diff --git a/unravel/docs/_build/doctrees/environment.pickle b/unravel/docs/_build/doctrees/environment.pickle index d939c419..9a930883 100644 Binary files a/unravel/docs/_build/doctrees/environment.pickle and b/unravel/docs/_build/doctrees/environment.pickle differ diff --git a/unravel/docs/_build/html/_modules/unravel/image_io/nii_info.html b/unravel/docs/_build/html/_modules/unravel/image_io/nii_info.html index 9549fd32..ed9c685c 100644 --- a/unravel/docs/_build/html/_modules/unravel/image_io/nii_info.html +++ b/unravel/docs/_build/html/_modules/unravel/image_io/nii_info.html @@ -375,6 +375,7 @@

Source code for unravel.image_io.nii_info

 def parse_args():
     parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
     parser.add_argument('-i', '--input', help='path/img.nii.gz', action=SM)
+    parser.add_argument('-v', '--verbose', help='Increase verbosity.', action='store_true', default=False)
     parser.epilog = __doc__
     return parser.parse_args()
diff --git a/unravel/docs/_build/html/_modules/unravel/voxel_stats/z_score.html b/unravel/docs/_build/html/_modules/unravel/voxel_stats/z_score.html index 50eda80e..2400354e 100644 --- a/unravel/docs/_build/html/_modules/unravel/voxel_stats/z_score.html +++ b/unravel/docs/_build/html/_modules/unravel/voxel_stats/z_score.html @@ -412,7 +412,7 @@

Source code for unravel.voxel_stats.z_score

     parser.add_argument('-amas', '--atlas_mask', help='path/atlas_mask.nii.gz (can use tmas and/or amas)', default=None, action=SM)
     parser.add_argument('-n', '--no_tmask', help='Provide flag to avoid use of tmas', action='store_true')
     parser.add_argument('-fri', '--fixed_reg_in', help='Reference nii header from ``reg``. Default: reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz', default="reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz", action=SM)
-    parser.add_argument('-a', '--atlas', help='path/atlas.nii.gz for warping mask to atlas space (Default: path/gubra_ano_combined_25um.nii.gz)', default='/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz', action=SM)
+    parser.add_argument('-a', '--atlas', help='path/atlas.nii.gz. It is used as a fixed image for warping a brain mask to atlas space (Default: path/gubra_ano_combined_25um.nii.gz)', default='/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz', action=SM)
     parser.add_argument('-inp', '--interpol', help='Type of interpolation (nearestNeighbor, multiLabel [default]).', default='multiLabel', action=SM)
     parser.add_argument('-v', '--verbose', help='Increase verbosity', default=False, action='store_true')
     parser.epilog = __doc__
diff --git a/unravel/docs/_build/html/_modules/unravel/warp/to_atlas.html b/unravel/docs/_build/html/_modules/unravel/warp/to_atlas.html
index ec3b36bc..b98d7a3f 100644
--- a/unravel/docs/_build/html/_modules/unravel/warp/to_atlas.html
+++ b/unravel/docs/_build/html/_modules/unravel/warp/to_atlas.html
@@ -399,7 +399,7 @@ 
Source code for unravel.warp.to_atlas
     parser.add_argument('-c', '--chann_idx', help='.czi channel index. Default: 1', default=1, type=int, action=SM)
     parser.add_argument('-x', '--xy_res', help='Native x/y voxel size in microns (Default: get via metadata)', default=None, type=float, action=SM)
     parser.add_argument('-z', '--z_res', help='Native z voxel size in microns (Default: get via metadata)', default=None, type=float, action=SM)
-    parser.add_argument('-a', '--atlas', help='path/atlas.nii.gz (Default: /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz)', default='/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz', action=SM)
+    parser.add_argument('-a', '--atlas', help='path/atlas.nii.gz for use as the fixed image (Default: /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz)', default='/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz', action=SM)
     parser.add_argument('-dt', '--dtype', help='Desired dtype for output (e.g., uint8, uint16). Default: uint16', default="uint16", action=SM)
     parser.add_argument('-fri', '--fixed_reg_in', help='Reference nii header from ``reg``. Default: reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz', default="reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz", action=SM)
     parser.add_argument('-r', '--reg_res', help='Resolution of registration inputs in microns. Default: 50', default='50',type=int, action=SM)