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nifti_1_header Struct Reference

#include <nifti1.h>


Data Fields
int	sizeof_hdr
char	data_type [10]
char	db_name [18]
int	extents
short	session_error
char	regular
char	dim_info
short	dim [8]
float	intent_p1
float	intent_p2
float	intent_p3
short	intent_code
short	datatype
short	bitpix
short	slice_start
float	pixdim [8]
float	vox_offset
float	scl_slope
float	scl_inter
short	slice_end
char	slice_code
char	xyzt_units
float	cal_max
float	cal_min
float	slice_duration
float	toffset
int	glmax
int	glmin
char	descrip [80]
char	aux_file [24]
short	qform_code
short	sform_code
float	quatern_b
float	quatern_c
float	quatern_d
float	qoffset_x
float	qoffset_y
float	qoffset_z
float	srow_x [4]
float	srow_y [4]
float	srow_z [4]
char	intent_name [16]
char	magic [4]

Detailed Description

INTRODUCTION TO NIFTI-1: ------------------------ The twin (and somewhat conflicting) goals of this modified ANALYZE 7.5 format are: (a) To add information to the header that will be useful for functional neuroimaging data analysis and display. These additions include:

More basic data types.
Two affine transformations to specify voxel coordinates.
"Intent" codes and parameters to describe the meaning of the data.
Affine scaling of the stored data values to their "true" values.
Optional storage of the header and image data in one file (.nii). (b) To maintain compatibility with non-NIFTI-aware ANALYZE 7.5 compatible software (i.e., such a program should be able to do something useful with a NIFTI-1 dataset -- at least, with one stored in a traditional .img/.hdr file pair).

Most of the unused fields in the ANALYZE 7.5 header have been taken, and some of the lesser-used fields have been co-opted for other purposes. Notably, most of the data_history substructure has been co-opted for other purposes, since the ANALYZE 7.5 format describes this substructure as "not required".

NIFTI-1 FLAG (MAGIC STRINGS): ---------------------------- To flag such a struct as being conformant to the NIFTI-1 spec, the last 4 bytes of the header must be either the C String "ni1" or "n+1"; in hexadecimal, the 4 bytes 6E 69 31 00 or 6E 2B 31 00 (in any future version of this format, the '1' will be upgraded to '2', etc.). Normally, such a "magic number" or flag goes at the start of the file, but trying to avoid clobbering widely-used ANALYZE 7.5 fields led to putting this marker last. However, recall that "the last shall be first" (Matthew 20:16).

If a NIFTI-aware program reads a header file that is NOT marked with a NIFTI magic string, then it should treat the header as an ANALYZE 7.5 structure.

NIFTI-1 FILE STORAGE: -------------------- "ni1" means that the image data is stored in the ".img" file corresponding to the header file (starting at file offset 0).

"n+1" means that the image data is stored in the same file as the header information. We recommend that the combined header+data filename suffix be ".nii". When the dataset is stored in one file, the first byte of image data is stored at byte location (int)vox_offset in this combined file. The minimum allowed value of vox_offset is 352; for compatibility with some software, vox_offset should be an integral multiple of 16.

GRACE UNDER FIRE: ---------------- Most NIFTI-aware programs will only be able to handle a subset of the full range of datasets possible with this format. All NIFTI-aware programs should take care to check if an input dataset conforms to the program's needs and expectations (e.g., check datatype, intent_code, etc.). If the input dataset can't be handled by the program, the program should fail gracefully (e.g., print a useful warning; not crash).

SAMPLE CODES: ------------ The associated files nifti1_io.h and nifti1_io.c provide a sample implementation in C of a set of functions to read, write, and manipulate NIFTI-1 files. The file nifti1_test.c is a sample program that uses the nifti1_io.c functions. -----------------------------------------------------------------------------

Definition at line 127 of file nifti1.h.

Field Documentation

char nifti_1_header::aux_file[24]

auxiliary filename.

Definition at line 167 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), and nifti_convert_nim2nhdr().

short nifti_1_header::bitpix

Number bits/voxel.

Definition at line 149 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nim2nhdr(), nifti_simple_init_nim(), and swap_nifti_header().

float nifti_1_header::cal_max

Max display intensity

Definition at line 158 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::cal_min

Min display intensity

Definition at line 159 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

char nifti_1_header::data_type[10]

++UNUSED++

Definition at line 132 of file nifti1.h.

Referenced by disp_nifti_1_header().

short nifti_1_header::datatype

Defines data type!

