Release notes from jnifti

JNIfTI Toolbox v0.6 - Epica

2020-06-24T02:26:39Z

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

v0.5

2019-09-14T05:48:16Z

change comment markers to make it compatible for both matlab and octave

JNIfTI Toolbox v0.5 - Ascendance

2019-09-15T18:03:02Z

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 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).

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');

Release notes from jnifti

JNIfTI Toolbox v0.6 - Epica

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

Overview

Installation

Usage

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

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

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

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

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

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

v0.5

JNIfTI Toolbox v0.5 - Ascendance

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

Overview

Installation

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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