AFNI program: nifti_tool
Output of -help
nifti_tool - display, modify or compare nifti headers
- display, modify or compare nifti structures in datasets
- copy a dataset by selecting a list of volumes from the original
- copy a dataset, collapsing any dimensions, each to a single index
- display a time series for a voxel, or more generally, the data
from any collapsed image, in ASCII text
This program can be used to display information from nifti datasets,
to modify information in nifti datasets, to look for differences
between two nifti datasets (like the UNIX 'diff' command), and to copy
a dataset to a new one, either by restricting any dimensions, or by
copying a list of volumes (the time dimension) from a dataset.
Only one action type is allowed, e.g. one cannot modify a dataset
and then take a 'diff'.
one can display - any or all fields in the nifti_1_header structure
- any or all fields in the nifti_image structure
- any or all fields in the nifti_analyze75 structure
- the extensions in the nifti_image structure
- the time series from a 4-D dataset, given i,j,k
- the data from any collapsed image, given dims. list
one can check - perform internal check on the nifti_1_header struct
(by nifti_hdr_looks_good())
- perform internal check on the nifti_image struct
(by nifti_nim_is_valid())
one can modify - any or all fields in the nifti_1_header structure
- any or all fields in the nifti_image structure
- swap all fields in NIFTI or ANALYZE header structure
add/rm - any or all extensions in the nifti_image structure
remove - all extensions and descriptions from the datasets
one can compare - any or all field pairs of nifti_1_header structures
- any or all field pairs of nifti_image structures
one can copy - an arbitrary list of dataset volumes (time points)
- a dataset, collapsing across arbitrary dimensions
(restricting those dimensions to the given indices)
one can create - a new dataset out of nothing
Note: to learn about which fields exist in either of the structures,
or to learn a field's type, size of each element, or the number
of elements in the field, use either the '-help_hdr' option, or
the '-help_nim' option. No further options are required.
See -help_hdr, -help_hdr1, -help_hdr2, -help_ana,
-help_nim, -help_nim1, -help_nim2.
------------------------------
usage styles:
nifti_tool -help : show this help
nifti_tool -help_hdr : show nifti_2_header field info
nifti_tool -help_hdr1 : show nifti_1_header field info
nifti_tool -help_hdr2 : show nifti_2_header field info
nifti_tool -help_nim : show nifti_image (2) field info
nifti_tool -help_nim1 : show nifti1_image field info
nifti_tool -help_nim2 : show nifti2_image field info
nifti_tool -help_ana : show nifti_analyze75 field info
nifti_tool -help_datatypes : show datatype table
nifti_tool -ver : show the current version
nifti_tool -ver_man : show man page formatted version
nifti_tool -see_also : show the 'SEE ALSO' string
nifti_tool -hist : show the modification history
nifti_tool -nifti_ver : show the nifti library version
nifti_tool -nifti_hist : show the nifti library history
nifti_tool -with_zlib : was library compiled with zlib
nifti_tool -check_hdr -infiles f1 ...
nifti_tool -check_nim -infiles f1 ...
nifti_tool -copy_brick_list -infiles f1'[indices...]'
nifti_tool -copy_collapsed_image I J K T U V W -infiles f1
nifti_tool -make_im -prefix new_im.nii
nifti_tool -disp_hdr [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_hdr1 [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_hdr2 [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_nim [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_ana [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_exts -infiles f1 ...
nifti_tool -disp_cext -infiles f1 ...
nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...
nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...
nifti_tool -mod_hdr [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1
nifti_tool -mod_hdr2 [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1
nifti_tool -mod_nim [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1
nifti_tool -swap_as_nifti -overwrite -infiles f1
nifti_tool -swap_as_analyze -overwrite -infiles f1
nifti_tool -swap_as_old -overwrite -infiles f1
nifti_tool -add_afni_ext 'extension in quotes' [...] -infiles f1
nifti_tool -add_comment_ext 'extension in quotes' [...] -infiles f1
nifti_tool -add_comment_ext 'file:FILENAME' [...] -infiles f1
nifti_tool -rm_ext INDEX [...] -infiles f1 ...
