def get_distmat(hemi, parcellation, scale, fn=None):
if hemi not in ('lh', 'rh'):
raise ValueError(f'Invalid hemishere designation {hemi}')
if USE_CACHED and fn is not None:
fn = DISTDIR / parcellation / 'nomedial' / f'{scale}_{hemi}_dist.npy'
dist = np.load(fn, allow_pickle=False, mmap_mode='c').astype('float32')
else:
surf = nndata.fetch_fsaverage('fsaverage5', data_dir=ROIDIR)['pial']
subj, spath = nnsurf.check_fs_subjid('fsaverage5')
medial = Path(spath) / subj / 'label'
medial_labels = [
'unknown', 'corpuscallosum', '???',
'Background+FreeSurfer_Defined_Medial_Wall'
]
if parcellation == 'vertex':
medial_path = medial / f'{hemi}.Medial_wall.label'
dist = surface.get_surface_distance(getattr(surf, hemi),
medial=medial_path,
use_wb=False,
verbose=True)
else:
annot = _get_annot(parcellation, scale)
dist = surface.get_surface_distance(getattr(surf, hemi),
getattr(annot, hemi),
medial_labels=medial_labels,
use_wb=False,
verbose=True)
return dist
def _mod_medial(data, remove=True, val=0):
"""
Removes (inserts) medial wall from (into) `data` from fsaverage5 surface
Parameters
----------
data : (20484,) array_like
Surface data
remove : bool, optional
Whether to remove medial wall instead of inserting it. Assumes input
has (does not have) medial wall. Default: True
val : float, optional
What value to insert if `remove=False`. Default: 0
Returns
-------
out : np.ndarray
Provided surface `data` with medial wall removed/inserted
"""
subj, path = check_fs_subjid('fsaverage5')
lh, rh = [
nib.freesurfer.read_label(
os.path.join(path, subj, 'label', f'{h}.Medial_wall.label'))
for h in ('lh', 'rh')
]
lhm, rhm = np.ones(10242, dtype=bool), np.ones(10242, dtype=bool)
lhm[lh], rhm[rh] = False, False
if remove:
x, y = np.split(data, 2)
return np.hstack((x[lhm], y[rhm]))
else:
x, y = np.split(data, [np.sum(lhm)])
xd, yd = np.ones(10242) * val, np.ones(10242) * val
xd[lhm], yd[rhm] = x, y
return np.hstack((xd, yd))
def get_vertex_yeo(*args, **kwargs):
"""
Returns Yeo RSN affiliations for fsaverage5 surface
Returns
-------
labels : (2,) namedtuple
Where the first entry ('vertices') is the vertex-level RSN affiliations
and the second entry ('parcels') is the parcel-level RSN affiliations
"""
# check for FreeSurfer installation and get path to fsaverage5 label dir
subjdir = Path(nnsurf.check_fs_subjid('fsaverage5')[-1]).resolve()
labeldir = subjdir / 'fsaverage5' / 'label'
# load Yeo2011 network affiliations and store in expected output
network_labels, parcel_labels = [], []
for hemi in ('lh', 'rh'):
annot = labeldir / f'{hemi}.Yeo2011_7Networks_N1000.annot'
labels, ctab, names = nib.freesurfer.read_annot(annot)
network_labels.append(labels)
parcel_labels.append(range(len(names)))
return NETWORKS(np.hstack(network_labels), np.hstack(parcel_labels))
"""
from pathlib import Path
from netneurotools import datasets as nndata, freesurfer as nnsurf
from parspin import surface, utils as putils
ROIDIR = Path('./data/raw/rois').resolve()
DISTDIR = Path('./data/derivatives/geodesic').resolve()
N_PROC = 24 # parallelization of distance calculation
SURFACE = 'pial' # surface on which to calculate distance
if __name__ == '__main__':
parcellations = putils.get_cammoun_schaefer(data_dir=ROIDIR)
surf = nndata.fetch_fsaverage('fsaverage5', data_dir=ROIDIR)[SURFACE]
subj, spath = nnsurf.check_fs_subjid('fsaverage5')
medial = Path(spath) / subj / 'label'
medial_labels = [
'unknown', 'corpuscallosum', '???',
'Background+FreeSurfer_Defined_Medial_Wall'
]
# get parcel distance matrices with this horrible nested for-loop :scream:
for name, annotations in parcellations.items():
for scale, annot in annotations.items():
for hemi in ['lh', 'rh']:
for allow_med in [True, False]:
med = 'medial' if allow_med else 'nomedial'
out = DISTDIR / name / med / f'{scale}_{hemi}_dist.csv'
if out.exists():
continue