def test_patch(subject, **kargs):
from src.utils import preproc_utils as pu
SUBJECTS_DIR, MMVT_DIR, FREESURFER_HOME = pu.get_links()
flat_patch_cut_vertices = utils.load(op.join(MMVT_DIR, subject, 'flat_patch_cut_vertices.pkl'))
for hemi in utils.HEMIS:
# verts, faces = read_patch(hemi, SUBJECTS_DIR)
# write_patch(op.join(MMVT_DIR, 'fsaverage', 'surf', '{}.flat.test.pial'.format(hemi)), verts, faces)
# fs_verts, fs_faces = utils.read_pial('fsaverage', MMVT_DIR, hemi, surface_type='inflated')
print('Reading inflated surf')
fs_verts, fs_faces = nib.freesurfer.read_geometry(op.join(SUBJECTS_DIR, subject, 'surf', '{}.inflated'.format(hemi)))
# flat_verts, flat_faces = read_patch(hemi, SUBJECTS_DIR, surface_type='inflated')
# good_verts = set(np.unique(flat_faces))
# bad_verts = np.setdiff1d(np.arange(0, flat_verts.shape[0]), good_verts)
# bad_faces_inds = set(utils.flat_list_of_lists([verts_faces_lookup[hemi][v] for v in bad_verts]))
patch_fname = op.join(SUBJECTS_DIR, subject, 'surf', '{}.inflated.patch'.format(hemi))
print('Writing patch')
flat_patch_cut_vertices_hemi = set(flat_patch_cut_vertices[hemi])
write_patch(patch_fname, [(ind, v) for ind, v in enumerate(fs_verts) if ind not in flat_patch_cut_vertices_hemi], set())#flat_faces)
print('Reading patch')
patch_verts, patch_faces = read_patch(subject, hemi, SUBJECTS_DIR, surface_type='inflated', patch_fname=patch_fname)
print('Writing ply')
patch_verts *= 0.1
utils.write_ply_file(patch_verts, patch_faces, op.join(MMVT_DIR, subject, 'surf', '{}.flat.pial.test.ply').format(hemi))
print('Finish!')
import os.path as op
import time
import nibabel as nib
import numpy as np
import scipy.ndimage
from skimage import measure
from src.utils import utils
from src.utils import preproc_utils as pu
from src.preproc import anatomy as anat
SUBJECTS_DIR, MMVT_DIR, FREESURFER_HOME = pu.get_links()
def create_surf(subject, subcortical_code, subcortical_name):
aseg = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'aseg.mgz')).get_data()
t1_header = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'T1.mgz')).header
aseg[aseg != subcortical_code] = 255
aseg[aseg == subcortical_code] = 10
aseg = np.array(aseg, dtype=np.float)
aseg_smooth = scipy.ndimage.gaussian_filter(aseg, sigma=1)
verts_vox, faces, _, _ = measure.marching_cubes(aseg_smooth, 100)
# Doesn't seem to fix the normals directions that should be out...
faces = measure.correct_mesh_orientation(aseg_smooth, verts_vox, faces)
verts = utils.apply_trans(t1_header.get_vox2ras_tkr(), verts_vox)
fol = utils.make_dir(op.join(MMVT_DIR, subject, 'subcortical_test'))
ply_file_name = op.join(fol, '{}.ply'.format(subcortical_name))
utils.write_ply_file(verts, faces, ply_file_name, False)
import os
import os.path as op
import numpy as np
import shutil
import time
import csv
from mne.label import _read_annot
from src.utils import utils
from src.utils import preproc_utils as pu
SUBJECTS_DIR, MMVT_DIR, FREESURFER_HOME = pu.get_links()
APARC2ASEG = 'mri_aparc2aseg --s {subject} --annot {atlas} --o {atlas}+aseg.mgz'
def create_freeview_cmd(subject, args):#, atlas, bipolar, create_points_files=True, way_points=False):
blender_freeview_fol = op.join(MMVT_DIR, subject, 'freeview')
freeview_command = 'freeview -v T1.mgz:opacity=0.3 ' + \
'{0}+aseg.mgz:opacity=0.05:colormap=lut:lut={0}ColorLUT.txt '.format(args.atlas)
if args.elecs_names:
groups = set([utils.elec_group(name, args.bipolar) for name in args.elecs_names])
freeview_command += '-w ' if args.way_points else '-c '
postfix = '.label' if args.way_points else '.dat'
for group in groups:
freeview_command += group + postfix + ' '
utils.make_dir(blender_freeview_fol)
with open(op.join(blender_freeview_fol, 'run_freeview.sh'), 'w') as sh_file:
sh_file.write(freeview_command)
print(freeview_command)
