Sorry, I ran the --debug flag after running the first command. It is not
the cause of the error. Here is the output after testavg has been deleted.
make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07
cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30
cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40
cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52
cann53 cann54 cann55 cann56 --out testavg --debug
set verbose = 1
if ( $getting_subjects ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( ! $?SUBJECTS ) then
if ( ! 1 ) then
if ( ! $?SUBJECTS_DIR ) then
if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then
if ( ! $?FREESURFER_HOME ) then
if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then
if ( ! -e /usr/local/freesurfer_4.0 ) then
if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR ;
if ( 0 == 0 ) set sdout =
/data/kang/work/struct/alex/freesurfer/subjects_cann
set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann
goto check_params_return ;
goto check_params_return
set ddir = ${sdout}/${average_subject}
set ddir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
mkdir -p ${ddir} ${ddir}/surf ${ddir}/mri ${ddir}/mri/transforms
${ddir}/scripts ${ddir}/label ${ddir}/stats
mkdir -p /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/surf
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/mri
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/mri/transforms
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/label
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/stats
set LF = ${ddir}/scripts/make_average_surface.log
set LF =
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
) mv
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log.bak
echo $VERSION | tee -a $LF
echo $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
$Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
date | tee -a $LF
date
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
Fri Oct 26 12:30:42 EST 2007
pwd | tee -a $LF
pwd
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
/data/kang/work/struct/alex/freesurfer/subjects_cann
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
echo "output ddir is $sdout" | tee -a $LF
echo output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
id | tee -a $LF
id
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003
Alex,
It looks like the subject 'testavg' already exists. To overwrite it,
add --force to the make_average_subject, or choose a different name for
the --out arg (or delete the 'testavg' subject).
Nick
On Fri, 2007-10-26 at 11:03 +1000, Alexander Fornito wrote:
Hi all,
I've been having problems with make_average_subject. The command and
error
are below. Below this is the same command with the output generated by
the
--debug flag.
I am running version 4.0 (redhat) on Linux Debian.
I'd appreciate any help on this.
Thanks,
Alex
make_average_surface --subjects cann01 cann02 cann04 cann05 cann06
cann07
cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30
cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40
cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52
cann53 cann54 cann55 cann56 --out testavg
$Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
Fri Oct 26 11:03:31 EST 2007
/data/kang/work/struct/alex/freesurfer/subjects_cann
setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003
make_average_subject --subjects cann01 cann02 cann04 cann05 cann06
cann07
cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30
cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40
cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52
cann53 cann54 cann55 cann56 --out testavg --debug
set verbose = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( ! $?SUBJECTS_DIR ) then
if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then
if ( ! $?FREESURFER_HOME ) then
if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then
if ( ! -e /usr/local/freesurfer_4.0 ) then
if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR
if ( 0 == 0 ) set sdout =
/data/kang/work/struct/alex/freesurfer/subjects_cann
set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann
set outdir = $sdout/$average_subject
set outdir =
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
if ( -e $outdir && ! $Force ) then
if ( -e /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg &&
!
0 ) then
echo "ERROR: $outdir already exists, select a new average subject name"
echo ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
already exists, select a new average subject name
ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
already exists, select a new average subject name
echo " or delete and rerun"
echo or delete and rerun
or delete and rerun
exit 1 ;
exit 1
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer