mvpa2.atlases.warehouse.FSLProbabilisticAtlas

class mvpa2.atlases.warehouse.FSLProbabilisticAtlas(thr=0.0, strategy='all', sort=True, *args, **kwargs)

Probabilistic FSL atlases

Attributes

coordT
extent
levels
origin
resolution
spaceT
version
voxdim

Methods

__call__(\*args)
find(\*args, \*\*kwargs)	Just a shortcut to the only level.
get_map(target[, strategy, axes_order])	Return a probability map as an array
get_maps(target[, axes_order, key_attr, ...])	Return a dictionary of probability maps for the target
label_point(coord[, levels])	Return labels for the given spatial point at specified levels
label_voxel(c[, levels])	Return labels for the voxel
levels_listing()
load_atlas(filename)	Load atlas from a file
query(index[, query_voxel])	Generic query method.
set_coordT(coordT)	Set coordT transformation.

Parameters:

thr : float

Value to threshold at

strategy : str

Possible values

all - all entries above thr max - entry with maximal value

sort : bool

Either to sort entries for ‘all’ strategy according to probability

filename : str

Filename for the xml definition of the atlas

resolution : None or float

Some atlases link to multiple images at different resolutions. if None – best resolution is selected using 0th dimension resolution

image_file : None or str

If None, overrides filename for the used imagefile, so it could load a custom (re-registered) atlas maps

coordT

Optional transformation to apply first

default_levels : None or slice or list of int

What levels by default to operate on

load_maps : bool

Load spatial maps for the atlas.

Attributes

coordT
extent
levels
origin
resolution
spaceT
version
voxdim

Methods

__call__(\*args)
find(\*args, \*\*kwargs)	Just a shortcut to the only level.
get_map(target[, strategy, axes_order])	Return a probability map as an array
get_maps(target[, axes_order, key_attr, ...])	Return a dictionary of probability maps for the target
label_point(coord[, levels])	Return labels for the given spatial point at specified levels
label_voxel(c[, levels])	Return labels for the voxel
levels_listing()
load_atlas(filename)	Load atlas from a file
query(index[, query_voxel])	Generic query method.
set_coordT(coordT)	Set coordT transformation.

find(*args, **kwargs)

Just a shortcut to the only level.

See find for more info

get_map(target, strategy='unique', axes_order='xyz')

Return a probability map as an array

Parameters:

target : int or str or re._pattern_type

If int, map for given index is returned. Otherwise, .find is called with unique=True to find matching area

strategy : str in (‘unique’, ‘max’)

If ‘unique’, then if multiple areas match, exception would be raised. In case of ‘max’, each voxel would get maximal value of probabilities from all matching areas

axes_order : str in (‘xyz’, ‘zyx’)

In what order axes of the returned array should follow.

get_maps(target, axes_order='xyz', key_attr=None, overlaps=None)

Return a dictionary of probability maps for the target

Each key is a Label instance, and value is the probability map

Parameters:

target : str or re._pattern_type

.find is called with a target and unique=False to find all matches

axes_order : str in (‘xyz’, ‘zyx’)

In what order axes of the returned array should follow.

key_attr : None or str

What to use for the keys of the dictionary. If None, Label instance would be used as a key. If some attribute provided (e.g. ‘text’, ‘abbr’, ‘index’), corresponding attribute of the Label instance would be taken as a key.

overlaps : None or {‘max’}

How to treat overlaps in maps. If None, nothing is done and maps might have overlaps. If ‘max’, then maps would not overlap and competing maps will be resolved based on maximal value (e.g. if maps contain probabilities).

label_voxel(c, levels=None)

Return labels for the voxel

Parameters:

c : tuple of coordinates (xyz)

- levels : just for API consistency (heh heh). Must be 0 for FSL atlases