def loadsurf_mne(fname, surftype, quiet=True):
from dataset import SurfData
sverts_lh, sfaces_lh = mne.surface.read_surface(
parse.hemineutral(fname) % 'lh')
sverts_rh, sfaces_rh = mne.surface.read_surface(
parse.hemineutral(fname) % 'rh')
return SurfData(sverts_lh, sfaces_lh, sverts_rh, sfaces_rh, surftype)
def loadsurf_gifti(fname,surftype,quiet=True):
from nibabel import gifti
from dataset import SurfData
fname = '%s.%sgii'%(fname,'%s')
fname = match_gifti_intent(fname, 'surface')
surf_lh = gifti.read(parse.hemineutral(fname)%'lh')
surf_rh = gifti.read(parse.hemineutral(fname)%'rh')
sverts_lh,sfaces_lh = surf_lh.darrays[0].data, surf_lh.darrays[1].data
sverts_rh,sfaces_rh = surf_rh.darrays[0].data, surf_rh.darrays[1].data
return SurfData(sverts_lh,sfaces_lh,sverts_rh,sfaces_rh,surftype)
def loadsurf_gifti(fname, surftype, quiet=True):
from nibabel import gifti
from dataset import SurfData
fname = '%s.%sgii' % (fname, '%s')
fname = match_gifti_intent(fname, 'surface')
surf_lh = gifti.read(parse.hemineutral(fname) % 'lh')
surf_rh = gifti.read(parse.hemineutral(fname) % 'rh')
sverts_lh, sfaces_lh = surf_lh.darrays[0].data, surf_lh.darrays[1].data
sverts_rh, sfaces_rh = surf_rh.darrays[0].data, surf_rh.darrays[1].data
return SurfData(sverts_lh, sfaces_lh, sverts_rh, sfaces_rh, surftype)
def loadannot_gifti(parcname,
subject,
subjects_dir,
labnam=None,
surf_type='pial',
surf_struct=None,
quiet=False):
import numpy as np
from nibabel import gifti
fname = os.path.join(subjects_dir, subject, 'label',
'lh.%s.%sgii' % (parcname, '%s'))
fname = match_gifti_intent(fname, 'label')
annot_lh = gifti.read(parse.hemineutral(fname) % 'lh')
annot_rh = gifti.read(parse.hemineutral(fname) % 'rh')
#unpack the annotation data
labdict_lh = parse.appendhemis(annot_lh.labeltable.get_labels_as_dict(),
"lh_")
labv_lh = map(labdict_lh.get, annot_lh.darrays[0].data)
labdict_rh = parse.appendhemis(annot_rh.labeltable.get_labels_as_dict(),
"rh_")
labv_rh = map(labdict_rh.get, annot_rh.darrays[0].data)
labv = labv_lh + labv_rh
#return labv
#The objective is now to create MNE label files for these on the fly
vertices = np.vstack((surf_struct.lh_verts, surf_struct.rh_verts))
mne_labels = []
for lab in labnam:
cur_lab_verts = np.flatnonzero(np.array(labv) == lab)
cur_lab_pos = vertices[cur_lab_verts]
cur_lab = mne.Label(cur_lab_verts,
pos=cur_lab_pos / 1000,
hemi=lab[:2],
name=parse.demangle_hemi(lab))
mne_labels.append(cur_lab)
return mne_labels
def loadannot_gifti(parcname, subject, subjects_dir, labnam=None, surf_type='pial',
surf_struct=None, quiet=False):
import numpy as np
from nibabel import gifti
fname = os.path.join(subjects_dir, subject, 'label', 'lh.%s.%sgii'%(parcname,'%s'))
fname = match_gifti_intent(fname, 'label')
annot_lh = gifti.read(parse.hemineutral(fname)%'lh')
annot_rh = gifti.read(parse.hemineutral(fname)%'rh')
#unpack the annotation data
labdict_lh=parse.appendhemis(annot_lh.labeltable.get_labels_as_dict(),"lh_")
labv_lh=map(labdict_lh.get,annot_lh.darrays[0].data)
labdict_rh=parse.appendhemis(annot_rh.labeltable.get_labels_as_dict(),"rh_")
labv_rh=map(labdict_rh.get,annot_rh.darrays[0].data)
labv=labv_lh+labv_rh
#return labv
#The objective is now to create MNE label files for these on the fly
vertices = np.vstack((surf_struct.lh_verts, surf_struct.rh_verts))
mne_labels = []
for lab in labnam:
cur_lab_verts = np.flatnonzero(np.array(labv)==lab)
cur_lab_pos = vertices[cur_lab_verts]
cur_lab = mne.Label(cur_lab_verts, pos=cur_lab_pos/1000, hemi=lab[:2],
name = parse.demangle_hemi(lab))
mne_labels.append(cur_lab)
return mne_labels
def loadsurf_mne(fname,surftype,quiet=True):
from dataset import SurfData
sverts_lh,sfaces_lh=mne.surface.read_surface(parse.hemineutral(fname)%'lh')
sverts_rh,sfaces_rh=mne.surface.read_surface(parse.hemineutral(fname)%'rh')
return SurfData(sverts_lh,sfaces_lh,sverts_rh,sfaces_rh,surftype)