vol2subfield --debug --i mean_func.nii.gz --reg M80301954_20190314 --sf /pl/active/ics/data/projects/hutchisonlab/studies/alcohol/AIM/FreeSurfer_data/fs_files/M80301954_20190314/mri/ThalamicNuclei.v12.T1.mgz --o BOLD_thalamus.mgz >> vol2subfield_debug.txt
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --i
shift

switch ( $flag )
switch ( --i )
if ( $#argv < 1 ) goto arg1err ;
if ( 7 < 1 ) goto arg1err
set invol = $argv[1] ; shift ;
set invol = mean_func.nii.gz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --reg
shift

switch ( $flag )
switch ( --reg )
if ( $#argv < 1 ) goto arg1err ;
if ( 5 < 1 ) goto arg1err
set reg = $argv[1] ; shift ;
set reg = M80301954_20190314
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 4 != 0 )

set flag = $argv[1] ; shift ;
set flag = --sf
shift

switch ( $flag )
switch ( --sf )
if ( $#argv < 1 ) goto arg1err ;
if ( 3 < 1 ) goto arg1err
set subfieldvol = $argv[1] ; shift ;
set subfieldvol = /pl/active/ics/data/projects/hutchisonlab/studies/alcohol/AIM/FreeSurfer_data/fs_files/M80301954_20190314/mri/ThalamicNuclei.v12.T1.mgz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 2 != 0 )

set flag = $argv[1] ; shift ;
set flag = --o
shift

switch ( $flag )
switch ( --o )
if ( $#argv < 1 ) goto arg1err ;
if ( 1 < 1 ) goto arg1err
set outvol = $argv[1] ; shift ;
set outvol = BOLD_thalamus.mgz
shift
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 ( $#invol == 0 ) then
if ( 1 == 0 ) then
if ( $#subfieldvol == 0 ) then
if ( 1 == 0 ) then
if ( $#reg == 0 ) then
if ( 1 == 0 ) then

set subject = `reg2subject --r $reg`
set subject = `reg2subject --r $reg`
reg2subject --r M80301954_20190314
set orig = $SUBJECTS_DIR/$subject/mri/orig.mgz
set orig = /pl/active/ics/data/projects/hutchisonlab/studies/alcohol/AIM/FreeSurfer_data/fs_files/ERROR: cannot find M80301954_20190314/mri/orig.mgz
set: Variable name must contain alphanumeric characters.