That link works for me, but I've attached rtview to this email just in case.
doug
On 06/04/2012 11:03 AM, Michael Bannert wrote:
Dear freesurfer community,
I tried to download rtview but it didn't work. I used the following
URL: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
... as described here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21560.html
I need this function to interpret retinotopic mapping data. I followed
the instructions for running retinotopic mapping using Freesurfer 5 I
found here (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
) and everything seems to work fine but I find it hard to interpret
the results and to determine the boundaries between visual areas.
Could you please tell me where the file can be found? (Or is there a
more elegant way to get a nice color wheel in Freesurfer 5?)
Thank you very much!
Michael
PS: The URL for the FsFast tutorial data still seems to be incorrect
as well. See also
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23019.html
--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of
Tübingen & BCCN Tübingen
Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phone: +49 - (0)7071 / 29 - 89031
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
#!/bin/tcsh -f
# rtview
set VERSION = '$Id$';
set srcsubject = ();
set trgsubject = ();
set realvol = ();
set imagvol = ();
set hemi = ();
set regfile = ();
set hfile = ();
set stimtype = ();
set tmpdir = ();
set cleanup = 1;
set LF = ();
set tclcmd0 = $FREESURFER_HOME/lib/tcl/twocond-views.tcl
set inputargs = ($argv);
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
if($#hfile) then
set srcdir = `dirname $hfile`
else
set srcdir = `dirname $realvol`
endif
if($#tmpdir == 0) set tmpdir = $srcdir/tmpdir.rtview
mkdir -p $tmpdir
if($#LF == 0) set LF = $tmpdir/rtview.log
if($LF != /dev/null) rm -f $LF
echo "Log file for rtview" >> $LF
date | tee -a $LF
echo "" | tee -a $LF
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo "cd `pwd`" | tee -a $LF
echo $0 $inputargs | tee -a $LF
echo "" | tee -a $LF
uname -a | tee -a $LF
set tkimagvol = $tmpdir/tkimag.mgh
set tkrealvol = $tmpdir/tkreal.mgh
rm -f $tkimagvol $tkrealvol
if($#hfile) then
set imagvol = $tmpdir/imag.mgh
set realvol = $tmpdir/real.mgh
mri_convert $hfile --frame 1 $tkimagvol; # 2nd frame
if($status) exit 1;
mri_convert $hfile --frame 2 $tkrealvol; # 3rd frame
if($status) exit 1;
endif
if(! -e $tkimagvol) then
# Multiply by fsig because that is what
mris_calc -o $tkimagvol $fsigvol mul $imagvol
if($status) exit 1;
mris_calc -o $tkrealvol $fsigvol mul $realvol
if($status) exit 1;
endif
foreach cmpx (real imag)
set cmpxvol = $tmpdir/tk"$cmpx".mgh
if($#regfile) then
# Input is a volume, use vol2surf
set cmpxmgh = $tmpdir/map-$cmpx-$hemi.mgh
mri_vol2surf --reg $regfile --mov $cmpxvol --hemi $hemi --o $cmpxmgh \
--mapmethod nnf
if($status) exit 1;
else
set cmpxmgh = $cmpxvol
endif
# Convert to wfile (and maybe change subjects)
set cmpxw = $tmpdir/map-$cmpx-$hemi.w
mri_surf2surf --hemi $hemi --sval $cmpxmgh --tval $cmpxw \
--tfmt paint --srcsubject $srcsubject --trgsubject $trgsubject
if($status) exit 1;
end
#mri_fieldsign --eccen eccen/lh.real.mgh eccen/lh.imag.mgh \
#--polar polar/lh.real.mgh polar/lh.imag.mgh \
# --fs lh.fieldsign.mgh --s els --hemi lh --sphere --old --fwhm 10
setenv angle_offset 0
setenv revpolarflag 0
unsetenv flatzrot
unsetenv flatscale
unsetenv statflag
unsetenv statname
setenv colscale 0
unsetenv colscalebarflag
#setenv eccendir eccen
#setenv polardir polar
setenv floatstem map
setenv realname -real; # map-real-?h.w
setenv complexname -imag; # map-imag-?h.w
setenv fthresh 0.4
setenv fslope 1.3
setenv fmid 0.8
setenv offset 0.4; # for gray scale
setenv hemi $hemi
setenv curv $hemi.curv
setenv nosave 1
setenv noexit
setenv dir $tmpdir
setenv polardir $tmpdir
setenv eccendir $tmpdir
setenv smoothsteps 2
#set tclcmd = $tmpdir/rtview.tcl
#rm -f $tclcmd
#echo "set noexit 1" >> $tclcmd
#cat $tclcmd0 >> $tclcmd
#echo "set dir $tmpdir" >> $tclcmd
#echo "set floatstem map" >> $tclcmd
set tclcmd = $FREESURFER_HOME/lib/tcl/$stimtype-views.tcl
