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Manpage of analyzeheader
analyzeheader
Section: User Commands (1)
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NAME
analyzeheader - Create or read an Analyze 7.5 header file.
SYNOPSIS
analyzeheader
[options]
DESCRIPTION
Analyze image header, provides support for the most common header
fields. Some fields, such as patient_id, are not currently
supported. The program allows three nonstandard options: the field
image_dimension.funused1 is the image scale. The intensity
of each pixel in the associated .img file is (image
value from file) * scale. Also, the origin of the Talairach
coordinates (midline of the anterior commisure) are encoded in the
field data_history.originator. These changes are included for
compatibility with SPM. Finally, the PICo seed point may be stored in
the fields unused8, unused9 and unused10.
All headers written with this program are big endian by default.
EXAMPLES
analyzeheader -datadims 128 128 60 -voxeldims 1.7 1.7 2.3 -datatype
double > subjectA.hdr
Initialize a new header from an existing file, and apply options
analyzeheader -initfromheader subjectA.hdr -datatype float
> subjectB.hdr
The header subjectB.hdr is identical to subjectA.hdr except that its data type
is float.
Get the data / voxel dimensions of an image as a string, suitable for passing to another
Camino program.
analyzeheader -printimagedims subjectA.hdr
The above command prints the data and voxel dimensions of the image,
"-datadims 128 128 60 -voxeldims 1.7 1.7 2.3".
This can be used with Camino programs that require this
information. For example,
dteig < subjectA.dt.Bdouble | pdview `analyzeheader -printimagedims subjectA.hdr`
To get relevant arguments for other programs, do
analyzeheader -printprogargs image.hdr program
where program is one of: shredder, scanner2voxel, vcthreshselect, pdview, track. The program
will print the args for the relevant program and exit. The list of suggested args for all of these
programs is available via the following command:
analyzeheader -readheader image.hdr
OPTIONS
- -readheader <file>
-
Reads header information from file and prints to stdout. If this
option is not specified, then the program writes a header based on the
other arguments.
- -printimagedims <file>
-
Prints image data and voxel dimensions as Camino arguments and exits.
- -printprogargs <file> <prog>
-
Prints data dimension (and type, if relevant) arguments for a specific
Camino program, where prog is one of shredder, scanner2voxel, vcthreshselect,
pdview, track.
- -printintelbyteorder <file>
-
Prints 1 if the header is little-endian, 0 otherwise.
- -printbigendian <file>
-
Prints 1 if the header is big-endian, 0 otherwise.
- -initfromheader <file>
-
Reads header information from file and intializes a new header with the
values read from the file. You may replace any combination of fields in the new header
by specifying subsequent options.
- -datadims <x> <y> <z>
-
Dimensions of the data in the img file, in voxels.
- -voxeldims <xv> <yv> <zv>
-
Dimensions of the voxels in mm.
- -nimages <number>
-
Number of images in the img file. Default 1.
- -datatype <byte | char | [u]short | [u]int | float | complex
-
| double>
The char datatype is 8 bit (not the 16 bit char of Java), as specified
by the Analyze 7.5 standard. The byte, ushort and uint types are not part of the Analyze
specification but are supported by SPM.
- -offset <value>
-
According to the Analyze 7.5 standard, this is the byte offset in the .img
file at which voxels start. This value can be negative to specify that
the absolute value is applied for every image in the file.
- -gl <min> <max>
-
Minimum and maximum greylevels. Stored as shorts in the header.
- -scaleslope <value>
-
Intensities in the image are scaled by this factor by SPM and
MRICro. Default is 1.0.
- -scaleinter <value>
-
Constant to add to the image intensities. Used by SPM and MRIcro.
- -description <string>
-
No spaces, max length 79 bytes. Will be null terminated automatically.
- -centre <x> <y> <z>
-
Voxel specifying origin of Talairach coordinate system for SPM,
default [0 0 0].
- -picoseed <x> <y> <z>
-
Voxel specifying the seed (for PICo maps), default [0 0 0].
- -intelbyteorder
-
Write header in intel byte order (little-endian).
- -networkbyteorder
-
Write header in network byte order (big-endian). This is the default for new headers.
AUTHORS
Philip Cook <camino@cs.ucl.ac.uk>
SEE ALSO
track(1), procstreamlines(1), rgbscalarimg(1), vtkstreamlines(1)
BUGS
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- EXAMPLES
-
- OPTIONS
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
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