Using the converted data in Neuroglancer ======================================== .. _info: The Neuroglancer *info* file ---------------------------- See the `info JSON file specification `_ from Neuroglancer. .. _half_voxel_shift: 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.