def _apply_vek_prob(data_dir=None):
"""
Applies probabilistic von Economo & Koskinas FreeSurfer classifier
Uses `fsaverage5` surface; requires FreeSurfer installation.
Parameters
----------
data_dir : str or os.PathLike, optional
Path where probabilistic von Economo & Koskinas classifier should be
downloaded. Also determines where generated annotation files are
saved.
Returns
-------
surface : (2,) namedtuple
Where the first entry ('lh') is the left hemisphere annotation file and
the second entry ('rh') is the right hemisphere annotation file
"""
vek = nndata.fetch_voneconomo(data_dir=data_dir)
annots = []
for hemi in ('lh', 'rh'):
gcs = Path(getattr(vek['gcs'], hemi))
ctab = Path(getattr(vek['ctab'], hemi))
annot = (gcs.parent / 'atl-vonEconomoKoskinas_space-fsaverage5_hemi-{}'
'_deterministic.annot'.format(hemi[0].capitalize()))
annot = nnsurf.apply_prob_atlas('fsaverage5',
str(gcs),
hemi,
ctab=str(ctab),
annot=str(annot))
annots.append(annot)
return vek['gcs'].__class__(*annots)
annot = 'atl-Cammoun2012_space-fsaverage_res-{}_hemi-{}_deterministic.annot'
if __name__ == '__main__':
#####
# get the GCS files and apply them onto the fsaverage surface
gcs = datasets.fetch_cammoun2012('gcs')
for scale, gcsfiles in gcs.items():
for fn in gcsfiles:
hemi = re.search('hemi-([RL])', fn).group(1)
scale = re.search('res-(.*)_hemi-', fn).group(1)
out = op.join(op.dirname(fn), annot.format(scale, hemi))
freesurfer.apply_prob_atlas('fsaverage',
fn,
hemi.lower() + 'h',
ctab=fn.replace('.gcs', '.ctab'),
annot=out)
#####
# get scale 500 parcellation files and combine
dirname = op.dirname(fn)
lh = sorted(glob.glob(op.join(dirname, '*res-500*_hemi-L*annot')))
rh = sorted(glob.glob(op.join(dirname, '*res-500*_hemi-R*annot')))
annot = op.join(dirname, annot.format('500', '{}'))
parc500 = combine_cammoun_500(lh, rh, 'fsaverage', annot=annot)
for fn in lh + rh:
os.remove(fn)
#####
# map all the WRONG .annot files to the correct ordering