nifti_tool -strip_extras -infiles f1 ...
nifti_tool -diff_hdr [-field FIELDNAME] [...] -infiles f1 f2
nifti_tool -diff_hdr1 [-field FIELDNAME] [...] -infiles f1 f2
nifti_tool -diff_hdr2 [-field FIELDNAME] [...] -infiles f1 f2
nifti_tool -diff_nim [-field FIELDNAME] [...] -infiles f1 f2
------------------------------
selected examples:
A. checks header (for problems):
1. nifti_tool -check_hdr -infiles dset0.nii dset1.nii
2. nifti_tool -check_hdr -infiles *.nii *.hdr
3. nifti_tool -check_hdr -quiet -infiles *.nii *.hdr
B. show header differences:
1. nifti_tool -diff_hdr -infiles dset0.nii dset1.nii
2. nifti_tool -diff_hdr1 -infiles dset0.nii dset1.nii
3. nifti_tool -diff_hdr2 -field dim -field intent_code \
-infiles dset0.nii dset1.nii
4. nifti_tool -diff_hdr1 -new_dims 3 10 20 30 0 0 0 0 \
-infiles my_dset.nii MAKE_IM
C. display structures or fields:
1. nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii
2. nifti_tool -disp_hdr1 -field dim -field descrip -infiles dset.nii
3. nifti_tool -disp_hdr2 -field dim -field descrip -infiles dset.nii
4. nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii
5. nifti_tool -disp_cext -infiles dset0.nii dset1.nii dset2.nii
6. nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii
7. nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii
8. nifti_tool -disp_ana -infiles analyze.hdr
9. nifti_tool -disp_nim -infiles nifti.nii
10. nifti_tool -disp_hdr -field HDR_SLICE_TIMING_FIELDS \
-infiles epi.nii
11. nifti_tool -disp_hdr -field NIM_SLICE_TIMING_FIELDS \
-infiles epi.nii
D. create a new dataset from nothing:
1. nifti_tool -make_im -prefix new_im.nii
2. nifti_tool -make_im -prefix float_im.nii \
-new_dims 3 10 20 30 0 0 0 0 -new_datatype 16
3. nifti_tool -mod_hdr -mod_field descrip 'dataset with mods' \
-new_dims 3 10 20 30 0 0 0 0 \
-prefix new_desc.nii -infiles MAKE_IM
4. Given a raw data file VALS.dat of 80x40x20 floats, with
grid spacing 0.5mm x 1mm x 2mm, make a 2-file NIFTI dataset
and overwrite the all-zero data with 'VALS.dat'.
Use -mod_hdr to specify that the output type is 2-files.
nifti_tool -infiles MAKE_IM -prefix newdata.hdr \
-new_dims 3 80 40 20 0 0 0 0 \
-new_datatype 16 \
-mod_hdr -mod_field pixdim '1 0.5 1 2 1 1 1 1' \
-mod_hdr -mod_field magic ni1
cp VALS.dat newdata.img
E. copy dataset, brick list or collapsed image:
0. nifti_tool -copy_image -prefix new.nii -infiles dset0.nii
1. nifti_tool -cbl -prefix new.nii -infiles dset0.nii
2. nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'
3. nifti_tool -cbl -prefix new_partial.nii \
-infiles dset0.nii'[3..$(2)]'
4. nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii
5. nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \
-prefix new_5_0_17_2.nii
F. modify the header (modify fields or swap entire header):
1. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field dim '4 64 64 20 30 1 1 1 1'
2. nifti_tool -mod_hdr2 -prefix dnew -infiles dset2.nii \
-mod_field dim '4 64 64 20 30 1 1 1 1'
3. nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field descrip 'beer, brats and cheese, mmmmm...'
