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 greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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