JNIfTI Toolbox - Fast and portable NIfTI-1/2 reader and NIfTI-to-JNIfTI converter

• Copyright (C) 2019-2024 Qianqian Fang <q.fang at neu.edu>
• License: GNU General Public License version 3 (GPL v3) or Apache License 2.0, see License*.txt
• Version: 0.6 (Epica)
• URL: http://github.com/NeuroJSON/jnifti

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 (http://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/jnifti'). 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 process gzip-compressed NIfTI/Analyze files in Octave and MATLAB with -nojvm, one need to install the open-source JSONLab and ZMat toolboxes, both supporting MATLAB and Octave. They can be downloaded at

• JSONLab: http://github.com/NeuroJSON/jsonlab
• ZMat: http://github.com/NeuroJSON/zmat

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 JNIfTI files in Octave, one must install the ZMat toolbox, as listed above.

Usage

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

Example:

  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', header);   % 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');

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