Ubuntu Manpage: gifti_tool - gifti_tool - create, display, modify or compare GIFTI datasets

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

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.

NAME

DESCRIPTION

SEE ALSO