Skip to content

JNIfTI Toolbox v0.8 - Tree of Life

Latest
Latest
Compare
Choose a tag to compare
@fangq fangq released this 23 Mar 18:31
· 0 commits to master since this release
v0.8
79fc08d

image

JNIfTI Toolbox - Fast and portable NIfTI-1/2 reader/writer for MATLAB and Octave

Click here to register and download JNIfTI Toolbox v0.8

ChangeLog

JNIFTY v0.8 (Tree of Life), FangQ <q.fang (a) neu.edu> ==

2025-03-23 [e243cc7] [doc] update README, make examples self-contained
2025-03-23*[905f87e] [release] update all units for v0.8 release, use 'z' flag in octavezmat, support JNIFTI Draft 2
2025-02-05 [1faaf18] [bug] fix int16 type typo, fangq/iso2mesh#83
2024-10-02 [096136c] [doc] update upstream repository to NeuroJSON
2024-03-27 [f3a535d] [doc] add DESCRIPTION and INDEX
2024-03-27*[aec438c] [format] reformat the code with miss_hit
2024-01-15*[ce0d20a] [bug] fix loading nii.gz with extension
2023-02-23*[1aa7dcf] make jnifty compatible with MATLAB R2010b
2023-02-21 [4c2185f] separate nii header to jnii header conversion
2022-03-12 [e61b802] remove redundant line
2022-03-11 [f062d50] add DataInfo header, add usemap option to memmapstream

Overview

This is a fully functional NIfTI-1/2 reader/writer that supports both
MATLAB and GNU Octave, and is capable of reading/writing both non-compressed
and compressed NIfTI files (.nii, .nii.gz) as well as two-part Analyze7.5/NIfTI
files (.hdr/.img and .hdr.gz/.img.gz).

More importantly, this is a toolbox that converts NIfTI data to its JSON-based
replacement, JNIfTI (.jnii for text-based and .bnii for binary-based), defined
by the JNIfTI specification (https://github.com/NeuroJSON/jnifti). JNIfTI is a
much more flexible, human-readable and extensible file format compared to the
more rigid and opaque NIfTI format, making the data much easier to manipulate
and share.

Installation

The JNIfTI toolbox includes a stand-alone NIfTI-1/2 parser that works on both
MATLAB and GNU Octave without needing additional components. To just reading and
writing the un-compressed NIfTI and Analyze7.5 files (.nii, .hdr/.img), one
only needs to run addpath('/path/to/jnifty'). For MATLAB, JNIfTI toolbox
utilizes memmapfile-based disk-reading, making it very fast. For Octave,
memmapfile is currently not implemented, so, a full reading is required.

The JNIfTI toolbox is also capable of reading/writing gzip-compressed NIfTI and
Analyze7.5 files (.nii.gz, .hdr.gz, .img.gz). This feature is supported in MATLAB
directly without needing another toolbox (MATLAB must be in the JVM-enabled mode).

To save NIfTI-1/2 data as JNIfTI files, one needs to install JSONLab. The JNIfTI
data format supports internal compression (as oppose to external compression such
as *.gz files).

To create or read compressed NIfTI/JNIfTI files in Octave, one may install the
ZMat toolbox (https://github.com/NeuroJSON/zmat), although it is optional.

Usage

nii2jnii - To convert a NIfTI-1/2 file to a JNIfTI file or data structure

Example:

  img = uint16(reshape(1:10*30*20, [10, 30, 20]));  % create sample data
  savenifti(img, 'test.nii');              % save sample data as an example nii file
  savenifti(img, 'test.nii.gz');           % save sample data as an example nii.gz file

  nii=nii2jnii('test.nii', 'nii');         % read a .nii file as a nii structure
  nii=nii2jnii('test.nii.gz');             % read a .nii.gz file as a jnii structure
  nii2jnii('test.nii.gz', 'newdata.jnii') ;% read a .nii.gz file and convert to a text-JNIfTI file
  nii2jnii('test.nii.gz', 'newdata.bnii','compression','zlib'); % read a .nii.gz file and convert to a binary-JNIfTI file with compression

loadnifti - To read a NIfTI-1/2 (.nii or .nii.gz) file (alias to nii2jnii)

Example:

  nii=loadnifti('test.nii.gz');             % read a .nii.gz file as a jnii structure
  nii=loadnifti('test.nii', 'nii');         % read a .nii file as a nii structure

savenifti - To write an image as NIfTI-1/2 (.nii or .nii.gz) file

Example:

  savenifti(img, 'test.nii.gz');        % save an array img to a compressed nifti file
  savenifti(img, 'test.nii', 'nifti2'); % save an array img to a nifti-2 file file
  savenifti(img, 'test.nii', nii.hdr);  % save an array img with an existing header

loadjnifti - To read a JNIfTI (.jnii or .bnii) file

Example:

  jnii = nii2jnii('test.nii.gz');
  savejnifti(jnii, 'magic10.bnii', 'Compression', 'gzip');
  newjnii = loadjnifti('magic10.bnii');

savejnifti - To write a JNIfTI structure into a file (.jnii or .bnii)

Example:

  jnii = jnifticreate(uint8(magic(10)), 'Name', '10x10 magic matrix');
  savejnifti(jnii, 'magic10.jnii');
  savejnifti(jnii, 'magic10_debug.bnii', 'Compression', 'gzip');
  savejnifti(jnii, 'test.jnii', 'Compression', 'zlib');
  savejnifti(jnii, 'test.bnii', 'Compression', 'zlib');

jnii2nii - To convert a JNIfTI file or data structure to a NIfTI-1/2 file

Example:

  nii = jnii2nii('test.jnii');             % read a .jnii file as an nii structure
  nii = jnii2nii('test.bnii');             % read a .bnii file as an nii structure
  jnii2nii('test.jnii', 'newdata.nii.gz'); % read a text-JNIfTI file to an .nii.gz file
  jnii2nii('test.bnii', 'newdata.nii');    % read a text-JNIfTI file to an .nii file
Assets 2
Loading