unravel.voxel_stats.vstats_prep module#
Use vstats_prep
(vp
) from UNRAVEL to load an immunofluo image, subtract its background, and warp it to atlas space.
- Prereqs:
reg
- Input examples (path is relative to ./sample??; 1st glob match processed):
*.czi, ochann/*.tif, ochann, *.tif, *.h5, or *.zarr
- Output example:
./sample??/atlas_space/sample??_cfos_rb4_30um_CCF_space.nii.gz
- Next commands for voxel-wise stats:
Preprocess atlas space IF images with
vstats_z_score
(recommended for c-Fos-IF) or aggregate them withutils_agg_files
.
Usage:#
vstats_prep -i *.czi -o cfos_rb4_30um_CCF_space.nii.gz [-sa 3] [-rb 4] [–channel 1] [–reg_res 50] [-fri reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz] [-a atlas/atlas_CCFv3_2020_30um.nii.gz] [-dt uint16] [-zo 1] [-inp bSpline] [-md parameters/metadata.txt] [–threads 8] [-mi] [-d list of paths] [-p sample??] [-v]