CiftiLib
A C++ library for CIFTI-2 and CIFTI-1 files
cifti::nifti_1_header Struct Reference

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. More...

#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.
  • "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.


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