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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
Alex,
The make_average_<something> scripts are such that they will exit on any error encountered (via the -e arg to tcsh at the top of the script). It appears make_average_surface is exiting after executing the command:
id | tee - a /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
Can you run the above command (after fixing where it was cut-off in this email) and then run:
echo $status
after that. It will probably not display 0. Is the disk full where that log file is being written to? I am trying to think of reasons why 'id' would exit with a non-zero status.
Nick
On Fri, 2007-10-26 at 12:21 +1000, Alexander Fornito wrote:
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
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
Sorry, what's the error in there?
Alexander Fornito wrote:
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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Alexander Fornito -
Doug Greve -
Nick Schmansky