Provided by: gifti-bin_1.0.9-6build2_amd64 bug

NAME

       gifti_tool - gifti_tool  - create, display, modify or compare GIFTI datasets

DESCRIPTION

       ------------------------------------------------------------    gifti_tool     -   create,
       display, modify or compare GIFTI datasets

              general examples:

       1. read in a GIFTI dataset (set verbose level?
              show GIFTI dataset?)

              gifti_tool -infile dset.gii gifti_tool -infile dset.gii -verb 3 gifti_tool  -infile
              dset.gii -show_gifti

              2. copy a GIFTI dataset

              a. create a simple copy, and check for differences

              gifti_tool -infile dset.gii -write_gifti copy.gii diff dset.gii copy.gii

              b. copy only 3 DataArray indices: 4, 0, 5

       gifti_tool -infile time_series.gii -write_gifti ts3.gii
              \

              -read_DAs 4 0 5

              OR

       gifti_tool -infile time_series.gii'[4,0,5]'
              \

              -write_gifti ts3.gii

              3. write datasets in other formats

              a. FreeSurfer-style .asc surface dataset

              gifti_tool -infile pial.gii -write_asc pial.asc

              b. .1D time series surface dataset

              gifti_tool -infile time_series.gii -write_1D ts.1D

              4. create a new gifti dataset from nothing, where

              a. - the dataset has 3 DataArray elements

              -  the  data  will  be  of  type 'short' (NIFTI_TYPE_INT16) - the intent codes will
              reflect a t-test - the data will be 2-dimensional (per DataArray), 5 by 2 shorts  -
              memory  will be allocated for the data (a modification option) - the result will be
              written to created.gii

       gifti_tool -new_dset
              \

       -new_numDA 3 -new_dtype NIFTI_TYPE_INT16 \
              -new_intent NIFTI_INTENT_TTEST           \ -new_ndim 2  -new_dims  5  2  0  0  0  0
              \ -mod_add_data -write_gifti created.gii

              b. - the dataset has 12 DataArray elements (40 floats each)

              - the data is partitioned over 2 files (so 6*40 floats in each)

       ** Note: since dataset creation does not add data (without
              -mod_add_data),  this  operation  will  not create or try to overwrite the external
              datafiles.

       gifti_tool -new_dset -new_numDA 12
              \

       -new_ndim 1 -new_dims 40 0 0 0 0 0
              \

       -set_extern_filelist ext1.bin ext2.bin
              \

              -write_gifti points_to_extern.gii

              5. modify a gifti dataset

              a. apply various modifications at the GIFTI level and to all DAs

              - set the Version attribute at the GIFTI level - set 'Date' as GIFTI MetaData, with
              value  of today's date - set 'Description' as GIFTI MetaData, with some value - set
              all DA Intent attributes to be an F-test - set 'Name' as an attribute of  all  DAs,
              with some value - read created.gii, and write to first_mod.gii

       gifti_tool -mod_gim_atr Version 1.0
              \

       -mod_gim_meta Date "`date`"
              \

       -mod_gim_meta Description 'modified surface'
              \

       -mod_DA_atr Intent NIFTI_INTENT_FTEST
              \

       -mod_DA_meta Name 'same name for all DAs'
              \

              -infile created.gii -write_gifti first_mod.gii

              b. modify the 'Name' attribute is DA index #42 only

       gifti_tool -mod_DA_meta Name 'data from pickle #42'
              \

       -mod_DAs 42
              \

              -infile stats.gii -write_gifti mod_stats.gii

              c. set the data to point to a single external data file, without

              overwriting  the external file on write (so use -no_data), and where the DataArrays
              will point to sequential partitions of the file

       gifti_tool -infiles created.gii -no_data
              \

       -set_extern_filelist ex_data.bin
              \

              -write_gifti extern.gii

              d. convert a POINTSET/TRIANGLE Base64 format dataset to one where

              to one where the data is external (raw binary):

       gifti_tool -infiles inflated.gii
              \

       -set_extern_filelist points.data tri.data \
              -write_gifti inflated.external.gii

              e. convert a 5 run time series dataset from internal Base64 format

              to one where the data is external (raw binary):

              as one external file:

       gifti_tool -infiles epi.5runs.gii
              \

       -set_extern_filelist data.5runs.bin
              \

              -write_gifti epi.ext.5runs.gii

              as 5 external files (1 per run):

       gifti_tool -infiles epi.5runs.gii
              \

              -set_extern_filelist data.5runs.r{1,2,3,4,5}.bin \ -write_gifti epi.ext.5runs.gii

              f. convert the previous external dataset back to internal form

              (i.e. it should be the same as epi.5runs.gii)

       gifti_tool -infiles epi.ext.5runs.gii
              \

       -encoding BASE64
              \

              -write_gifti epi.int.5runs.gii

              6. compare 2 gifti datasets

              a. compare GIFTI structures, compare data, and report all diffs

       gifti_tool -compare_gifti -compare_data -compare_verb 3 \
              -infiles created.gii first_mod.gii

              b. report approximate comparison: focusing on data, but allowing

              for small, fractional differences varying per datatype

       gifti_tool -approx_gifti -compare_verb 3 \
              -infiles created.gii first_mod.gii

