR/$subject/surf/$hemi.$surf
if(! -e $surffile) then
echo "ERROR ($sessid): cannot find $surffile" |& tee -a $LF
exit 1;
endif
##############################################################
set SURFER = tksurfer$usenew
if(! $nowait ) then
setenv noexit
else
unsetenv noexit
endif
setenv hemi $hemi
setenv offset 0.4
if($Medial) then
setenv med
else
unsetenv med
endif
if($Lateral) then
setenv lat
else
unsetenv lat
endif
if($Ventral) then
setenv ven
else
unsetenv ven
endif
if( $#usenew == 0 ) then
setenv statflag 1
else
unsetenv statflag
endif
setenv statname
setenv colscale 1
setenv colscalebarflag 1
setenv invphaseflag 0
setenv truncphaseflag 0
if($UseAvgCurv) then
setenv curv $hemi.avg_curv
set fname = $SUBJECTS_DIR/$subject/surf/$curv
if(! -e $fname ) then
echo "ERROR: cannot find average curvature file $curv for $subject"
exit 1;
endif
setenv curvsteps 10
else
setenv curv $hemi.curv
endif
setenv floatstem $Stat
pushd $StatDir > /dev/null
setenv dir .
if($norgb) then
setenv nosave 1
else
setenv nosave 0
if($#rgbstem == 0) then
setenv rgbname $Stat
else
setenv rgbname $rgbstem
endif
mkdir -p $dir/rgb
if(! -d $dir/rgb) then
echo "ERROR: cannot create $dir/rgb"
exit 1;
endif
endif
if($rtopy) then
if($#angleoffset == 0) set angleoffset = 0;
setenv angle_offset $angleoffset;
setenv revpolarflag 0
unsetenv flatzrot
unsetenv flatscale
unsetenv statflag
unsetenv statname
setenv colscale 0
unsetenv colscalebarflag
setenv eccendir eccen
setenv polardir polar
setenv realname -real
setenv complexname -imag
setenv fs fieldsign/fieldsign$angleoffsetcode-$hemi
setenv fm fieldsign/fieldsignmask$angleoffsetcode-$hemi
setenv fthresh 0.4
setenv fslope 1.3
setenv fmid 0.8
endif
set rmtclcmd = 0;
if(! $flat ) then
if(! $rtopy) then
if($#usenew == 1) then
set tclcmd = /tmp/surf-sess-$$.tcl
rm -f $tclcmd
if($#usertcl != 0) cat $usertcl >> $tclcmd
echo "set val $wfile" >> $tclcmd
echo "sclv_read_binary_values 0" >> $tclcmd
if ($#smoothsteps != 0) then
echo "smooth_val $smoothsteps" >> $tclcmd
endif
echo "set curv $curv" >> $tclcmd
echo "read_binary_curv; " >> $tclcmd
echo "set curvflag 1; " >> $tclcmd
echo "source $FREESURFER_HOME/lib/tcl/readenv.tcl" >> $tclcmd
echo "file mkdir $rgbwd/rgb" >> $tclcmd
echo "file mkdir $rgbwd/rgb" >> $tclcmd
set outdir = $rgbwd/rgb
echo "open_window" >> $tclcmd
echo "sclv_set_current_field 0" >> $tclcmd
echo 'puts "Taking Snapshots..."' >> $tclcmd
echo "make_lateral_view" >> $tclcmd
echo "redraw" >> $tclcmd
echo "set rgb $outdir/${rgbstem}_${hemi}_lat.rgb" >> $tclcmd
echo "save_rgb" >> $tclcmd
echo "rotate_brain_x 90" >> $tclcmd
if (${hemi} == 'rh') then
echo "rotate_brain_z 180" >> $tclcmd
endif
echo "redraw" >> $tclcmd
echo "set rgb $outdir/${rgbstem}_${hemi}_ven.rgb" >> $tclcmd
echo "save_rgb" >> $tclcmd
echo "make_lateral_view" >> $tclcmd
echo "rotate_brain_y 180" >> $tclcmd
echo "redraw" >> $tclcmd
echo "set rgb $outdir/${rgbstem}_${hemi}_med.rgb" >> $tclcmd
echo "save_rgb" >> $tclcmd
echo "exit" >> $tclcmd
set rmtclcmd = 1;
echo "------------ tcl file -----------" |& tee -a $LF
cat $tclcmd |& tee -a $LF
echo "---------------------------------" |& tee -a $LF
else
if($#usertcl != 0) then
set tclcmd = /tmp/surf-sess-$$.tcl
cat $usertcl >> $tclcmd
echo twocond-views.tcl >> $tclcmd
set rmtclcmd = 1;
else
set tclcmd = twocond-views.tcl
endif
endif
else
set tclcmd = $rtopymode-views.tcl
endif
else
if(! $rtopy) then
set tclcmd0 = twocond-flat.tcl
else
set tclcmd0 = $rtopymode-flat.tcl
endif
if($#usertcl != 0) then
set tclcmd = /tmp/surf-sess-$$.tcl
cat $usertcl >> $tclcmd
echo $tclcmd0 >> $tclcmd
set rmtclcmd = 1;
else
set tclcmd = $tclcmd0;
endif
setenv use_vertex_arrays 0
setenv patchname $patch
endif
# Construct the tksurfer command-line #
set cmd = ($SURFER -$name $hemi $surf -tcl $tclcmd)
echo "----------------------------------------------------------" |& tee -a $LF
pwd |& tee -a $LF
echo $cmd |& tee -a $LF
