atlases.fsl

Module: atlases.fsl

Inheritance diagram for mvpa.atlases.fsl:

FSL atlases interfaces

Classes

FSLAtlas

class mvpa.atlases.fsl.FSLAtlas(*args, **kwargs)

Bases: mvpa.atlases.base.XMLBasedAtlas

Base class for FSL atlases

See also

Please refer to the documentation of the base class for more information:

XMLBasedAtlas

Parameters:

• filename (string) – 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
• query_voxel (bool) – By default [x,y,z] assumes coordinates in space, but if query_voxel is True, they are assumed to be voxel coordinates
• coordT – Optional transformation to apply first
• levels (None or slice or list of int) – What levels by default to operate on

FSLLabelsAtlas

class mvpa.atlases.fsl.FSLLabelsAtlas(*args, **kwargs)

Bases: mvpa.atlases.base.XMLBasedAtlas

Not sure what this one was for

not implemented

FSLProbabilisticAtlas

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

Bases: mvpa.atlases.fsl.FSLAtlas

Probabilistic FSL atlases

See also

Please refer to the documentation of the base class for more information:

FSLAtlas

Parameters:

• thr (float) – Value to threshold at
• strategy (basestring) – 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 (string) – 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
• query_voxel (bool) – By default [x,y,z] assumes coordinates in space, but if query_voxel is True, they are assumed to be voxel coordinates
• coordT – Optional transformation to apply first
• levels (None or slice or list of int) – What levels by default to operate on

find(*args, **kwargs)

Just a shortcut to the only level.

See find for more info

getMap(target, strategy='unique')

Return a probability map

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

getMaps(target)

Return a list of probability maps for the target

Parameter:target (str or re._pattern_type) – .find is called with a target and unique=False to find all matches

labelVoxel(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) –