unravel.region_stats.rstats_mean_IF module

Use rstats_mean_IF from UNRAVEL to measure mean intensity of immunofluorescence staining in brain regions in atlas space.

Inputs:

• *.nii.gz

• path/atlas.nii.gz

Outputs:

• ./rstats_mean_IF/image_name.csv with regional mean intensity values for each image

Next:

• cd rstats_mean_IF

• rstats_mean_IF_summary

Usage:

rstats_mean_IF -i ‘<asterisk>.nii.gz’ -a path/atlas [–regions 1 2 3] [-v]

unravel.region_stats.rstats_mean_IF.parse_args()

unravel.region_stats.rstats_mean_IF.calculate_mean_intensity(atlas, image, regions=None)

Calculates mean intensity for each region in the atlas.

unravel.region_stats.rstats_mean_IF.write_to_csv(data, output_file)

Writes the data to a CSV file.

unravel.region_stats.rstats_mean_IF.main()