Definition at line 148 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), nifti_simple_init_nim(), and swap_nifti_header().

char nifti_1_header::db_name[18]

++UNUSED++

Definition at line 133 of file nifti1.h.

Referenced by disp_nifti_1_header().

char nifti_1_header::descrip[80]

any text you like.

Definition at line 166 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), and nifti_convert_nim2nhdr().

short nifti_1_header::dim[8]

Data array dimensions.

Definition at line 140 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), nifti_simple_init_nim(), and swap_nifti_header().

char nifti_1_header::dim_info

MRI slice ordering.

Definition at line 137 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), and nifti_convert_nim2nhdr().

int nifti_1_header::extents

++UNUSED++

Definition at line 134 of file nifti1.h.

Referenced by disp_nifti_1_header(), and swap_nifti_header().

int nifti_1_header::glmax

++UNUSED++

Definition at line 162 of file nifti1.h.

Referenced by disp_nifti_1_header(), and swap_nifti_header().

int nifti_1_header::glmin

++UNUSED++

Definition at line 163 of file nifti1.h.

Referenced by disp_nifti_1_header(), and swap_nifti_header().

short nifti_1_header::intent_code

NIFTI_INTENT_* code.

Definition at line 147 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

char nifti_1_header::intent_name[16]

'name' or meaning of data.

Definition at line 183 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), and nifti_convert_nim2nhdr().

float nifti_1_header::intent_p1

1st intent parameter.

Definition at line 141 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::intent_p2

2nd intent parameter.

Definition at line 143 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::intent_p3

3rd intent parameter.

Definition at line 145 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

char nifti_1_header::magic[4]

MUST be "ni1\0" or "n+1\0".

Definition at line 185 of file nifti1.h.

Referenced by disp_nifti_1_header(), and nifti_convert_nim2nhdr().

float nifti_1_header::pixdim[8]

Grid spacings.

Definition at line 151 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), nifti_simple_init_nim(), and swap_nifti_header().

short nifti_1_header::qform_code

NIFTI_XFORM_* code.

Definition at line 169 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::qoffset_x

Quaternion x shift.

Definition at line 175 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::qoffset_y

Quaternion y shift.

Definition at line 176 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::qoffset_z

Quaternion z shift.

Definition at line 177 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::quatern_b

Quaternion b param.

Definition at line 172 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::quatern_c

Quaternion c param.

Definition at line 173 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::quatern_d

Quaternion d param.

Definition at line 174 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

char nifti_1_header::regular

++UNUSED++

Definition at line 136 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nim2nhdr(), and nifti_simple_init_nim().

float nifti_1_header::scl_inter

Data scaling: offset.

Definition at line 154 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::scl_slope

Data scaling: slope.

Definition at line 153 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

short nifti_1_header::session_error

++UNUSED++

Definition at line 135 of file nifti1.h.

Referenced by disp_nifti_1_header(), and swap_nifti_header().

short nifti_1_header::sform_code

NIFTI_XFORM_* code.

Definition at line 170 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

int nifti_1_header::sizeof_hdr

MUST be 348

Definition at line 131 of file nifti1.h.

Referenced by disp_nifti_1_header(), is_nifti_file(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), nifti_simple_init_nim(), and swap_nifti_header().

char nifti_1_header::slice_code

Slice timing order.

Definition at line 156 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), and nifti_convert_nim2nhdr().

float nifti_1_header::slice_duration

Time for 1 slice.

Definition at line 160 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

short nifti_1_header::slice_end

Last slice index.

Definition at line 155 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

short nifti_1_header::slice_start

First slice index.

Definition at line 150 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::srow_x[4]

1st row affine transform.

Definition at line 179 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::srow_y[4]

2nd row affine transform.

Definition at line 180 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::srow_z[4]

3rd row affine transform.

Definition at line 181 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::toffset

Time axis shift.

Definition at line 161 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

float nifti_1_header::vox_offset

Offset into .nii file

Definition at line 152 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), nifti_convert_nim2nhdr(), and swap_nifti_header().

char nifti_1_header::xyzt_units

Units of pixdim[1..4]

Definition at line 157 of file nifti1.h.

Referenced by disp_nifti_1_header(), nifti_convert_nhdr2nim(), and nifti_convert_nim2nhdr().

The documentation for this struct was generated from the following file:

nifti1.h

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nifti_1_header Struct Reference

Data Fields

Detailed Description

Field Documentation