3. cp old_dset.hdr nifti_swap.hdr
nifti_tool -swap_as_nifti -overwrite -infiles nifti_swap.hdr
4. cp old_dset.hdr analyze_swap.hdr
nifti_tool -swap_as_analyze -overwrite -infiles analyze_swap.hdr
5. nifti_tool -swap_as_old -prefix old_swap.hdr -infiles old_dset.hdr
nifti_tool -diff_hdr1 -infiles nifti_swap.hdr old_swap.hdr
G. strip, add or remove extensions:
(in example #3, the extension is copied from a text file)
1. nifti_tool -strip_extras -overwrite -infiles *.nii
2. nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \
-prefix dnew -infiles dset0.nii
3. nifti_tool -add_comment 'file:my.extension.txt' \
-prefix dnew -infiles dset0.nii
4. nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii
5. nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \
-infiles dset0.nii
H. convert to a different datatype (from whatever is there):
(possibly warn or fail if conversion is not perfect)
0. nifti_tool -copy_image -prefix copy.nii -infiles dset0.nii
1. nifti_tool -copy_image -infiles dset0.nii \
-prefix copy_f32.nii \
-convert2dtype NIFTI_TYPE_FLOAT32 \
-convert_fail_choice warn
2. nifti_tool -copy_image -infiles dset0.nii \
-prefix copy_i32.nii \
-convert2dtype NIFTI_TYPE_INT32 \
-convert_fail_choice fail
------------------------------
options for check actions:
-check_hdr : check for a valid nifti_1_header struct
This action is used to check the nifti_1_header structure for
problems. The nifti_hdr_looks_good() function is used for the
test, and currently checks:
dim[], sizeof_hdr, magic, datatype
More tests can be requested of the author.
e.g. perform checks on the headers of some datasets
nifti_tool -check_hdr -infiles dset0.nii dset1.nii
nifti_tool -check_hdr -infiles *.nii *.hdr
e.g. add the -quiet option, so that only errors are reported
nifti_tool -check_hdr -quiet -infiles *.nii *.hdr
-check_nim : check for a valid nifti_image struct
This action is used to check the nifti_image structure for
problems. This is tested via both nifti_convert_n1hdr2nim()
and nifti_nim_is_valid(), though other functions are called
below them, of course. Current checks are:
dim[], sizeof_hdr, datatype, fname, iname, nifti_type
Note that creation of a nifti_image structure depends on good
header fields. So errors are terminal, meaning this check would
probably report at most one error, even if more exist. The
-check_hdr action is more complete.
More tests can be requested of the author.
e.g. nifti_tool -check_nim -infiles dset0.nii dset1.nii
e.g. nifti_tool -check_nim -infiles *.nii *.hdr
------------------------------
options for create action:
-make_im : create a new dataset from nothing
With this the user can create a new dataset of a basic style,
which can then be modified with other options. This will create
zero-filled data of the appropriate size.
The default is a 1x1x1 image of shorts. These settings can be
modified with the -new_dim option, to set the 8 dimension values,
and the -new_datatype, to provide the integral type for the data.
See -new_dim, -new_datatype and -infiles for more information.
Note that any -infiles dataset of the name MAKE_IM will also be
created on the fly.
-new_dim D0 .. D7 : specify the dim array for the a new dataset.
e.g. -new_dim 4 64 64 27 120 0 0 0
This dimension list will apply to any dataset created via
MAKE_IM or -make_im. All 8 values are required. Recall that
D0 is the number of dimensions, and D1 through D7 are the sizes.
-new_datatype TYPE : specify the dim array for the a new dataset.
e.g. -new_datatype 16
default: -new_datatype 4 (short)
This dimension list will apply to any dataset created via
MAKE_IM or -make_im. TYPE should be one of the NIFTI_TYPE_*
numbers, from nifti1.h.
------------------------------
options for copy actions:
-copy_image : copy a NIFTI dataset to a new one
This basic action allows the user to copy a dataset to a new one.
This offers a more pure NIFTI I/O copy, while still allowing for
options like alteration of the datatype.
-convert2dtype TYPE : convert input dset to given TYPE
This option allows one to convert the data to a new datatype
upon read. If both the input and new types are valid, the
the conversion will be attempted.
As values cannot always be copied correctly, one should decide
what to do in case of a conversion error. To control response
to a conversion error, consider options -convert_verify and
-convert_fail_choice.
For example, converting NIFTI_TYPE_FLOAT32 to NIFTI_TYPE_UINT16,
a value of 53000.0 would exceed the maximum short, while 7.25
could not be exactly represented as a short.