set cmd = (tksurfer $subject $hemi inflated -aparc -tcl $tclcmd)
echo $cmd
$cmd
if($cleanup) rm -f $tmpdir
exit 0
###############################################
############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "--s":
if($#argv < 1) goto arg1err;
set trgsubject = $argv[1]; shift;
set srcsubject = $trgsubject;
breaksw
case "--reg":
if($#argv < 1) goto arg1err;
set regfile = $argv[1]; shift;
if(! -e $regfile) then
echo "ERROR: cannot find $regfile"
exit 1;
endif
set srcsubject = `head -n 1 $regfile`
breaksw
case "--r":
case "--real":
if($#argv < 1) goto arg1err;
set realvol = $argv[1]; shift;
if(! -e $realvol) then
echo "ERROR: cannot find $realvol"
exit 1;
endif
breaksw
breaksw
case "--i":
case "--imag":
if($#argv < 1) goto arg1err;
set imagvol = $argv[1]; shift;
if(! -e $imagvol) then
echo "ERROR: cannot find $imagvol"
exit 1;
endif
breaksw
case "--fsig":
if($#argv < 1) goto arg1err;
set fsigvol = $argv[1]; shift;
if(! -e $fsigvol) then
echo "ERROR: cannot find $fsigvol"
exit 1;
endif
breaksw
case "--h":
if($#argv < 1) goto arg1err;
set hfile = $argv[1]; shift;
if(! -e $hfile) then
echo "ERROR: cannot find $hfile"
exit 1;
endif
breaksw
case "--hemi":
if($#argv < 1) goto arg1err;
set hemi = $argv[1]; shift;
breaksw
case "--lh":
set hemi = lh;
breaksw
case "--rh":
set hemi = rh;
breaksw
case "--log":
if($#argv < 1) goto arg1err;
set LF = $argv[1]; shift;
breaksw
case "--nolog":
case "--no-log":
set LF = /dev/null
breaksw
case "--tmpdir":
if($#argv < 1) goto arg1err;
set tmpdir = $argv[1]; shift;
set cleanup = 0;
breaksw
case "--no-cleanup":
case "--nocleanup":
set cleanup = 0;
breaksw
case "--polar":
set stimtype = polar
breaksw
case "--eccen":
set stimtype = eccen
breaksw
case "--cleanup":
set cleanup = 1;
breaksw
case "--debug":
set verbose = 1;
set echo = 1;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#stimtype == 0) then
echo "ERROR: must --eccen or --polar"
exit 1;
endif
if($#trgsubject == 0) set trgsubject = $srcsubject
if($#trgsubject == 0) then
echo "ERROR: must spec subject or reg"
exit 1;
endif
foreach subject ($srcsubject $trgsubject)
if(! -e $SUBJECTS_DIR/$subject) then
echo "ERROR: cannot find $subject"
exit 1;
endif
end
if($#hemi == 0) then
echo "ERROR: must spec hemi"
exit 1;
endif
if($#fsigvol == 0) then
echo "ERROR: must spec fsigvol"
exit 1;
endif
if($#realvol == 0) then
echo "ERROR: must spec real vol"
exit 1;
endif
if($#imagvol == 0) then
echo "ERROR: must spec imag vol"
exit 1;
endif
if(0 && $#hfile == 0) then
echo "ERROR: must spec hfile"
exit 1;
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo ""
echo "rtview"
echo ""
echo " --s subject : subject to use as display"
echo " --hemi hemi, --lh, --rh"
echo " --eccen or --polar"
echo " --real real : real (cosine) values"
echo " --imag imag : imaginary (sine) values"
echo " --fsig fsig : significances"
echo ""
echo " --reg regfile : for when real/imag/fsig are volumes "
echo ""
echo " --no-cleanup : don't delete tmp dir"
echo ""
# echo " --src srcsubject : map to this subject"
# echo " --h hfile : eg, eccen/h.nii"
# 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
View FSFAST version 5 retinotopy data using the color wheel. This is a
front-end for tksurfer. It sets up the environment for using the
color wheel.
The source data (real/imaginary/fsig) can be either in the volume or
the surface. If in the volume, then you need to supply a registration
file with --reg (and no need to supply a subject name with --s).
For displaying data already on the surface:
cd sess/bold/rtopy.lh
rtview --s subject --lh --eccen \
--real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii
rtview --s subject --lh --polar \
--real polar/real.nii --imag polar/imag.nii --fsig polar/fsig.nii
For displaying in the native volume:
cd sess/bold/rtopy.native
rtview --reg ../register.dof6.dat --lh --eccen \
--real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii
rtview --reg ../register.dof6.dat --lh --polar \
--real polar/real.nii --imag polar/imag.nii --fsig polar/fsig.nii
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