echo "----------------------------------------------------------" |& tee -a $LF
$cmd |& tee -a $LF
if($rmtclcmd) rm -f $tclcmd;
popd > /dev/null
##############################################################
if ($resetsubject) then
set subject = ();
endif
end # loop over hemispheres #
end # loop over Sesslist #
date | tee -a $LF
exit 0;
###############################################
############--------------##################
parse_args:
set cmdline = "$argv";
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "-c":
case "-contrast":
if ( $#argv == 0) goto arg1err;
set contrast = $argv[1]; shift;
breaksw
case "-map":
if ( $#argv == 0) goto arg1err;
set map = $argv[1]; shift;
breaksw
case "-subject":
if ( $#argv == 0) goto arg1err;
set subject = $argv[1]; shift;
breaksw
case "-surf":
if ( $#argv == 0) goto arg1err;
set surf = $argv[1]; shift;
breaksw
case "-new":
set usenew = ".new";
breaksw
case "-old":
set usenew = ();
breaksw
case "-space":
if ( $#argv == 0) goto arg1err;
set space = $argv[1]; shift;
breaksw
case "-spacedir":
if ( $#argv == 0) goto arg1err;
set spacedir = $argv[1]; shift;
breaksw
case "-hemi":
if ( $#argv == 0) goto arg1err;
set hemilist = ($hemilist $argv[1]); shift;
breaksw
case "-fthresh":
if ( $#argv == 0) goto arg1err;
setenv fthresh $argv[1]; shift;
breaksw
case "-fmid":
if ( $#argv == 0) goto arg1err;
setenv fmid $argv[1]; shift;
breaksw
case "-fslope":
if ( $#argv == 0) goto arg1err;
setenv fslope $argv[1]; shift;
breaksw
case "-smoothsteps":
if ( $#argv == 0) goto arg1err;
set smoothsteps = $argv[1]; shift;
breaksw
case "-a":
case "-analysis":
if ( $#argv == 0) goto arg1err;
set analysis = $argv[1]; shift;
breaksw
case "-angleoffset":
case "-ao":
if ( $#argv == 0) goto arg1err;
set angleoffset = $argv[1]; shift;
breaksw
case "-angleoffsetcode":
case "-aoc":
if ( $#argv == 0) goto arg1err;
set angleoffsetcode = $argv[1]; shift;
breaksw
case "-isxavg":
if ( $#argv == 0) goto arg1err;
set isxavgmethod = $argv[1]; shift;
set IsGroup = 1;
breaksw
case "-offset":
if ( $#argv == 0) goto arg1err;
set imageoffset = $argv[1]; shift;
breaksw
case "-umask":
if ( $#argv == 0) goto arg1err;
set umaskarg = "-umask $argv[1]";
umask $argv[1]; shift;
breaksw
case "-patch":
if ( $#argv == 0) goto arg1err;
set patch = $argv[1]; shift;
set flat = 1;
breaksw
case "-flat":
set flat = 1;
breaksw
case "-medonly":
set Medial = 1;
set Lateral = 0;
set Ventral = 0;
breaksw
case "-latonly":
set Medial = 0;
set Lateral = 1;
set Ventral = 0;
breaksw
case "-venonly":
set Medial = 0;
set Lateral = 0;
set Ventral = 1;
breaksw
case "-avgcurv":
set UseAvgCurv = 1;
breaksw
case "-code":
if ( $#argv == 0) goto arg1err;
set code = $argv[1]; shift;
breaksw
case "-tcl":
if ( $#argv == 0) goto arg1err;
set usertcl = $argv[1]; shift;
breaksw
case "-retinotopy":
case "-rtopy":
if ( $#argv == 0) goto arg1err;
set rtopymode = $argv[1]; shift;
set rtopy = 1;
breaksw
case "-rgbname":
if ( $#argv == 0) goto arg1err;
set rgbstem = $argv[1]; shift;
breaksw
case "-wfile":
if ( $#argv == 0) goto arg1err;
set wfilename = $argv[1]; shift;
breaksw
case "-norgb":
set norgb = 1;
breaksw
case "-nowait":
set nowait = 1;
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 "-nolog":
breaksw
case "-cwd":
set IsSess = 1; # otherwise, ignore getsesspath arguments
breaksw
case "-group":
echo "ERROR: cannot use -group with surf-sess"
exit 1;
breaksw
case "-s":
case "-sf":
case "-df":
case "-d":
case "-g":
set IsSess = 1; # otherwise, ignore getsesspath arguments
shift;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if ($#analysis == 0) then
echo "ERROR: no sxa name specified"|& tee -a $LF
exit 1
endif
set infofile = $analysis/analysis.info
if(! -e $infofile) then
echo "ERROR: cannot find $infofile"|tee -a $LF
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 $2}'`;
endif
if($rtopy && "$designtype" != "retinotopy") then
echo "ERROR: the design type of analysis $analysis is $designtype."
