nifti_1_header(3)
| nifti_1_header(3) | Library Functions Manual | nifti_1_header(3) |
NAME
nifti_1_header -
Data structure defining the fields in the nifti1 header. This binary header should be found at the beginning of a valid NIFTI-1 header file.
SYNOPSIS
#include <nifti1.h>
Public Attributes
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
Data structure defining the fields in the nifti1 header. This binary header should be found at the beginning of a valid NIFTI-1 header file.
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.
- 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).
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. -----------------------------------------------------------------------------
Member Data Documentation
char nifti_1_header::aux_file[24] auxiliary filename.
short nifti_1_header::bitpix Number bits/voxel.
float nifti_1_header::cal_max Max display intensity
float nifti_1_header::cal_min Min display intensity
char nifti_1_header::data_type[10] ++UNUSED++
short nifti_1_header::datatype Defines data type!
char nifti_1_header::db_name[18] ++UNUSED++
char nifti_1_header::descrip[80] any text you like.
short nifti_1_header::dim[8] Data array dimensions.
char nifti_1_header::dim_info MRI slice ordering.
int nifti_1_header::extents ++UNUSED++
int nifti_1_header::glmax ++UNUSED++
int nifti_1_header::glmin ++UNUSED++
short nifti_1_header::intent_code NIFTI_INTENT_* code.
char nifti_1_header::intent_name[16] 'name' or meaning of data.
float nifti_1_header::intent_p1 1st intent parameter.
float nifti_1_header::intent_p2 2nd intent parameter.
float nifti_1_header::intent_p3 3rd intent parameter.
char nifti_1_header::magic[4] MUST be 'ni1 ' or 'n+1 '.
float nifti_1_header::pixdim[8] Grid spacings.
short nifti_1_header::qform_code NIFTI_XFORM_* code.
float nifti_1_header::qoffset_x Quaternion x shift.
float nifti_1_header::qoffset_y Quaternion y shift.
float nifti_1_header::qoffset_z Quaternion z shift.
float nifti_1_header::quatern_b Quaternion b param.
float nifti_1_header::quatern_c Quaternion c param.
float nifti_1_header::quatern_d Quaternion d param.
char nifti_1_header::regular ++UNUSED++
float nifti_1_header::scl_inter Data scaling: offset.
float nifti_1_header::scl_slope Data scaling: slope.
short nifti_1_header::session_error ++UNUSED++
short nifti_1_header::sform_code NIFTI_XFORM_* code.
int nifti_1_header::sizeof_hdr MUST be 348
char nifti_1_header::slice_code Slice timing order.
float nifti_1_header::slice_duration Time for 1 slice.
short nifti_1_header::slice_end Last slice index.
short nifti_1_header::slice_start First slice index.
float nifti_1_header::srow_x[4] 1st row affine transform.
float nifti_1_header::srow_y[4] 2nd row affine transform.
float nifti_1_header::srow_z[4] 3rd row affine transform.
float nifti_1_header::toffset Time axis shift.
float nifti_1_header::vox_offset Offset into .nii file
char nifti_1_header::xyzt_units Units of pixdim[1..4]
Author
Generated automatically by Doxygen for nifti1_io from the source code.
| Sat Apr 16 2011 | nifti1_io |