[NEW 🐝] fsaverage surface

enigmatoolbox/datasets/__init__.py

@@ -1,10 +1,11 @@
-from .base import (load_conte69, load_sc, load_fc,
+from .base import (load_conte69, load_sc, load_fc, load_fsa,
  load_fsa5, load_subcortical, structural_covariance,
  fetch_ahba, risk_genes, load_example_data,
  load_summary_stats, load_fc_as_one, load_sc_as_one,
  nfaces, getaffine, load_mask, write_cifti)
 
 __all__ = ['load_conte69',
+ 'load_fsa',
  'load_fsa5',
  'load_subcortical',
  'load_sc',

enigmatoolbox/datasets/base.py

@@ -141,6 +141,45 @@ def load_fsa5(as_sphere=False, with_normals=True, join=False, with_sctx=False):
  return surfs[0], surfs[1]
 
 
+def load_fsa(as_sphere=False, with_normals=True, join=False):
+ """Load fsaverage surfaces (author: @saratheriver)
+
+ Parameters
+ ----------
+ as_sphere : bool, optional
+ Return spheres instead of cortical surfaces. Default is False.
+ with_normals : bool, optional
+ Whether to compute surface normals. Default is True.
+ join : bool, optional
+ If False, return one surface for left and right hemispheres. Otherwise,
+ return a single surface as a combination of both left and right
+ surfaces. Default is False.
+
+ Returns
+ -------
+ surf : tuple of BSPolyData or BSPolyData
+ Surfaces for left and right hemispheres. If ``join == True``, one surface with both hemispheres.
+ """
+ root_pth = os.path.dirname(__file__)
+ if as_sphere is True:
+ fname = 'fsa_sphere_{}.gii'
+ elif as_sphere is not True:
+ fname = 'fsa_{}.gii'
+
+ ipth = os.path.join(root_pth, 'surfaces', fname)
+ surfs = [None] * 2
+ for i, side in enumerate(['lh', 'rh']):
+ surfs[i] = read_surface(ipth.format(side))
+ if with_normals:
+ nf = wrap_vtk(vtkPolyDataNormals, splitting=False,
+ featureAngle=0.1)
+ surfs[i] = serial_connect(surfs[i], nf)
+
+ if join:
+ return combine_surfaces(*surfs)
+ return surfs[0], surfs[1]
+
+
 def load_subcortical(with_normals=False, join=False):
  """Load subcortical surfaces (author: @saratheriver)
 

enigmatoolbox/plotting/surface_plotting.py

@@ -14,7 +14,7 @@
 from .colormaps import colormaps
 from . import defaults_plotting as dp
 from .utils import _broadcast, _expand_arg, _grep_args, _gen_grid, _get_ranges
-from ..datasets import load_fsa5, load_conte69, load_subcortical
+from ..datasets import load_fsa, load_fsa5, load_conte69, load_subcortical
 from ..utils.parcellation import subcorticalvertices
 from ..mesh.mesh_io import read_surface
 from ..vtk_interface.decorators import wrap_input
@@ -436,7 +436,7 @@ def plot_cortical(array_name=None, surface_name='fsa5', color_bar=False,
  the left and right hemispheres. If list, plot one row per array.
  Default is None.
  surface_name : str, optional
- Name of surface {'fsa5', 'conte69}. Default is 'fsa5'.
+ Name of surface {'fsa', 'fsa5', 'conte69}. Default is 'fsa5'.
  color_bar : bool, optional
  Plot color bar for each array (row). Default is False.
  color_range : {'sym'}, tuple or sequence.
@@ -489,6 +489,8 @@ def plot_cortical(array_name=None, surface_name='fsa5', color_bar=False,
 
  if surface_name == "fsa5":
  surf_lh, surf_rh = load_fsa5()
+ elif surface_name == "fsa":
+ surf_lh, surf_rh = load_fsa()
  elif surface_name == "conte69":
  surf_lh, surf_rh = load_conte69()
 

matlab/scripts/surface_viewer/plot_cortical.m

@@ -10,7 +10,7 @@
 % data (double array) - vector of data, size = [1 x v]
 %
 % Name/value pairs:
-% surface_name (string, optional) - Name of surface {'fsa5', 'conte69}. 
+% surface_name (string, optional) - Name of surface {'fsa', 'fsa5', 'conte69}. 
 % Default is 'fsa5'.
 % label_text (string, optional) - Label text for colorbar. Default is empty.
 % background (string, double array, optional) - Background color. 
@@ -39,6 +39,8 @@
 % load surfaces
 if strcmp(in.surface_name, 'fsa5')
  surf = SurfStatAvSurf({'fsa5_lh', 'fsa5_rh'});
+elseif strcmp(in.surface_name, 'fsa')
+ surf = SurfStatAvSurf({'fsa_lh', 'fsa_rh'});
 elseif strcmp(in.surface_name, 'conte69')
  surf = SurfStatAvSurf({'conte69_lh', 'conte69_rh'});
 elseif strcmp(in.surface_name, 'ss')