Valid TYPE values include all NIFTI types, except for
FLOAT128 and any RGB or COMPLEX one.
For a list of potential values for TYPE, see the output from:
nifti_tool -help_datatypes
See also -convert_verify, -convert_fail_choice
-convert_fail_choice CHOICE : set what to do on conversion failures
Used with -convert2dtype and -convert_verify, this option
specifies how to behave when a datatype conversion is not exact
(e.g. 7.25 converted to a short integer would be 7).
Valid values for CHOICE are:
ignore : just let the failures happen
warn : warn about errors, but still convert
fail : bad conversions are terminal failures
This option implies -convert_verify, so they are not both needed.
See also -convert2dtype, -convert_verify
-convert_verify : verify that conversions were exact
Used with -convert2dtype, this option specifies that any
conversions should be verified for exactness. What to do in the
case of a bad conversion is controlled by -convert_fail_choice,
with a default of warning.
See also -convert2dtype, -convert_fail_choice
-copy_brick_list : copy a list of volumes to a new dataset
-cbl : (a shorter, alternative form)
This action allows the user to copy a list of volumes (over time)
from one dataset to another. The listed volumes can be in any
order and contain repeats, but are of course restricted to
the set of values {1, 2, ..., nt-1}, from dimension 4.
This option is a flag. The index list is specified with the input
dataset, contained in square brackets. Note that square brackets
are special to most UNIX shells, so they should be contained
within single quotes. Syntax of an index list:
notes:
- indices start at zero
- indices end at nt-1, which has the special symbol '$'
- single indices should be separated with commas, ','
e.g. -infiles dset0.nii'[0,3,8,5,2,2,2]'
- ranges may be specified using '..' or '-'
e.g. -infiles dset0.nii'[2..95]'
e.g. -infiles dset0.nii'[2..$]'
- ranges may have step values, specified in ()
example: 2 through 95 with a step of 3, i.e. {2,5,8,11,...,95}
e.g. -infiles dset0.nii'[2..95(3)]'
e.g. to copy sub-bricks 0 and 7:
nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'
e.g. to copy an entire dataset:
nifti_tool -cbl -prefix new_all.nii -infiles dset0.nii'[0..$]'
e.g. to copy every other time point, skipping the first three:
nifti_tool -cbl -prefix new_partial.nii \
-infiles dset0.nii'[3..$(2)]'
-copy_collapsed_image ... : copy a list of volumes to a new dataset
-cci I J K T U V W : (a shorter, alternative form)
This action allows the user to copy a collapsed dataset, where
some dimensions are collapsed to a given index. For instance, the
X dimension could be collapsed to i=42, and the time dimensions
could be collapsed to t=17. To collapse a dimension, set Di to
the desired index, where i is in {0..ni-1}. Any dimension that
should not be collapsed must be listed as -1.
Any number (of valid) dimensions can be collapsed, even down to a
a single value, by specifying enough valid indices. The resulting
dataset will then have a reduced number of non-trivial dimensions.
Assume dset0.nii has nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 }.
Note that this is a 4-dimensional dataset.
e.g. copy the time series for voxel i,j,k = 5,4,17
nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii
e.g. read the single volume at time point 26
nifti_tool -cci -1 -1 -1 26 -1 -1 -1 -prefix new_t26.nii
Assume dset1.nii has nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 }.
Note that this is a 6-dimensional dataset.
e.g. copy all time series for voxel i,j,k = 5,0,17, with v=2
(and add the command to the history)
nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist \
-prefix new_5_0_17_2.nii
e.g. copy all data where i=3, j=19 and v=2
(I do not claim to know a good reason to do this)
nifti_tool -cci 3 19 -1 -1 -1 2 -1 -prefix new_mess.nii
See '-disp_ci' for more information (which displays/prints the
data, instead of copying it to a new dataset).
------------------------------
options for display actions:
-disp_hdr : display nifti_*_header fields for datasets
This flag means the user wishes to see some of the nifti_*_header
fields in one or more nifti datasets. The user may want to specify
multiple '-field' options along with this. This option requires
one or more files input, via '-infiles'.
