unravel.warp.to_atlas module#
Use warp_to_atlas from UNRAVEL to warp a native image to atlas space.
- Prereqs:
reg- Input examples (path is relative to ./sample??; 1st glob match processed):
*.czi, cfos/*.tif, cfos, *.tif, *.h5, or *.zarr
Usage:#
warp_to_atlas -i cfos -o img_in_atlas_space.nii.gz [–channel 1] [-md path/metadata.txt] [-a atlas/atlas_CCFv3_2020_30um.nii.gz] [-dt uint16] [-fri reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz] [–reg_res 50] [-inp bSpline] [-zo 1] [-mi] [-d list of paths] [-p sample??] [-v]
- unravel.warp.to_atlas.copy_nii_header(source_img, new_img)[source]#
Copy header info from nii_img to new_img
- unravel.warp.to_atlas.to_atlas(sample_path, img, fixed_reg_in, atlas, output, interpol, dtype='uint16')[source]#
Warp the image to atlas space using ANTsPy.
- Parameters:
sample_path (-) – Path to the sample directory.
img (-) – 3D image.
fixed_reg_in (-) – Name of the fixed image for registration.
atlas (-) – Path to the atlas.
output (-) – Path to the output.
interpol (-) – Type of interpolation (linear, bSpline, nearestNeighbor, multiLabel).
dtype (-) – Desired dtype for output (e.g., uint8, uint16). Default: uint16