NIFTI_TOOL(1)															     NIFTI_TOOL(1)

NAME

       nifti_tool - multipurpose manipulation tool for NIfTI files

SYNOPSIS

       nifti_tool -help show this help

       nifti_tool -help_hdr show nifti_1_header field info

       nifti_tool -help_nim show nifti_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 -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 -copy_im -infiles f1

       nifti_tool -make_im -prefix new_im.nii

       nifti_tool -disp_hdr [-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_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_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_nim [-field FIELDNAME] [...] -infiles f1 f2

DESCRIPTION

       This tool can

	      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.

OPTIONS

       Check options

       -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 cur-
       rently 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 erros 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_nhdr2nim()  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

       Create options

       -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.

       Copy options

       -copy_brick_list   : copy a list of volumes to a new dataset

       -cbl		  : (a shorter, alternative form)

       -copy_im 	  : (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)]"

       This functionality applies only to 3 or 4-dimensional datasets.

       e.g. to copy a dataset: nifti_tool -copy_im -prefix new.nii -infiles dset0.nii

       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  dimen-
       sion 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).

       Display options

       -disp_hdr	  : display nifti_1_header fields for datasets

       This flag means the user wishes to see some of the nifti_1_header fields in one or more nifti datasets. The user may want to specify mutli-
       ple "-field" options along with this.  This option requires one or more files input, via "-infiles".

       If no "-field" option is present, all fields will be displayed.

       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

       -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.

       -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_exts	  : display all AFNI-type extensions

       This flag option is used to display all nifti_1_extension data, for only those extensions of type AFNI (code = 4).  The only  other  option
       used will be "-infiles".

       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:

	      This function applies only to 4-dimensional datasets.

	      The "-quiet" option can be used to suppress the text header, leaving only the data.

	      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.

       Modification options

       -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 recom-
       mended 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_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 -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).

       Add, remove options

       -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  "-over-
       write" 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..."  -pre-
       fix 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 "-over-
       write" 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 exensions 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

       Difference options

       -diff_hdr	 : display header field diffs between two datasets

       This option is used to find differences between two datasets.  If any fields are different, the	contents  of  those  fields  is  displayed
       (unless the "-quiet" option is used).

       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_1_header field differences: nifti_tool -diff_hdr -infiles dset0.nii dset1.nii

       e.g. to display selected nifti_1_header 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 infoma-
       tion.

       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  pre-
       sented above.

       See "-disp_hdr", 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_1_header fields Use "nifti_tool -help_nim" to get a list of nifti_image 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
       prefered, 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".

       Help options

       -help		 : show this help

       e.g.  nifti_tool -help

       -help_hdr	 : show nifti_1_header field info

       e.g.  nifti_tool -help_hdr

       -help_nim	 : show nifti_image field info

       e.g.  nifti_tool -help_nim

       -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

       -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

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 -field dim -field intent_code  -infiles dset0.nii dset1.nii

       2. nifti_tool -diff_hdr -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_hdr -field dim -field descrip -infiles dset.nii 3.
       nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii 4. nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii 5. nifti_tool -disp_ci
       23 0 172 -1 0 0 0 -infiles dset1_time.nii

       6. nifti_tool -disp_ana -infiles analyze.hdr 7. nifti_tool -disp_nim -infiles nifti.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

       E. copy dataset, brick list or collapsed image:

       1.  nifti_tool  -copy_im  -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_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_hdr -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 -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" fR -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

SEE ALSO

       libnifti(1), nifti1_test(1), nifti_stats(1).

       Homepage: http://niftilib.sourceforge.net

AUTHOR

       The NIfTI libraries were written by the NIfTI Data Format Working Group (DFWG, http://nifti.nimh.nih.gov/ ).

       This manual page was generated by a custom script, written by Michael Hanke <michael.hanke@gmail.com> (available within the Debian package)
       from the help output of the nifti_tool binary.'

Michael Hanke															     NIFTI_TOOL(1)