def test_define_subpath(self):
s = file_finder.SubjectFiles(
subpath=os.path.join('path', 'to', 'm2m_sub'))
assert s.subpath == os.path.join('path', 'to', 'm2m_sub')
assert s.subid == 'sub'
assert s.basedir == os.path.join('path', 'to')
assert s.fnamehead == os.path.join('path', 'to', 'sub.msh')
def test_cap_files(self):
s = file_finder.SubjectFiles(os.path.join('path', 'to', 'sub.msh'))
assert s.eeg_cap_folder == os.path.join('path', 'to', 'm2m_sub',
'eeg_positions')
assert s.eeg_cap_1010 == os.path.join('path', 'to', 'm2m_sub',
'eeg_positions',
'EEG10-10_UI_Jurak_2007.csv')
assert s.get_eeg_cap('test.csv') == os.path.join(
'path', 'to', 'm2m_sub', 'eeg_positions', 'test.csv')
def test_define_fnamehead_subpath(self):
s = file_finder.SubjectFiles(os.path.join('some', 'random',
'file.msh'),
subpath=os.path.join(
'path', 'to', 'm2m_sub'))
assert s.fnamehead == os.path.join('some', 'random', 'file.msh')
assert s.subid == 'sub'
assert s.basedir == os.path.join('path', 'to')
assert s.subpath == os.path.join('path', 'to', 'm2m_sub')
def main():
args = parse_arguments(sys.argv[1:])
m2m_dir = os.path.abspath(os.path.realpath(os.path.expanduser(args.m2mpath)))
if not os.path.isdir(m2m_dir):
raise IOError('Could not find directory: {0}'.format(args.m2mpath))
subject_files = file_finder.SubjectFiles(subpath=m2m_dir)
os.makedirs(args.out_folder, exist_ok=True)
for hemi in ['lh', 'rh']:
# I have a parallel implementation here
fn_atlas = os.path.join(
file_finder.templates.cat_atlases_surfaces,
f'{hemi}.aparc_{args.atlas}.freesurfer.annot'
)
labels, colors, names = nibabel.freesurfer.io.read_annot(fn_atlas)
if subject_files.seg_type == 'headreco':
read_fun = read_gifti_surface
elif subject_files.seg_type == 'mri2mesh':
read_fun = read_freesurfer_surface
if hemi == 'lh':
ref_surf = read_gifti_surface(file_finder.templates.cat_lh_sphere_ref)
sub_surf = read_fun(subject_files.lh_reg)
if hemi == 'rh':
ref_surf = read_gifti_surface(file_finder.templates.cat_rh_sphere_ref)
sub_surf = read_fun(subject_files.rh_reg)
labels_sub, _ = transformations._surf2surf(labels, ref_surf, sub_surf)
fn_out = os.path.join(
args.out_folder,
f'{hemi}.{subject_files.subid}_{args.atlas}.annot'
)
logger.info('Writing: ' + fn_out)
nibabel.freesurfer.io.write_annot(
fn_out,
labels_sub,
colors,
names,
fill_ctab=True
)
def test_tensor_file(self):
s = file_finder.SubjectFiles(os.path.join('path', 'to', 'sub.msh'))
assert s.tensor_file == os.path.join('path', 'to', 'd2c_sub',
'dti_results_T1space',
'DTI_conf_tensor.nii.gz')