Hi Doug, Here is the output Thanks. -Michelle BOTANICA:/usr/local/freesurfer/subjects/retinotopy/sj25/bold/rtopy.self.rh> rtview.sh --debug --s sj25 --lh --eccen --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii set echo = 1 ; breaksw breaksw
end end while ( $#argv != 0 ) while ( 10 != 0 ) set flag = $argv[1] ; shift ; set flag = --s shift switch ( $flag ) switch ( --s ) if ( $#argv < 1 ) goto arg1err ; if ( 9 < 1 ) goto arg1err set trgsubject = $argv[1] ; shift ; set trgsubject = sj25 shift set srcsubject = $trgsubject ; set srcsubject = sj25 breaksw breaksw end end while ( $#argv != 0 ) while ( 8 != 0 ) set flag = $argv[1] ; shift ; set flag = --lh shift switch ( $flag ) switch ( --lh ) set hemi = lh ; set hemi = lh breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = --eccen shift switch ( $flag ) switch ( --eccen ) set stimtype = eccen set stimtype = eccen breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 ) set flag = $argv[1] ; shift ; set flag = --real shift switch ( $flag ) switch ( --real ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set realvol = $argv[1] ; shift ; set realvol = eccen/real.nii shift if ( ! -e $realvol ) then if ( ! -e eccen/real.nii ) then echo "ERROR: cannot find $realvol" echo ERROR: cannot find eccen/real.nii ERROR: cannot find eccen/real.nii exit 1 ; exit 1 On Tue, Dec 13, 2011 at 11:39 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Can you run it with --debug and send me the terminal output? > > Michelle Umali wrote: >> >> Dear All, >> I am still having trouble generating polar and eccen maps with rtview. >> >> I did this: >> cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh >> rtview.sh --s sj07 --lh --eccen \ >> --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii >> >> The subjectname file is in $SUBJECTS_DIR/retinotopy/sj07 >> and I've tried when a copy of rtview is in >> $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh or in >> $SUBJECTS_DIR/retinotopy >> >> The error I got : ERROR: cannot find eccen/real.nii even though all >> the appropriate images exist in the directories and can be seen >> through tksurfer-sess. >> >> Where am I going wrong? >> >> Thanks. >> Michelle >> _______________________________________________ >> 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 > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
