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README.md
gzipdecode.m
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jnifticreate.m
jnii2nii.m
loadjnifti.m
loadnifti.m
memmapstream.m
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nii2jnii.m
niicodemap.m
niiformat.m
savebnii.m
savejnifti.m
savejnii.m
savenifti.m

README.md

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

  • Copyright (C) 2019 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: 0.5 (Ascendence)
  • URL: http://github.com/fangq/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/fangq/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

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');
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