JNIfTI Toolbox - Fast and portable NIfTI-1/2 reader and NIfTI-to-JNIfTI converter
- Copyright (C) 2019-2020 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/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
- JSONLab: http://github.com/fangq/jsonlab
- ZMat: http://github.com/fangq/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