This displays the header in its native format.
If no '-field' option is present, all fields will be displayed.
Using '-field HDR_SLICE_TIMING_FIELDS' will include header fields
related to slice timing.
Using '-field NIM_SLICE_TIMING_FIELDS' will include nifti_image
fields related to slice timing.
e.g. to display the contents of all fields:
nifti_tool -disp_hdr -infiles dset0.nii
nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii
e.g. to display the contents of select fields:
nifti_tool -disp_hdr -field dim -infiles dset0.nii
nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii
e.g. a special case to display slice timing fields:
nifti_tool -disp_hdr -field HDR_SLICE_TIMING_FIELDS
-infiles dset0.nii
-disp_hdr1 : display nifti_1_header fields for datasets
Like -disp_hdr, but only display NIFTI-1 format.
This attempts to convert other NIFTI versions to NIFTI-1.
-disp_hdr2 : display nifti_2_header fields for datasets
Like -disp_hdr, but only display NIFTI-2 format.
This attempts to convert other NIFTI versions to NIFTI-2.
-disp_nim : display nifti_image fields for datasets
This flag option works the same way as the '-disp_hdr' option,
except that the fields in question are from the nifti_image
structure.
e.g. a special case to display slice timing fields:
nifti_tool -disp_nim -field NIM_SLICE_TIMING_FIELDS
-infiles dset0.nii
-disp_ana : display nifti_analyze75 fields for datasets
This flag option works the same way as the '-disp_hdr' option,
except that the fields in question are from the nifti_analyze75
structure.
-disp_cext : display CIFTI-type extensions
This flag option is used to display all CIFTI extension data.
-disp_exts : display all AFNI-type extensions
This flag option is used to display all nifti_1_extension data,
for extensions of type AFNI (4), COMMENT (6) or CIFTI (32).
e.g. to display the extensions in datasets:
nifti_tool -disp_exts -infiles dset0.nii
nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii
-disp_ts I J K : display ASCII time series at i,j,k = I,J,K
This option is used to display the time series data for the voxel
at i,j,k indices I,J,K. The data is displayed in text, either all
on one line (the default), or as one number per line (via the
'-dci_lines' option).
Notes:
o This function applies only to 4-dimensional datasets.
o The '-quiet' option can be used to suppress the text header,
leaving only the data.
o This option is short for using '-disp_ci' (display collapsed
image), restricted to 4-dimensional datasets. i.e. :
-disp_ci I J K -1 -1 -1 -1
e.g. to display the time series at voxel 23, 0, 172:
nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii
nifti_tool -disp_ts 23 0 172 -dci_lines -infiles dset1_time.nii
nifti_tool -disp_ts 23 0 172 -quiet -infiles dset1_time.nii
-disp_collapsed_image : display ASCII values for collapsed dataset
-disp_ci I J K T U V W : (a shorter, alternative form)
This option is used to display all of the data from a collapsed
image, given the dimension list. The data is displayed in text,
either all on one line (the default), or as one number per line
(by using the '-dci_lines' flag).
The '-quiet' option can be used to suppress the text header.
e.g. to display the time series at voxel 23, 0, 172:
nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii
e.g. to display z-slice 14, at time t=68:
nifti_tool -disp_ci -1 -1 14 68 0 0 0 -infiles dset1_time.nii
See '-ccd' for more information, which copies such data to a new
dataset, instead of printing it to the terminal window.
------------------------------
options for modification actions:
-mod_hdr : modify nifti_1_header fields for datasets
This action is used to modify some of the nifti_1_header fields in
one or more datasets. The user must specify a list of fields to
modify via one or more '-mod_field' options, which include field
names, along with the new (set of) values.
The user can modify a dataset in place, or use '-prefix' to
produce a new dataset, to which the changes have been applied.
It is recommended to normally use the '-prefix' option, so as not
to ruin a dataset.
Note that some fields have a length greater than 1, meaning that
the field is an array of numbers, or a string of characters. In
order to modify an array of numbers, the user must provide the
correct number of values, and contain those values in quotes, so
that they are seen as a single option.
To modify a string field, put the string in quotes.
