diff --git a/recon_surf/rewrite_mc_surface.py b/recon_surf/rewrite_mc_surface.py index bcd86be8..8372f94f 100644 --- a/recon_surf/rewrite_mc_surface.py +++ b/recon_surf/rewrite_mc_surface.py @@ -18,7 +18,6 @@ import optparse import nibabel.freesurfer.io as fs from nibabel import load as nibload -from lapy._read_geometry import read_geometry def options_parse(): @@ -69,7 +68,7 @@ def resafe_surface(insurf: str, outsurf: str, pretess: str) -> None: Path and name of file the input surface was created on (e.g. filled-pretess127.mgz) """ - surf = read_geometry(insurf, read_metadata=True) + surf = fs.read_geometry(insurf, read_metadata=True) if not surf[2]["filename"]: # Set information with file used for surface construction (volume info and name) diff --git a/recon_surf/smooth_aparc.py b/recon_surf/smooth_aparc.py index 7380a856..fbd50e78 100644 --- a/recon_surf/smooth_aparc.py +++ b/recon_surf/smooth_aparc.py @@ -22,7 +22,6 @@ import numpy as np from numpy import typing as npt import nibabel.freesurfer.io as fs -from lapy._read_geometry import read_geometry from scipy import sparse @@ -269,7 +268,7 @@ def smooth_aparc( """ # read input files print("Reading in surface: {} ...".format(insurfname)) - surf = read_geometry(insurfname, read_metadata=True) + surf = fs.read_geometry(insurfname, read_metadata=True) print("Reading in annotation: {} ...".format(inaparcname)) aparc = fs.read_annot(inaparcname) print("Reading in cortex label: {} ...".format(incortexname)) diff --git a/recon_surf/spherically_project.py b/recon_surf/spherically_project.py index d18ab696..42a56e6d 100644 --- a/recon_surf/spherically_project.py +++ b/recon_surf/spherically_project.py @@ -21,7 +21,6 @@ import math from lapy.diffGeo import tria_mean_curvature_flow from lapy.triaMesh import TriaMesh -from lapy.read_geometry import read_geometry from lapy.solver import Solver HELPTEXT = """ @@ -320,7 +319,7 @@ def spherically_project_surface( Try to use the Cholesky decomposition from the cholmod. Defaults to True """ - surf = read_geometry(insurf, read_metadata=True) + surf = fs.read_geometry(insurf, read_metadata=True) projected = tria_spherical_project( TriaMesh(surf[0], surf[1]), flow_iter=3, use_cholmod=use_cholmod )