def convert_and_rename_subcortical_files(subject, fol, new_fol, lookup, mmvt_subcorticals_fol_name='subcortical'):
obj_files = glob.glob(op.join(fol, '*.srf'))
utils.delete_folder_files(new_fol)
for obj_file in obj_files:
num = int(op.basename(obj_file)[:-4].split('_')[-1])
new_name = lookup.get(num, '')
if new_name != '':
utils.srf2ply(obj_file, op.join(new_fol, '{}.ply'.format(new_name)))
verts, faces = utils.read_ply_file(op.join(new_fol, '{}.ply'.format(new_name)))
np.savez(op.join(new_fol, '{}.npz'.format(new_name)), verts=verts, faces=faces)
copy_subcorticals_to_mmvt(new_fol, subject, mmvt_subcorticals_fol_name)
def convert_and_rename_subcortical_files(subject, fol, new_fol, lookup):
obj_files = glob.glob(op.join(fol, '*.srf'))
utils.delete_folder_files(new_fol)
for obj_file in obj_files:
num = int(op.basename(obj_file)[:-4].split('_')[-1])
new_name = lookup.get(num, '')
if new_name != '':
utils.srf2ply(obj_file, op.join(new_fol, '{}.ply'.format(new_name)))
verts, faces = utils.read_ply_file(op.join(new_fol, '{}.ply'.format(new_name)))
np.savez(op.join(new_fol, '{}.npz'.format(new_name)), verts=verts, faces=faces)
copy_subcorticals_to_blender(new_fol, subject)
def convert_and_rename_subcortical_files(subject, fol, new_fol, lookup):
obj_files = glob.glob(op.join(fol, '*.srf'))
utils.delete_folder_files(new_fol)
for obj_file in obj_files:
num = int(op.basename(obj_file)[:-4].split('_')[-1])
new_name = lookup.get(num, '')
if new_name != '':
utils.srf2ply(obj_file, op.join(new_fol, '{}.ply'.format(new_name)))
verts, faces = utils.read_ply_file(op.join(new_fol, '{}.ply'.format(new_name)))
np.savez(op.join(new_fol, '{}.npz'.format(new_name)), verts=verts, faces=faces)
blender_fol = op.join(MMVT_DIR, subject, 'subcortical')
if op.isdir(blender_fol):
shutil.rmtree(blender_fol)
shutil.copytree(new_fol, blender_fol)
def read_surface(surf_name):
print('Reading {}'.format(surf_name))
try:
verts, faces = nib.freesurfer.read_geometry(surf_name)
except:
from src.utils import utils
import shutil
utils.print_last_error_line()
print('Trying to recreate the surface')
surf_wavefront_name = '{}.asc'.format(surf_name)
print('mris_convert {} {}'.format(surf_name, surf_wavefront_name))
utils.run_script('mris_convert {} {}'.format(surf_name,
surf_wavefront_name))
ply_fname = '{}.ply'.format(surf_name)
verts, faces = utils.srf2ply(surf_wavefront_name, ply_fname)
shutil.copyfile(surf_name, '{}.org'.format(surf_name))
nib.freesurfer.write_geometry(surf_name, verts, faces)
return verts, faces
def convert_hemis_srf_to_ply(subject, hemi='both', surf_type='pial'):
for hemi in utils.get_hemis(hemi):
ply_file = utils.srf2ply(op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.srf'.format(hemi, surf_type)),
op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type)))
utils.make_dir(op.join(MMVT_DIR, subject))
def convert_hemis_srf_to_ply(subject, hemi='both'):
for hemi in utils.get_hemis(hemi):
ply_file = utils.srf2ply(op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial.srf'.format(hemi)),
op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial.ply'.format(hemi)))
utils.make_dir(op.join(MMVT_DIR, subject))
shutil.copyfile(ply_file, op.join(MMVT_DIR, subject, '{}.pial.ply'.format(hemi)))
def convert_hemis_srf_to_ply(subject, hemi='both', surf_type='pial'):
for hemi in utils.get_hemis(hemi):
ply_file = utils.srf2ply(op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.srf'.format(hemi, surf_type)),
op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type)))
utils.make_dir(op.join(MMVT_DIR, subject))