              7. copy MetaData from one dataset to another

              (any old Value will be replaced if the Name already exists)

              - copy every (ALL) MetaData element at  the  GIFTI  level  -  copy  MetaData  named
              'Label' per DataArray element - only apply DataArray copies to indices 0, 3 and 6 -
              first input file is the source, second is the  destination  -  write  the  modified
              'destination.gii' dataset to meta_copy.gii

       gifti_tool -copy_gifti_meta ALL
              \

       -copy_DA_meta Label
              \

       -DA_index_list 0 3 6
              \

       -infiles source.gii destination.gii
              \

              -write_gifti meta_copy.gii

       ----------------------------------------------------------------------

              (all warranties are void in Montana, and after 4 pm on Tuesdays)

       ----------------------------------------------------------------------

              informational options:

       -help  : display this help

       -hist  : display the modification history of gifti_tool

       -ver   : display the gifti_tool version

       -gifti_hist
              : display thd modification history of gifticlib

       -gifti_ver
              : display gifticlib version

       -gifti_dtd_url
              : display the gifti DTD URL

       -gifti_zlib
              : display whether the zlib is linked in library

       ----------------------------------------

              general/input options

       -b64_check
              TYPE : set method for checking base64 errors

              e.g. -b64_check COUNT

              This  option sets the preference for how to deal with errors in Base64 encoded data
              (whether compressed or not).  The default is SKIPnCOUNT, which  skips  any  illegal
              characters, and reports a count of the number found.

       TYPE = NONE
              : no checks - assume all is well

       TYPE = DETECT
              : report whether errors were found

       TYPE = COUNT
              : count the number of bad chars

       TYPE = SKIP
              : ignore any bad characters

              TYPE = SKIPnCOUNT : ignore but count bad characters

              This default adds perhaps 10% to the reading time.

       -buf_size
              SIZE : set the buffer size (given to expat library)

              e.g. -buf_size 1024

       -DA_index_list I0 I1 ... : specify a list of DataArray indices

              e.g. -DA_index_list 0 e.g. -DA_index_list 0 17 19

              This  option  is used to specify a list of DataArray indices for use via some other
              option (such as -copy_DA_meta).

              Each DataArray element corresponding to one of the  given  indices  will  have  the
              appropriate  action  applied,  such  as  copying  a given MetaData element from the
              source dataset to the destination dataset.

              Note that this differs from -read_DAs, which specifies which DataArray elements  to
              even  read  in.   Both  options  could  be used in the same command, such as if one
              wanted to copy the 'Name' MetaData from index 17  of  a  source  dataset  into  the
              MetaData of the first DataArray in a dataset with only two DataArray elements.

       e.g. gifti_tool -infiles source.gii dest.gii
              \

       -write_gifti new_dest.gii
              \

       -copy_DA_meta Name
              \

       -read_DAs 17 17
              \

              -DA_index_list 0

              Note that DA_index_list applies to the indices _after_ the datasets are read in.

       -gifti_test
              : test whether each gifti dataset is valid

              This  performs  a  consistency  check  on  each  input  GIFTI  dataset.   Lists and
              dimensions must be consistent.

       -infile
              INPUT : specify one or more GIFTI datasets as input

              e.g.  -input  pial.gii  e.g.  -input  run1.gii   run2.gii   e.g.   -input   MAKE_IM
              (create  a new image) e.g. -input run1.gii'[3,4,5]'       (read DAs 3,4,5    ) e.g.
              -input  run1.gii'[0..16(2)]'     (read  evens   from   0   to   16)   e.g.   -input
              run1.gii'[4..$]'        (read all but 0..3)

       There are 2 special ways to specify input.
              One is via the

       name 'MAKE_IM'.
              That 'input' filename tell gifti_tool to

              create a new dataset, applying any '-new_*' options to it.

              (refer to options: -new_*)

              The  other  special  way  is to specify which DataArray elements should be read in,
              using  AFNI-style  syntax  within  '[]'.   The  quotes  prevent  the   shell   from
              interpreting the brackets.

              DataArray indices are zero-based.

              The list of DAs can be comma-delimited, and can use '..' or '-' to specify a range,
              and a value in parentheses to be used as a step.  The '$' character means the  last
              index (numDA-1).

       -no_data
              : do not read in data

              This option means not to read in the Data element in any DataArray, akin to reading
              only the header.

