NIfTi Input/Output

Author: Guy Williams (gbw1000 at wbic.cam.ac.uk)
Source: In nifti_io.jar
Installation: Download nifti_io.jar to the plugins folder, or subfolder, restart ImageJ, and there will be five new commands: File/Import/NIfTI-Analyze, File/Save As/Analyze (NIfTI-1), File/Save As/NIfTI-1, File/Save As/Analyze 7.5 and Analyze/Tools/Coordinate Viewer.
Description: These plugins are modified and rewritten versions of the Analyze_Reader and Analyze_Writer, plugins that support the NIfTI-1 Data Format, a modified and extended version of the Analyze file format.

The File/Import/NIfTI-Analyze command loads Analyze and Nifti-1 format files. If the <filename> provided (or selected) ends with ".hdr" or ".img" then <filename>.hdr will be parsed and used to appropriately load the raw image data found in '<filename>.img'. Otherwise the file is assumed to be in the concatenated nifti format. If the header information conforms to the nifti-1 standard, the information is stored in property "nifti" as an object of class NiftiHeader.

The File/Save As/Analyze (NIfTI-1) command saves the current image as a Nifti-1 .img/.hdr pair, File/Save As/NIfTI-1 saves as a combined header/image file (.nii), and File/Save As/Analyze 7.5 saves in Analyze 7.5 format.

Analyze/Tools/Coordinate Viewer tool can be used to display the interpretation of image coordinates based on coordinate mapping information in the NIfTI header.

History: 2005/08/19: First version
2005/10/26: Bug fixes
2006/07/05: Imports 64 bit data
2007/06/29: Compiles without Image5D plugin
2009/02/12: Opens 4D images as hyperstacks
2009/06/30: Opens gzip-ed images; bug fixes
2009/12/05: Saves virtual stacks (requires v1.43m or later)
2012/11/15: Fixed signed 16-bit import bug

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