# tests based on a newly create image (via nifti_tool)

set prefix = out.c21.c

# create a new image, and note outfile for other commands
nifti_tool -mod_hdr -mod_field descrip 'dataset with mods'      \
        -new_dim 3 10 20 30 0 0 0 0                             \
        -infiles MAKE_IM -prefix $prefix.10.nii
set tfile11 = $prefix.10.nii
nifti_tool -mod_hdr -mod_field slice_start 3 -mod_field slice_duration 0.04 \
        -infiles $tfile11 -overwrite

# create ASCII based image as alternate
nifti_tool -mod_nim -mod_field descrip 'try ASCII'              \
        -infiles $tfile11 -prefix $prefix.11.nia -debug 3
set tfile12 = $prefix.11.nia

# add some extensions, then display them
nifti_tool -add_ext 6 'adding extension type 6 (comment)' \
        -infiles $tfile12 -overwrite
nifti_tool -add_comment_ext 'and now for a formal comment' \
        -infiles $tfile12 -overwrite


nifti_tool -rm_ext 1 -infiles $tfile12 -debug 3 -overwrite

# ... and add an extension from a file
cat > $prefix.my_extension.txt << EOF
here is some formatted
  extension, added via some stupid text file
EOF
nifti_tool -add_afni_ext "file:$prefix.my_extension.txt" \
           -infiles $tfile12 -prefix $prefix.11.b.nii.gz
nifti_tool -diff_hdr1 -infiles $tfile11 $prefix.11.b.nii.gz



nifti_tool -disp_exts -infiles $prefix.11.b.nii.gz
nifti_tool -check_nim -infiles $prefix.11.b.nii.gz
nifti_tool -disp_hdr1 -infiles $prefix.11.b.nii.gz -field descrip
nifti_tool -disp_ana  -infiles $prefix.11.b.nii.gz
nifti_tool -strip_extras -infiles $tfile12 -debug 3 -overwrite


# and compare (as nim, we are not allowed to diff different hdr types)
nifti_tool -diff_nim -debug 3 -infiles $tfile11 $tfile12

# try swapping
nifti_tool -swap_as_nifti -debug 3 -infiles $tfile11 \
           -prefix $prefix.12.a.swap.nii
nifti_tool -swap_as_analyze -debug 3 -infiles $tfile11 \
           -prefix $prefix.12.b.swap.ana.nii
nifti_tool -swap_as_old -debug 3 -infiles $prefix.12.b.swap.ana \
           -prefix $prefix.13.c.swap.old.nii

# collapse third dimension
nifti_tool -debug 3 -infiles $tfile12                            \
           -cci -1 -1 17 0 0 0 0 -prefix $prefix.13.nia