       -no_updates
              : do not allow the library to modify metadata

              By  default,   the   library   may   update   some   metadata   fields,   such   as
              'gifticlib-version'.  The -no_updates option will prevent that operation.

       -read_DAs s0 ...
              : read DataArray list indices s0,... from input

              e.g.  -read_DAs  0  4  3  3  8 e.g. -input run1.gii -read_DAs 0 2 4 6 8 e.g. -input
              run1.gii'[0..8(2)]'              (same effect)

       Specify a list of DataArray indices to read.
              This is a

              simplified form of using brackets '[]' with -input names.

       -show_gifti
              : show final gifti image

              Display all of the dataset information on the screen (sans  data).   This  includes
              meta data and all DataArray elements.

       -verb  VERB : set verbose level   (default: 1)

              e.g. -verb 2

       Print extra information to the screen.
              The VERB level can

              be from 0 to 8, currently.

              Level 0 is considered 'quiet' mode, and should only report serious errors.  Level 1
              is the default.

       ----------------------------------------

              output options

       -encoding
              TYPE : set the data encoding for any output file

              e.g. -encoding BASE64GZIP

       TYPE = ASCII
              : ASCII encoding

       TYPE = BASE64
              : base64 binary

              TYPE = BASE64GZIP : base64 compressed binary

              This operation can also be performed via  -mod_DA_atr:  e.g.  -mod_DA_atr  Encoding
              BASE64GZIP

       -set_extern_filelist F1 F2 ... : store data in external files

              e.g.     -set_extern_filelist     run.1.data     run.2.data     run.3.data     e.g.
              -set_extern_filelist   runs.all.data    e.g.    -set_extern_filelist    points.data
              triangles.data

              Data is normally stored within the XML file as numerical text or Base64 encoded raw
              or compressed data.

              With use of this option, users can set to have data stored in external binary files
              (neither encoded nor compressed) upon a write operation.

              External file storage is subject to a couple of restrictions:

              - GIFTI requires that they are in the same directory

              - the library allows multiple DataArrays per file, but each

              DataArray  within the same file must have the same size (this is a gifticlib limit,
              not a GIFTI limit)

              OK : equal data in 1 file OK : equal data in k files, numDA is multiple of  k  BAD:
              equal  data in k files, numDA is NOT multiple of k OK : points/triangles in 2 files
              BAD: points/triangles in 1 file (sizes differ)

              The most basic use of this option is to convert data  from  internal  to  external.
              See examples 5d and 5e.

              Note that one can also create a GIFTI dataset out of nothing and use this option to
              point to existing external data files.   This  would  help  conversion  from  other
              dataset formats.  See example 5c.

              Note  that  one  can  convert  from  an  external  data  format to internal just by
              modifying the -encoding.  See example 5f.

       -write_1D
              DSET : write out data to AFNI style 1D file

              e.g. -write_1D stats.1D

       Currently, all DAs need to be of the same datatype.
              This

              restriction could be lifted if there is interest.

       -write_asc
              DSET : write out geometry to FreeSurfer style ASC file

              e.g. -write_asc pial.asc

              To write a surface file  in  FreeSurfer  asc  format,  it  must  contain  DataArray
              elements  of  intent NIFTI_INTENT_POINTSET and NIFTI_INTENT_TRIANGLE.  The POINTSET
              data is written as node coordinates and the TRIANGLE data as triangles (node  index
              triplets).

       -write_gifti DSET : write out dataset as gifti image

              e.g. -write_gifti new.pial.gii

       -zlevel
              LEVEL : set compression level (-1 or 0..9)

       This option sets the compression level used by zlib.
              Some

              LEVEL values are noteworthy:

       -1     : specify to use the default of zlib (currently 6)

       0      : no compression (but still needs a few extra bytes)

       1      : fastest but weakest compression

       6      : default (good speed/compression trade-off)

       9      : slowest but strongest compression

       ----------------------------------------

              modification options

              These  modification  options  will  affect every DataArray element specified by the
              -mod_DAs option.  If the option is not used, then ALL DataArray  elements  will  be
              affected.

       -mod_add_data
              : add data to empty DataArray elements

       Allocate data in every DataArray element.
              Datasets can be

       created without any stored data.
              This will allocate data

              and fill it with zeros of the given type.

       -mod_DA_atr
              NAME VALUE : set the NAME=VALUE attribute pair

              e.g. -mod_DA_atr Intent NIFTI_INTENT_ZSCORE

              This  option  will  set the DataArray attribute corresponding to NAME to the value,
              VALUE.   Attribute  name=value  pairs  are  specified  in  the   gifti   DTD   (see
              -gifti_dtd_url).

              One  NAME=VALUE pair can be specified per -mod_DA_atr option.  Multiple -mod_DA_atr
              options can be used.