echo " -retinotopy can only be used with retinotopy designs"
exit 1;
endif
if($rtopy && "$rtopymode" != fieldsign && \
"$rtopymode" != eccen && "$rtopymode" != polar) then
echo "ERROR: retinotopy mode must be either fieldsign, eccen, or polar"
exit 1;
endif
if($rtopymode == fieldsign) set rtopymode = fs;
if($#hemilist == 0) set hemilist = (lh rh);
foreach hs ($hemilist)
if($hs != lh && $hs != rh) then
echo "ERROR: hemi must be either lh or rh ($hs)";
exit 1;
endif
end
if($#contrast == 0 && ! $rtopy ) then
echo "ERROR: no contrast specified"|& tee -a $LF
exit 1
endif
if($#contrast != 0 && $rtopy) then
echo "ERROR: do not specify contrast with retinotopic designs"|& tee -a $LF
exit 1
endif
if($space != "tal" && $space != "sph" && $space != "native" ) then
echo "ERROR: no surf support for space $space "|& tee -a $LF
exit 1
endif
if($#surf == 0) set surf = inflated;
## Determine whether Group or Individual Data ##
foreach sess ($SessList)
set sessinfo = $sess/session.info
set IsGroup = `grep GroupAverage $sessinfo | wc -l`;
end
## Group Contingencies ##
if($IsGroup) then
if($space == "native") then
echo "ERROR: currently no support for painting group data in native
space"\
|& tee -a $LF
exit 1;
endif
if($#subject == 0) then
echo "ERROR: $sess is a group average, need -subject"|& tee -a $LF
exit 1;
endif
if($#isxavgmethod == 0) then
echo "ERROR: must supply -isxavg method with group data" |& tee -a $LF
exit 1;
endif
if($isxavgmethod != "fixed" && $isxavgmethod != "random") then
echo "ERROR: -isxavg must be either fixed or random" |& tee -a $LF
exit 1;
endif
endif
if($#spacedir == 0) set spacedir = $space;
if( ($space == sph || $space == tal) && $#subject == 0) then
echo "ERROR: space $space needs a subject designation"
exit 1;
endif
if(! $nowait && $Lateral && $Medial && $Ventral) then
set Medial = 0;
set Lateral = 1;
set Ventral = 0;
endif
if($#patch == 0) then
set patch = patch;
if($rtopy) set patch = occip.patch.flat
endif
if( $#angleoffset != 0 && ( ! $rtopy || \
($rtopymode != "polar" && $rtopymode != "eccen") )) then
echo "ERROR: can only use -angleoffset with retinotopy designs"
echo " and only with polar or eccen modes"
exit 1;
endif
if( $#angleoffsetcode != 0 && $rtopymode != "fs") then
echo "ERROR: can only use -angleoffsetcode with retinotopy designs"
echo " and only with fieldsign mode"
exit 1;
endif
if($#usertcl != 0) then
if(! -e $usertcl) then
echo "ERROR: cannot find $usertcl"
exit 1;
endif
# Get the full path #
set tmp1 = `dirname $usertcl`;
set tmp2 = `basename $usertcl`;
pushd $tmp1 > /dev/null
set tmp1 = `pwd`;
popd > /dev/null
set usertcl = $tmp1/$tmp2;
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo ""
echo "USAGE: surf-sess"
echo ""
echo "Required Arguments:";
echo " -analysis analysisname : session-level functional analysis name"
echo " -contrast contrastname : contrast name"
echo ""
echo "Optional Arguments:";
echo " -map mapname : <sig>, minsig, iminsig, t"
echo " -offset n : 0-based image offset"
echo " -hemi hemisphere : <lh rh>";
echo " -space spacename : space from which to surf (<native>, tal,
sph)"
echo " -spacedir spacedir : get data from spacedir"
echo " -subject subjectname : name of subject on which to paint (with
group)"
echo " -surf surfacename : name of surface upon which to visualize"
echo " -fthresh fthreshvalue : color map threshold ($fthresh)"
echo " -fmid fmidvalue : middle of the color map ($fmid)";
echo " -fslope fslopevalue : slope of the color scale ($fslope)";
echo " -smoothsteps nsteps : spatial smoothing ($smoothsteps)";
echo " -retinotopy map : eccen, polar, fieldsign";
echo " -flat : display on flattened cortex "
echo " (hemi.patch or hemi.occip.patch.flat for retinotopy)"
echo " -patch patchname : display on flattened hemi.patchname"
echo " -old : use old version of tksurfer"
echo ""
echo "Session Arguments (Required)"
echo " -sf sessidfile "
echo " -df srchdirfile "
echo " -s sessid "
echo " -d srchdir "
echo ""
echo "Session Arguments (Optional)"
echo " -umask umask : set unix file permission mask"
echo " -version : print version and exit"
echo ""
exit 1;
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