.TH mk_analyze_hdr "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
mk_analyze_hdr \- Make Analyze header file
.SH SYNOPSIS
mk_analyze_hdr [options] [output.nii]
.SH DESCRIPTION
Make header file according Analzye 7.5 format based on user-supplied parameters for geometry, data type, orientation, etc.
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Main Options
.TP 5
\fB\-\-dims\fR \fI<string>\fR, \fB\-D\fR \fI<string>\fR
Set dimensions in voxels
.TP 5
\fB\-\-voxel\fR \fI<string>\fR, \fB\-V\fR \fI<string>\fR
Set voxel size in [mm]
.TP 5
\fB\-\-offset\fR \fI<float>\fR, \fB\-O\fR \fI<float>\fR
Binary data file offset
.B [Default: disabled]
.TP 5
\fB\-\-byte\fR, \fB\-b\fR
8 bits, unsigned (this is the default)
.TP 5
\fB\-\-char\fR, \fB\-c\fR
8 bits, signed
.TP 5
\fB\-\-short\fR, \fB\-s\fR
16 bits, signed
.TP 5
\fB\-\-ushort\fR, \fB\-u\fR
16 bits, unsigned
.TP 5
\fB\-\-int\fR, \fB\-i\fR
32 bits signed
.TP 5
\fB\-\-float\fR, \fB\-f\fR
32 bits floating point
.TP 5
\fB\-\-double\fR, \fB\-d\fR
64 bits floating point

.TP 5
\fB\-\-big-endian\fR, \fB\-B\fR
Big endian data
\fB[This is the default]\fR
.TP 5
\fB\-\-little-endian\fR, \fB\-L\fR
Little endian data
.TP 5
\fB\-\-axial\fR
Set slice orientation to axial (this is the default)
.TP 5
\fB\-\-axial-flip\fR
Set slice orientation to reverse axial
.TP 5
\fB\-\-sagittal\fR
Set slice orientation to sagittal
.TP 5
\fB\-\-sagittal-flip\fR
Set slice orientation to reverse sagittal
.TP 5
\fB\-\-coronal\fR
Set slice orientation to corona;
.TP 5
\fB\-\-coronal-flip\fR
Set slice orientation to reverse coronal
.TP 5
\fB\-\-legacy\fR
Legacy mode; do not write 'SRI1' tag into header
.TP 5
\fB\-\-SRI1\fR
Force 'SRI1' tag even if not present in imported header
.TP 5
\fB\-\-import\fR \fI<string>\fR, \fB\-I\fR \fI<string>\fR
Import data from given header file.
.B [Default: NONE]
.TP 5
\fB\-\-description\fR \fI<string>\fR
Set description string [max. 80 characters]
.B [Default: NONE]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH ACKNOWLEDGMENTS
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.