The NIFTI-2 file format

In a previous post, the nifti-1 file format was presented. An update of this format has recently been produced by the Data Format Working Group (dfwg). The updated version retains generally the same amount of information as the previous, with the crucial difference that it allows far more datapoints in each dimension, thus permitting that the same overall file structure is used to store, for instance, surface-based scalar data, or large connectivity matrices. Neither of these had originally been intended at the time the analyze or the nifti-1 formats were developed. While packages as FreeSurfer developed their own formats for surface-based scalar data, a more general solution was still pending.

Compatible, but not as before

Users who participated of the transition from analyze to nifti-1 may remember that the same libraries used to read analyze would read nifti, perhaps with a few minor difficulties, but the bulk of the actual data would be read by most analyze-compliant applications. This was possible because a large part of the relevant information in the header was kept exactly in the same position counted from the beginning of the file. An application could read information at a given byte position and locate it without error, or without finding something else.

This time things are different. While a large degree of compatibility exists, this compatibility helps more the developer than the end user. If before, an application made to read only analyze could read nifti-1, this time an application made to read nifti-1 will not read nifti-2 without a few, even if minor, changes to the application source code. To put in other words, the new version of the format is not bitwise compatible with the previous one. The reasons for this “almost compatibility” will become clear below.

Changing types

The limitation that became evident with the new uses found for the nifti format refer particularly to the maximum number of points (e.g., voxels) in each dimension. This limitation stems from the field short dim[8], which allows only 2 bytes (16 bits) for each dimension; since only positive values are accepted (short is signed), this imposes a cap: no more than 215-1 = 32767 voxels per dimension. In the nifti-2 format, this was replaced by int64_t dim[8], which guarantees 8 bytes (64 bits) per dimension, and so, a much larger number of points per dimension, that is, 263-1 = 9,223,372,036,854,775,807.

This change alone already renders the nifti-2 not bitwise compatible with the nifti-1. Yet, other changes were made, some as a consequence of the modifications to dim[8], such as slice_start and slice_end, both too promoted from short to int64_t. Other changes were made so as to improve the general ability to store data with higher precision. A complete table listing the modifications of the field types is below:

NIFTI-1 NIFTI-2
short dim[8] int64_t dim[8]
float intent_p1 double intent_p1
float intent_p2 double intent_p2
float intent_p3 double intent_p3
float pixdim[8] double pixdim[8]
float vox_offset int64_t vox_offset
float scl_slope double scl_slope
float scl_inter double scl_inter
float cal_max double cal_max
float cal_min double cal_min
float slice_duration double slice_duration
float toffset double toffset
short slice_start int64_t slice_start
short slice_end int64_t slice_end
char slice_code int32_t slice_code
char xyzt_units int32_t xyzt_units
short intent_code int32_t intent_code
short qform_code int32_t qform_code
short sform_code int32_t sform_code
float quatern_b double quatern_b
float quatern_c double quatern_c
float quatern_d double quatern_d
float srow_x double srow_x
float srow_y double srow_y
float srow_z double srow_z
char magic[4] char magic[8]

Fields removed, fields reordered, fields added

Seven fields that only existed in the nifti-1 for compatibility with the old analyze format were removed entirely. These are:

  • char data_type[10]
  • char db_name[18]
  • int extents
  • short session_error
  • char regular
  • int glmax
  • int glmax

Another change is that the fields were reordered, which is an improvement over the nifti-1: the magic string, for instance, is now at the beginning of the file, which helps testing what kind of file it is. All constraints that were imposed on the nifti-1 to allow compatibility with the analyze were finally dropped. At the far end of the header, a field with 15 bytes was included for padding the header to a total size of 540, and to ensure 16-byte alignment after the 4 final bytes that indicate extra information are included.

Overview of the new header structure

With the modifications above, the overall structure of the he nifti-2 became:

Type Name Offset Size Description
int sizeof_hdr 0B 4B Size of the header. Must be 540 (bytes).
char magic[8] 4B 8B Magic string, defining a valid signature.
int16_t data_type 12B 2B Data type.
int16_t bitpix 14B 2B Number of bits per voxel.
int64_t dim[8] 16B 64B Data array dimensions.
double intent_p1 80B 8B 1st intent parameter.
double intent_p2 88B 8B 2nd intent parameter.
double intent_p3 96B 8B 3rd intent parameter.
double pixdim[8] 104B 64B Grid spacings (unit per dimension).
int64_t vox_offset 168B 8B Offset into a .nii file.
double scl_slope 176B 8B Data scaling, slope.
double scl_inter 184B 8B Data scaling, offset.
double cal_max 192B 8B Maximum display intensity.
double cal_min 200B 8B Minimum display intensity.
double slice_duration 208B 8B Time for one slice.
double toffset 216B 8B Time axis shift.
int64_t slice_start 224B 8B First slice index.
int64_t slice_end 232B 8B Last slice index.
char descrip[80] 240B 80B Any text.
char aux_file[24] 320B 24B Auxiliary filename.
int qform_code 344B 4B Use the quaternion fields.
int sform_code 348B 4B Use of the affine fields.
double quatern_b 352B 8B Quaternion b parameter.
double quatern_c 360B 8B Quaternion c parameter.
double quatern_d 368B 8B Quaternion d parameter.
double qoffset_x 376B 8B Quaternion x shift.
double qoffset_y 384B 8B Quaternion y shift.
double qoffset_z 392B 8B Quaternion z shift.
double srow_x[4] 400B 32B 1st row affine transform.
double srow_y[4] 432B 32B 2nd row affine transform.
double srow_z[4] 464B 32B 3rd row affine transform.
int slice_code 496B 4B Slice timing order.
int xyzt_units 500B 4B Units of pixdim[1..4].
int intent_code 504B 4B nifti intent.
char intent_name[16] 508B 16B Name or meaning of the data.
char dim_info 524B 1B Encoding directions.
char unused_str[15] 525B 15B Unused, to be padded with with zeroes.
Total size 540B

NIFTI-1 or NIFTI-2?

For the developer writing input/output functions to handle nifti files, a simple check can be used to test the version and the endianness of the file: the first four bytes are read (int sizeof_hdr): if equal to 348, then it is a nifti-1 file; if equal to 540, then it is a nifti-2 file. If equal to neither, then swap the bytes, as if reading in the non-native endianness, and repeat the test; if this time the size of the header is found as 348 or 540, the version is determined, and this also implies that all bytes in the file need to be swapped to match the endianness of the current architecture. If, however, the first four bytes do not contain 348 or 540 in either endianness, then it is not a valid nifti file.

Once the version and the endianness have been determined, if it is a nifti-1 file, jump to byte 344 and check if the content is 'ni1' (or '6E 69 31 00' in hexadecimal), indicating a pair .hdr/.img, or if it is 'n+1' ('6E 2B 31 00'), indicating a single .nii file. If, however, it is a nifti-2 file, just read the next 8 bytes and check if the content is 'n+2' ('6E 2B 32 00') followed by '0D 0A 1A 0A' (hex).

Storing extra information

Just like the nifti-1, the four bytes after the end of the nifti-2 header are used to indicate extensions and more information. Thus, the actual data begins after the byte 544. See the post on the nifti-1 for details. The cifti-2 file format (used extensively by the Human Connectome Project) is built on top of the nifti-2 format, and uses this extra information.

More information

The official definition of the nifti-2 format is available as a c header file (nifti2.h) here and mirrored here.

One thought on “The NIFTI-2 file format

  1. Pingback: The NIFTI file format | Brainder.

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