Using the converted data in Neuroglancer¶
The Neuroglancer info file¶
See the info JSON file specification from Neuroglancer.
Different conventions for coordinate transformations¶
Beware that Neuroglancer departs from the NIfTI convention in associating physical coordinates to voxels: Neuroglancer associates physical coordinates to the corner of a voxel, whereas NIfTI specifies that they refer to the centre of a voxel. Therefore, images will be offset by half a voxel relative to meshes if you do not compensate for this offset.
For standalone meshes, this offset can be compensated for by using the
transform
URL parameter. For pre-computed segmentation meshes however, there
is no way of specifying a different transform
for the image and the
associated meshes: the offset must be applied to the vertex coordinates. This
can be achieved by using the --coord-transform
option.
Please note that if you want to display images correctly with respect to
physical coordinates (e.g. stereotaxic coordinates), you have to use the
transform
parameter as well. The transform.json
which is output by
volume-to-precomputed
does take the half-voxel shift into account.