The '-mod_field' option takes a field_name and a list of values.
e.g. to modify the contents of various fields:
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field qoffset_x -17.325
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field dim '4 64 64 20 30 1 1 1 1'
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field descrip 'beer, brats and cheese, mmmmm...'
e.g. to modify the contents of multiple fields:
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field qoffset_x -17.325 -mod_field slice_start 1
e.g. to modify the contents of multiple files (must overwrite):
nifti_tool -mod_hdr -overwrite -mod_field qoffset_x -17.325 \
-infiles dset0.nii dset1.nii
-mod_hdr2 : modify nifti_2_header fields for datasets
This action option is like -mod_hdr, except that this -mod_hdr2
option applies to NIFTI-2 datasets, while -mod_hdr applies to
NIFTI-1 datasets.
The same -mod_field options are then applied to specify changes.
-mod_nim : modify nifti_image fields for datasets
This action option is used the same way that '-mod_hdr' is used,
except that the fields in question are from the nifti_image
structure.
-strip_extras : remove extensions and descriptions from datasets
This action is used to attempt to 'clean' a dataset of general
text, in order to make it more anonymous. Extensions and the
nifti_image descrip field are cleared by this action.
e.g. to strip all *.nii datasets in this directory:
nifti_tool -strip_extras -overwrite -infiles *.nii
-swap_as_nifti : swap the header according to nifti_1_header
Perhaps a NIfTI header is mal-formed, and the user explicitly
wants to swap it before performing other operations. This action
will swap the field bytes under the assumption that the header is
in the NIfTI format.
** The recommended course of action is to make a copy of the
dataset and overwrite the header via -overwrite. If the header
needs such an operation, it is likely that the data would not
otherwise be read in correctly.
-swap_as_analyze : swap the header according to nifti_analyze75
Perhaps an ANALYZE header is mal-formed, and the user explicitly
wants to swap it before performing other operations. This action
will swap the field bytes under the assumption that the header is
in the ANALYZE 7.5 format.
** The recommended course of action is to make a copy of the
dataset and overwrite the header via -overwrite. If the header
needs such an operation, it is likely that the data would not
otherwise be read in correctly.
-swap_as_old : swap the header using the old method
As of library version 1.35 (3 Aug, 2008), nifticlib now swaps all
fields of a NIfTI dataset (including UNUSED ones), and it swaps
ANALYZE datasets according to the nifti_analyze75 structure.
This is a significant different in the case of ANALYZE datasets.
The -swap_as_old option was added to compare the results of the
swapping methods, or to undo one swapping method and replace it
with another (such as to undo the old method and apply the new).
------------------------------
options for adding/removing extensions:
-add_afni_ext EXT : add an AFNI extension to the dataset
This option is used to add AFNI-type extensions to one or more
datasets. This option may be used more than once to add more than
one extension.
If EXT is of the form 'file:FILENAME', then the extension will
be read from the file, FILENAME.
The '-prefix' option is recommended, to create a new dataset.
In such a case, only a single file may be taken as input. Using
'-overwrite' allows the user to overwrite the current file, or
to add the extension(s) to multiple files, overwriting them.
e.g. to add a generic AFNI extension:
nifti_tool -add_afni_ext 'wow, my first extension' -prefix dnew \
-infiles dset0.nii
e.g. to add multiple AFNI extensions:
nifti_tool -add_afni_ext 'wow, my first extension :)' \
-add_afni_ext 'look, my second...' \
-prefix dnew -infiles dset0.nii
e.g. to add an extension, and overwrite the dataset:
nifti_tool -add_afni_ext 'some AFNI extension' -overwrite \
-infiles dset0.nii dset1.nii
-add_comment_ext EXT : add a COMMENT extension to the dataset
This option is used to add COMMENT-type extensions to one or more
datasets. This option may be used more than once to add more than
one extension. This option may also be used with '-add_afni_ext'.
If EXT is of the form 'file:FILENAME', then the extension will
be read from the file, FILENAME.
The '-prefix' option is recommended, to create a new dataset.
