mk_nifti_hdr(1) Make NIFTI header file


mk_nifti_hdr [options] [output.nii]


Make header file according to NIFTI file format based on user-supplied parameters for geometry, data type, orientation, etc.


Global Toolkit Options (these are shared by all CMTK tools)

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write toolkit version to standard output.
Write the current command line to standard output.
--verbose-level <integer>
Set verbosity level.
--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
--threads <integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options

--dims <string>, -D <string>
Set dimensions in voxels. Provided as 'DimsX,DimsY,DimsZ'
--voxel <string>, -V <string>
Set voxel size. Provided as 'PixX,PixY,PixZ' [in mm]
--offset <float>, -O <float>
Binary data file offset [Default: disabled]
--byte, -b
8 bits, unsigned (this is the default)
--char, -c
8 bits, signed
--short, -s
16 bits, signed
--ushort, -u
16 bits, unsigned
--int, -i
32 bits signed
--float, -f
32 bits floating point
--double, -d
64 bits floating point

In an imported header, reset the image-to-physical coordinate mapping to an identity matrix.
Create attached header for use in single-file images. Image data must be concatenated directly onto the created header file.
--import <string>, -I <string>
Import data from given header file. [Default: NONE]
--description <string>
Set description string [max. 80 characters] [Default: NONE]


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko


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CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.