def create_annotation_from_fsaverage(subject, aparc_name='aparc250', fsaverage='fsaverage',
overwrite_annotation=False, overwrite_morphing=False, do_solve_labels_collisions=False,
morph_labels_from_fsaverage=True, fs_labels_fol='', n_jobs=6):
annotations_exist = np.all([op.isfile(op.join(SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format(hemi,
aparc_name))) for hemi in HEMIS])
existing_freesurfer_annotations = ['aparc.DKTatlas40.annot', 'aparc.annot', 'aparc.a2009s.annot']
if '{}.annot'.format(aparc_name) in existing_freesurfer_annotations:
morph_labels_from_fsaverage = False
do_solve_labels_collisions = False
if not annotations_exist:
utils.make_dir(op.join(SUBJECTS_DIR, subject, 'label'))
annotations_exist = fu.create_annotation_file(subject, aparc_name, subjects_dir=SUBJECTS_DIR, freesurfer_home=FREE_SURFER_HOME)
if morph_labels_from_fsaverage:
utils.morph_labels_from_fsaverage(subject, SUBJECTS_DIR, aparc_name, n_jobs=n_jobs,
fsaverage=fsaverage, overwrite=overwrite_morphing, fs_labels_fol=fs_labels_fol)
if do_solve_labels_collisions:
solve_labels_collisions(subject, aparc_name, fsaverage, n_jobs)
# Note that using the current mne version this code won't work, because of collissions between hemis
# You need to change the mne.write_labels_to_annot code for that.
if overwrite_annotation or not annotations_exist:
try:
utils.labels_to_annot(subject, SUBJECTS_DIR, aparc_name, overwrite=overwrite_annotation)
except:
print("Can't write labels to annotation! Trying to solve labels collision")
solve_labels_collisions(subject, aparc_name, fsaverage, n_jobs)
try:
utils.labels_to_annot(subject, SUBJECTS_DIR, aparc_name, overwrite=overwrite_annotation)
except:
print("Can't write labels to annotation! Solving the labels collision didn't help...")
print(traceback.format_exc())
return utils.both_hemi_files_exist(op.join(
SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format('{hemi}', aparc_name)))
def create_annotation_from_fsaverage(subject, aparc_name='aparc250', fsaverage='fsaverage', remote_subject_dir='',
overwrite_annotation=False, overwrite_morphing=False, do_solve_labels_collisions=False,
morph_labels_from_fsaverage=True, fs_labels_fol='', n_jobs=6):
annotations_exist = np.all([op.isfile(op.join(SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format(hemi,
aparc_name))) for hemi in HEMIS])
if not annotations_exist:
utils.make_dir(op.join(SUBJECTS_DIR, subject, 'label'))
remote_annotations_exist = np.all([op.isfile(op.join(remote_subject_dir, 'label', '{}.{}.annot'.format(
hemi, aparc_name))) for hemi in HEMIS])
if remote_annotations_exist:
for hemi in HEMIS:
shutil.copy(op.join(remote_subject_dir, 'label', '{}.{}.annot'.format(hemi, aparc_name)),
op.join(SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format(hemi, aparc_name)))
return True
existing_freesurfer_annotations = ['aparc.DKTatlas40.annot', 'aparc.annot', 'aparc.a2009s.annot']
if '{}.annot'.format(aparc_name) in existing_freesurfer_annotations:
morph_labels_from_fsaverage = False
do_solve_labels_collisions = False
if not annotations_exist:
utils.make_dir(op.join(SUBJECTS_DIR, subject, 'label'))
annotations_exist = fu.create_annotation_file(subject, aparc_name, subjects_dir=SUBJECTS_DIR, freesurfer_home=FREE_SURFER_HOME)
if morph_labels_from_fsaverage:
lu.morph_labels_from_fsaverage(subject, SUBJECTS_DIR, MMVT_DIR, aparc_name, n_jobs=n_jobs,
fsaverage=fsaverage, overwrite=overwrite_morphing, fs_labels_fol=fs_labels_fol)
if do_solve_labels_collisions:
solve_labels_collisions(subject, aparc_name, fsaverage, n_jobs)
# Note that using the current mne version this code won't work, because of collissions between hemis
# You need to change the mne.write_labels_to_annot code for that.
if overwrite_annotation or not annotations_exist:
try:
utils.labels_to_annot(subject, SUBJECTS_DIR, aparc_name, overwrite=overwrite_annotation)
except:
print("Can't write labels to annotation! Trying to solve labels collision")
print(traceback.format_exc())
solve_labels_collisions(subject, aparc_name, fsaverage, n_jobs)
try:
utils.labels_to_annot(subject, SUBJECTS_DIR, aparc_name, overwrite=overwrite_annotation)
except:
print("Can't write labels to annotation! Solving the labels collision didn't help...")
print(traceback.format_exc())
return utils.both_hemi_files_exist(op.join(
SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format('{hemi}', aparc_name)))
def parcelate_cortex(subject, aparc_name, overwrite=False, overwrite_ply_files=False, minimum_labels_num=50):
dont_do_anything = True
ret = {'pial':True, 'inflated':True}
utils.labels_to_annot(subject, SUBJECTS_DIR, aparc_name, overwrite=False)
for surface_type in ['pial', 'inflated']:
files_exist = True
for hemi in HEMIS:
blender_labels_fol = op.join(MMVT_DIR, subject,'{}.{}.{}'.format(aparc_name, surface_type, hemi))
files_exist = files_exist and op.isdir(blender_labels_fol) and \
len(glob.glob(op.join(blender_labels_fol, '*.ply'))) > minimum_labels_num
# if surface_type == 'inflated':
if overwrite or not files_exist:
dont_do_anything = False
matlab_command = op.join(BRAINDER_SCRIPTS_DIR, 'splitting_cortical.m')
matlab_command = "'{}'".format(matlab_command)
sio.savemat(op.join(BRAINDER_SCRIPTS_DIR, 'params.mat'),
mdict={'subject': subject, 'aparc':aparc_name, 'subjects_dir': SUBJECTS_DIR,
'scripts_dir': BRAINDER_SCRIPTS_DIR, 'freesurfer_home': FREE_SURFER_HOME,
'surface_type': surface_type})
cmd = 'matlab -nodisplay -nosplash -nodesktop -r "run({}); exit;"'.format(matlab_command)
script_ret = utils.run_script(cmd)
if script_ret == '':
return False
# convert the obj files to ply
lookup = convert_perecelated_cortex(subject, aparc_name, surface_type, overwrite_ply_files)
matlab_labels_vertices = True
if surface_type == 'pial':
matlab_labels_vertices = save_matlab_labels_vertices(subject, aparc_name)
labels_num = sum([len(lookup[hemi]) for hemi in HEMIS])
labels_files_num = sum([len(glob.glob(op.join(MMVT_DIR, subject,'{}.{}.{}'.format(
aparc_name, surface_type, hemi), '*.ply'))) for hemi in HEMIS])
labels_dic_fname = op.join(MMVT_DIR, subject,'labels_dic_{}_{}.pkl'.format(aparc_name, hemi))
print('labels_files_num == labels_num: {}'.format(labels_files_num == labels_num))
print('isfile(labels_dic_fname): {}'.format(op.isfile(labels_dic_fname)))
print('matlab_labels_vertices files: {}'.format(matlab_labels_vertices))
ret[surface_type] = labels_files_num == labels_num and op.isfile(labels_dic_fname) and matlab_labels_vertices
if dont_do_anything:
return True
else:
return ret['pial'] and ret['inflated']