In such a case, only a single file may be taken as input. Using
'-overwrite' allows the user to overwrite the current file, or
to add the extension(s) to multiple files, overwriting them.
e.g. to add a comment about the dataset:
nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \
-prefix dnew \
-infiles dset0.nii
e.g. to add multiple extensions:
nifti_tool -add_comment 'add a comment extension' \
-add_afni_ext 'and an AFNI XML style extension' \
-add_comment 'dataset copied from dset0.nii' \
-prefix dnew -infiles dset0.nii
-rm_ext INDEX : remove the extension given by INDEX
This option is used to remove any single extension from the
dataset. Multiple extensions require multiple options.
notes - extension indices begin with 0 (zero)
- to view the current extensions, see '-disp_exts'
- all extensions can be removed using ALL or -1 for INDEX
e.g. to remove the extension #0:
nifti_tool -rm_ext 0 -overwrite -infiles dset0.nii
e.g. to remove ALL extensions:
nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii
nifti_tool -rm_ext -1 -prefix dset1 -infiles dset0.nii
e.g. to remove the extensions #2, #3 and #5:
nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite \
-infiles dset0.nii
------------------------------
options for showing differences:
-diff_hdr : display header field diffs between two datasets
This option is used to find differences between two NIFTI-*
dataset headers. If any fields are different, the contents of
those fields are displayed (unless the '-quiet' option is used).
The NIFTI versions must agree.
-diff_hdr1 : display header diffs between NIFTI-1 datasets
This option is used to find differences between two NIFTI-1
dataset headers.
-diff_hdr2 : display header diffs between NIFTI-2 datasets
This option is used to find differences between two NIFTI-2
dataset headers.
A list of fields can be specified by using multiple '-field'
options. If no '-field' option is given, all fields will be
checked.
Exactly two dataset names must be provided via '-infiles'.
e.g. to display all nifti_2_header field differences:
nifti_tool -diff_hdr2 -infiles dset0.nii dset1.nii
e.g. to display selected field differences:
nifti_tool -diff_hdr -field dim -field intent_code \
-infiles dset0.nii dset1.nii
-diff_nim : display nifti_image field diffs between datasets
This option works the same as '-diff_hdr', except that the fields
in question are from the nifti_image structure.
------------------------------
miscellaneous options:
-debug LEVEL : set the debugging level
Level 0 will attempt to operate with no screen output, but errors.
Level 1 is the default.
Levels 2 and 3 give progressively more information.
e.g. -debug 2
-field FIELDNAME : provide a field to work with
This option is used to provide a field to display, modify or
compare. This option can be used along with one of the action
options presented above.
Special cases of FIELDNAME that translate to lists of fields:
HDR_SLICE_TIMING_FIELDS : fields related to slice timing
slice_code : code for slice acquisition order
slice_start : first slice applying to slice_code
slice_end : last slice applying to slice_code
slice_duration : time to acquire one slice
dim_info : slice/phase/freq_dim (2+2+2 lower bits)
dim : dimensions of data
pixdim : grid/dimension spacing (e.g. time)
xyzt_units : time/space units for pixdim (3+3 bits)
See '-disp_hdr', above, for complete examples.
HDR_SLICE_TIMING_FIELDS : fields related to slice timing
slice_code : code for slice acquisition order
slice_start : first slice applying to slice_code
slice_end : last slice applying to slice_code
slice_duration : time to acquire one slice
slice_dim : slice dimension (unset or in 1,2,3)
phase_dim : phase dimension (unset or in 1,2,3)
freq_dim : freq dimension (unset or in 1,2,3)
dim : dimensions of data
pixdim : grid/dimension spacing (e.g. time)
xyzt_units : time/space units for pixdim (3+3 bits)
See '-disp_nim', above, for complete examples.
e.g. nifti_tool -field descrip
e.g. nifti_tool -field descrip -field dim
-infiles file0... : provide a list of files to work with
This parameter is required for any of the actions, in order to
provide a list of files to process. If input filenames do not
have an extension, the directory we be searched for any
appropriate files (such as .nii or .hdr).
Note: if the filename has the form MAKE_IM, then a new dataset
will be created, without the need for file input.
