m2m_download_annotation

Download the Allen mouse brain annotation for the Adult Mouse (3D), and setting the correct RAS+ direction and spacing.

usage: m2m_download_annotation.py [-h] [-r {10,25,50,100}] [-m FILE_MAT]
                                  [-R REFERENCE]
                                  output output_labels

Positional Arguments

output: Output nifti filename (.nii or .nii.gz)
output_labels: Output labels information file (.txt or .label) (Can be used by ITKSnap)

Named Arguments

-r, --resolution

Possible choices: 10, 25, 50, 100

Template resolution in micron. Default=100

Default: 100

-m, --file_mat

Path to the transform matrix (.mat)

-R, --reference

Path to the reference volume (.nii.gz)