Scalar Image File Format¶
Scalar value image includes the following data types:
brain_region: label image with integer values as voxel type
gray_level: raw imaging data, integer or float values as voxel type
longitude: computed depth information of the atlas, integer values as voxel type
hemisphere: hemisphere dataset with int8 or uint8 values as voxel type (0: undefined, 1: left, 2: right)
Specification¶
The meta data stored in the NRRD file should follow the specification below:
Field |
Value Type |
Suggested Value |
Comments |
---|---|---|---|
dimension |
integer |
3 |
dimension of the image is always 3 for volumetric data |
encoding |
string |
gzip |
use ‘gzip’ for compressing the data |
endian |
string |
little |
use ‘little’ for x86 machines |
kinds |
list of string |
[‘domain’, ‘domain’, ‘domain’] |
use ‘domain’ to indicate that the axis is image axis |
sizes |
list of integer |
[{size_x}, {size_y}, {size_z}] |
the size of the volume in x, y, z dimension |
space directions |
3d matrix |
A 3D matrix indicating the orientation of the image data, with the value indicating the spacing of the voxel |
|
space origin |
list of float |
[{origin_x}, {origin_y}, {origin_z}] |
physical coordinates of the image origin |
space |
string |
{x_orientation}-{y_orientation}-{z_orientation} |
the orientation of the image data, should be consistent with the space direction |
type |
string |
{voxel type} |
the type of the values stored in the voxels (e.g. unsigned/signed int, float, etc.) |
Example:
{
u'space origin': ['-46.540000915527344', '-152.15999984741211', '-152'],
u'space directions': [['16', '0', '0'], ['0', '16', '0'], ['0', '0', '16']],
u'sizes': [308, 495, 464],
u'space': 'left-posterior-superior',
u'encoding': 'gzip',
u'endian': 'little',
u'kinds': ['domain', 'domain', 'domain'],
u'type': 'unsigned short',
u'dimension': 3
}