See '-mod_hdr', above, for complete examples.
e.g. nifti_tool -infiles file0.nii
e.g. nifti_tool -infiles file1.nii file2 file3.hdr
-mod_field NAME 'VALUE_LIST' : provide new values for a field
This parameter is required for any the modification actions.
If the user wants to modify any fields of a dataset, this is
where the fields and values are specified.
NAME is a field name (in either the nifti_1_header structure or
the nifti_image structure). If the action option is '-mod_hdr',
then NAME must be the name of a nifti_1_header field. If the
action is '-mod_nim', NAME must be from a nifti_image structure.
VALUE_LIST must be one or more values, as many as are required
for the field, contained in quotes if more than one is provided.
Use 'nifti_tool -help_hdr' to get a list of nifti_2_header fields
Use 'nifti_tool -help_hdr1' to get a list of nifti_1_header fields
Use 'nifti_tool -help_hdr2' to get a list of nifti_2_header fields
Use 'nifti_tool -help_nim' to get a list of nifti_image fields
Use 'nifti_tool -help_nim1' to get a list of nifti1_image fields
Use 'nifti_tool -help_nim2' to get a list of nifti2_image fields
Use 'nifti_tool -help_ana' to get a list of nifti_analyze75 fields
See '-mod_hdr', above, for complete examples.
e.g. modifying nifti_1_header fields:
-mod_field descrip 'toga, toga, toga'
-mod_field qoffset_x 19.4 -mod_field qoffset_z -11
-mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'
-keep_hist : add the command as COMMENT (to the 'history')
When this option is used, the current command will be added
as a NIFTI_ECODE_COMMENT type extension. This provides the
ability to keep a history of commands affecting a dataset.
e.g. -keep_hist
-overwrite : any modifications will be made to input files
This option is used so that all field modifications, including
extension additions or deletions, will be made to the files that
are input.
In general, the user is recommended to use the '-prefix' option
to create new files. But if overwriting the contents of the
input files is preferred, this is how to do it.
See '-mod_hdr' or '-add_afni_ext', above, for complete examples.
e.g. -overwrite
-prefix : specify an output file to write change into
This option is used to specify an output file to write, after
modifications have been made. If modifications are being made,
then either '-prefix' or '-overwrite' is required.
If no extension is given, the output extension will be '.nii'.
e.g. -prefix new_dset
e.g. -prefix new_dset.nii
e.g. -prefix new_dset.hdr
-quiet : report only errors or requested information
This option is equivalent to '-debug 0'.
------------------------------
basic help options:
-help : show this help
e.g. nifti_tool -help
-help_hdr : show nifti_2_header field info
e.g. nifti_tool -help_hdr
-help_hdr1 : show nifti_1_header field info
e.g. nifti_tool -help_hdr1
-help_hdr2 : show nifti_2_header field info
e.g. nifti_tool -help_hdr2
-help_nim : show nifti_image field info (currently NIFTI-2)
e.g. nifti_tool -help_nim
-help_nim1 : show nifti1_image field info
e.g. nifti_tool -help_nim1
-help_nim2 : show nifti2_image field info
e.g. nifti_tool -help_nim2
-help_ana : show nifti_analyze75 field info
e.g. nifti_tool -help_ana
-help_datatypes [TYPE] : display datatype table
e.g. nifti_tool -help_datatypes
e.g. nifti_tool -help_datatypes N
This displays the contents of the nifti_type_list table.
An additional 'D' or 'N' parameter will restrict the type
name to 'DT_' or 'NIFTI_TYPE_' names, 'T' will test.
-ver : show the program version number
e.g. nifti_tool -ver
-ver_man : show the version, formatted for a man page
e.g. nifti_tool -ver_man
-see_also : show the 'SEE ALSO' string for man pages
e.g. nifti_tool -see_also
-hist : show the program modification history
e.g. nifti_tool -hist
-nifti_ver : show the nifti library version number
e.g. nifti_tool -nifti_ver
-nifti_hist : show the nifti library modification history
e.g. nifti_tool -nifti_hist
-with_zlib : print whether library was compiled with zlib
e.g. nifti_tool -with_zlib
------------------------------
R. Reynolds
version 2.13 (February 27, 2022)
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