       -mod_DA_meta NAME VALUE : set the NAME=VALUE pair in DA's MetaData

              e.g. -mod_DA_meta Description 'the best dataset, ever'

              Add a MetaData entry to each DataArray element for this NAME and VALUE.  If  'NAME'
              already exists, the old value is replaced by VALUE.

       -mod_DAs i0 i1 ...
              : specify the set of DataArrays to modify

              e.g. -mod_DAs 0 4 5

       Specify the list of DataArray elements to modify.
              All the

       -mod_* options apply to this list of DataArray indices.
              If

              no -mod_DAs option is used, the operations apply to ALL DataArray elements.

              Note that the indices are zero-based, 0 .. numDA-1.

       -mod_gim_atr
              NAME VALUE : set the GIFTI NAME=VALUE attribute pair

              e.g. -mod_gim_atr Version 3.141592

              Set the GIFTI element attribute corresponding to NAME to the value, VALUE.

              Given  that  numDA  is  computed  and  version will rarely change, this option will
              probably not feel much love.

       -mod_gim_meta NAME VALUE : add this pair to the GIFTI MetaData

              e.g. -mod_gim_meta date "`date`"

              Add a MetaData entry to each DataArray element for this NAME and  VALUE  pair.   If
              NAME exists, VALUE will replace the old value.

       -mod_to_float
              : change all DataArray data to float

              Convert  all  DataArray  elements  of  all  datasets to datatype NIFTI_TYPE_FLOAT32
              (4-byte floats).  If the data does not actually exist, only the attribute  will  be
              set.   Otherwise all of the data will be converted.  There are some types for which
              this operation may not be appropriate.

       ----------------------------------------

              creation (new dataset) options

       -new_dset
              : create a new GIFTI dataset

       -new_numDA
              NUMDA : new dataset will have NUMDA DataArray elements e.g. -new_numDA 3

       -new_intent INTENT: DA elements will have intent INTENT
              e.g. -new_intent NIFTI_INTENT_FTEST

       -new_dtype
              TYPE : set datatype to TYPE e.g. -new_dtype NIFTI_TYPE_FLOAT32

       -new_ndim NUMDIMS : set Dimensionality to NUMDIMS (see -new_dims)

       -new_dims D0...D5 : set dims[] to these 6 values
              e.g. -new_ndim 2 -new_dims 7 2 0 0 0 0

       -new_data
              : allocate space for data in created dataset

       ----------------------------------------

              comparison options

       -approx_gifti
              : approximate comparison of GIFTI dsets

              This compares all data elements of  the  two  GIFTI  structures.   The  attributes,
              MetaData, etc. are ignored if they do not pertain directly to the data.

              The  comparisons  allow  for  small,  fractional  differences,  which depend on the
              datatype.

       -compare_gifti
              : specifies to compare two GIFTI datasets

              This  compares  all  elements  of  the  two  GIFTI  structures.   The   attributes,
              LabelTabels,  MetaData  are  compared,  and  then  each  of  the included DataArray
              elements.  All sub-structures of the DataArrays are compared, except for the actual
              'data', which requires the '-compare_data' flag.

              There  must  be  exactly  2  input datasets to use this option.  See example #7 for
              sample usage.

       -compare_data
              : flag to request comparison of the data

              Data comparison is done per DataArray element.

              Comparing data is a separate operation from comparing GIFTI.  Neither  implies  the
              other.

       -compare_verb LEVEL
              : set the verbose level of comparisons

       Data comparison is done per DataArray element.
              Setting the

              verb level will have the following effect:

              0  : quiet, only return whether there was a difference 1 : show whether there was a
              difference 2 : show whether there was a difference  per  DataArray  3  :  show  all
              differences

       ----------------------------------------

              MetaData copy options

       -copy_gifti_meta MD_NAME
              : copy MetaData with name MD_NAME

              e.g. -copy_gifti_meta AFNI_History

              Copy  the  MetaData  with the given name from the first input dataset to the second
              (last).  This applies to  MetaData  at  the  GIFTI  level  (not  in  the  DataArray
              elements).

       -copy_DA_meta MD_NAME
              : copy MetaData with name MD_NAME

              e.g. -copy_DA_meta intent_p1

              Copy  the  MetaData  with the given name from the first input dataset to the second
              (last).  This applies to MetaData at DataArray level.

              This will apply to all DataArray elements, unless the -DA_index_list option is used
              to specify a zero-based index list.

              see also -DA_index_list

       ------------------------------------------------------------  see  the GIfTI community web
       site at:

              http://www.nitrc.org/projects/gifti

       R          Reynolds,           National           Institutes           of           Health
       ------------------------------------------------------------

SEE ALSO

       The  full documentation for gifti_tool is maintained as a Texinfo manual.  If the info and
       gifti_tool programs are properly installed at your site, the command

              info gifti_tool

       should give you access to the complete manual.