It really thinks that eccen/real.nii does not exist. What does ls -l eccen/real.nii return?
Michelle Umali wrote: > 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 > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
