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