pip install nifti-zarrConvert a nifti file to a nifti-zarr storage.
from niizarr import nii2zarr
nii2zarr("path/to/nifti.nii.gz", "s3://path/to/bucket")Convert a nifti-zarr storage to a nifti file.
The pyramid level can be selected with level=L, where 0 is the base/finest level.
from niizarr import zarr2nii
zarr2nii("s3://path/to/bucket", "path/to/nifti.nii.gz", level=0)Load a nifti-zarr into a nibabel.Nifti1Image object.
from niizarr import zarr2nii
nivol = zarr2nii("s3://path/to/bucket", level=0)usage: nii2zarr [-h]
[--chunk CHUNK]
[--unchunk-channels]
[--unchunk-time]
[--levels LEVELS]
[--method {gaussian,laplacian}]
[--fill FILL]
[--compressor {blosc,zlib}]
[--label]
[--no-label]
[--no-time]
[--no-pyramid-axis {x,y,z}]
[--zarr-version {2,3}]
[--ome-version {0.4,0.5}]
input [output]
Convert nifti to nifti-zarr.
positional arguments:
input Input nifti file.
output Output zarr directory.
When not specified, write to input directory.
optional arguments:
-h, --help Show this help message and exit.
--chunk CHUNK Spatial chunk size.
--unchunk-channels Save all chanels in a single chunk.
Unchunk if you want to display all channels
as a single RGB layer in neuroglancer.
Chunked by default, unless datatype is RGB.
--unchunk-time Save all timepoints in a single chunk.
Unchunk if you want to display all timepoints
as a single RGB layer in neuroglancer.
Chunked by default.
--levels LEVELS Number of levels in the pyramid.
If -1 (default), use as many levels as possible.
--method {gaussian,laplacian} Pyramid method.
--fill FILL Missing value.
--compressor {blosc,zlib} Compressor.
--label Segmentation volume.
--no-label Not a segmentation volume.
--no-time No time dimension.
--no-pyramid-axis {x,y,z} Thick slice axis that should not be downsampled.
--zarr-version {2,3} Zarr format version.
--ome-version {0.4,0.5} OME-Zarr specification version.
usage: zarr2nii [-h] [--level LEVEL] input [output]
Convert nifti-zarr to nifti.
positional arguments:
input Input zarr directory
output Output nifti file.
When not provided, write to the same directory as input
optional arguments:
-h, --help Show this help message and exit.
--level LEVEL Pyramid level to extract (default: 0 = finest).