f.read.analyze.header: read Analyze header file

In AnalyzeFMRI: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format

Description

Reads the ANALYZE image format .hdr header file into a list.

Usage

f.read.analyze.header(file)

Arguments

file	The .hdr file to be read

Value

A list containing the information in the fields of the .hdr file.

file.name	name of the .img file
swap	TRUE or FALSE variable indicating whether files are big or little endian
....... HEADER KEY ..........
sizeof.hdr	This field implies that Analyze format was originally intended to be extensible, but in practice this did not happen, and instead the file size (and hence the value of this field) is 348. Software commonly tests the value in this field to detect whether the byte ordering is Big-Endian or Little-Endian.
data.type	character vector indicating data storage type for each voxel
db.name	database name
extents	Should be 16384, the image file is created as contiguous with a minimum extent size
session.error
regular	Must be ‘r’ to indicate that all images and volumes are the same size
hkey.un0
....... IMAGE DIMENSION ..........
dim	vector of the image dimensions: dim[1] Number of dimensions in database, usually 4; dim[2] Image X dimension (slice width), number of pixels in an image row; dim[3] Image Y dimension (slice height), number of pixel rows in slice; dim[4] Volume Z dimension (volume depth), number of slices in a volume; dim[5] Time points, number of volumes in database dim[6] ?? dim[7] ?? dim[8] ??
vox.units	3 characters to specify the spatial units of measure for a voxel (mm., um., cm.)
cal.units	7 characters to specify the name of the calibration unit i.e. pixel,voxel
unused1	??
datatype	integer indicator of data storage type for this image: 0 (None or Unknown), 1 (Binary), 2 (Unsigned-char), 4 (Signed-short), 8 (Signed-int), 16 (float), 32 (Complex), 64 (Double), 128 (RGB), 255 (All)
bitpix	number of bits per pixel: 1 (packed binary, slices begin on byte boundaries), 8 (unsigned char, gray scale), 16 (signed short), 32 (signed integers or float), or 24 (RGB, 8 bits per channel)s
dim.un0	unused
pixdim	Parallel vector to dim, giving real world measurements in mm. and ms. pixdim[1]: ?? pixdim[2]: voxel width in mm. pixdim[3]: voxel height in mm. pixdim[4]: slice thickness (interslice distance) in mm. pixdim[5]: timeslice in ms. pixdim[6]: ?? pixdim[7]: ?? pixdim[8]: ??
vox.offset	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 voxel in the file
funused1	specify the range of calibration values. SPM extends the Analyze format by using a scaling factor for the image from the header
funused2	SPM2 image intensity zero intercept
funused3	??
cal.max	Max display intensity, calibration value, values of 0.0 for both fields imply that no calibration max and min values are used
cal.min	Min display intensity, calibration value
compressed	??
verified	??
glmax	The maximum pixel values for the entire database
glmin	The minimum pixel values for the entire database
....... DATA HISTORY ..........
descrip	any text you like
aux.file	auxiliary filename
orient	planar slice orientation for this dataset: 0 transverse unflipped; 1 coronal unflipped; 2 sagittal unflipped; 3 transverse flipped; 4 coronal flipped; 5 sagittal flipped
originator	image central voxel coordinates. SPM uses this Analyze header field in an unorthodox way. originator[1]: SPM99 X near Anterior Commissure, originator[2]: SPM99 Y near Anterior Commissure, originator[3]: SPM99 Z near Anterior Commissure, originator[4]:??, originator[5]:??
generated	??
scannum	??
patient.id	??
exp.date	??
exp.time	??
hist.un0	??
views	??
vols.added	??
start.field	??
field.skip	??
omax	??
omin	??
smax	??
smin	??

See Also

f.analyze.file.summary

Examples

f.read.analyze.header(system.file("example.hdr", package="AnalyzeFMRI"))

Example output

Loading required package: R.matlab
R.matlab v3.6.2 (2018-09-26) successfully loaded. See ?R.matlab for help.

Attaching package: 'R.matlab'

The following objects are masked from 'package:base':

    getOption, isOpen

Loading required package: fastICA
Loading required package: tcltk
Loading required package: tkrplot
Warning messages:
1: no DISPLAY variable so Tk is not available 
2: loading Rplot failed 
$file.name
[1] "/usr/lib/R/site-library/AnalyzeFMRI/example.img"

$swap
[1] 1

$sizeof.hdr
[1] 348

$data.type
[1] "signed short"

$db.name
[1] "audvis.4.2.mc.vol."

$extents
[1] 16384

$session.error
[1] 0

$regular
[1] "r"

$hkey.un0
[1] ""

$dim
[1]  4 64 64 21  1  0  0  0

$vox.units
[1] "mm"

$cal.units
[1] "pixels"

$unused1
[1] 0

$datatype
[1] 4

$bitpix
[1] 16

$dim.un0
[1] 0

$pixdim
[1] 4 4 4 6 0 0 0 0
attr(,"Csingle")
[1] TRUE

$vox.offset
[1] 0
attr(,"Csingle")
[1] TRUE

$funused1
[1] 1
attr(,"Csingle")
[1] TRUE

$funused2
[1] 0
attr(,"Csingle")
[1] TRUE

$funused3
[1] 0
attr(,"Csingle")
[1] TRUE

$cal.max
[1] 14553
attr(,"Csingle")
[1] TRUE

$cal.min
[1] 0
attr(,"Csingle")
[1] TRUE

$compressed
[1] 0
attr(,"Csingle")
[1] TRUE

$verified
[1] 0
attr(,"Csingle")
[1] TRUE

$glmax
[1] 14553

$glmin
[1] 0

$descrip
[1] "audvis.4.2.mc.vol.1.img"

$aux.file
[1] ""

$orient
[1] ""

$originator
[1] 0 0 0 0 0

$generated
[1] ""

$scannum
[1] ""

$patient.id
[1] ""

$exp.date
[1] ""

$exp.time
[1] ""

$hist.un0
[1] "LAS"

$views
[1] 0

$vols.added
[1] 0

$start.field
[1] 0

$field.skip
[1] 0

$omax
[1] 0

$omin
[1] 0

$smax
[1] 0

$smin
[1] 0

AnalyzeFMRI documentation built on Oct. 5, 2021, 5:06 p.m.