def sanity_check():
subject = 'mg101'
template_system = 'hc029'
# mg101 RMF3 to hc029
tk_ras = [7.3, 37.9, 59]
ras = [6.08, 73.07, 17.80]
vox = [121, 69, 166]
template_tk_ras_true = np.array([6.18, 52.26, 21.46])
template_vox_true = np.array([122, 107, 180])
template_tk_ras, trans = fu.transform_subject_to_subject_coordinates(
subject, template_system, tk_ras, SUBJECTS_DIR, return_trans=True)
template_tk_ras2 = apply_trans(trans, tk_ras)
assert (all(np.isclose(template_tk_ras, template_tk_ras2, rtol=1e-3)))
lta = fu.read_lta_file(
op.join(SUBJECTS_DIR, subject, 'mri',
't1_to_{}.lta'.format(template_system)))
lta[np.isclose(trans, np.zeros(lta.shape))] = 0
print(lta - trans)
# template_lta_tk_ras = lta_transfer_ras2ras(subject, tk_ras)
# assert(all(np.isclose(template_tk_ras_true, template_tk_ras, rtol=1e-3)))
subject = 'mg112'
# ROF1 - 2
tk_ras = [2.00, 29.00, 8.00]
ras = [-6.88, 50.40, -7.31]
template_tk_ras = fu.transform_subject_to_subject_coordinates(
subject, template_system, tk_ras, SUBJECTS_DIR)
print('asdf')
def lta_transfer_vox2vox(subject, coords):
lta_fname = op.join(SUBJECTS_DIR, subject, 'mri',
't1_to_{}_vox2vox.lta'.format(template_system))
if not op.isfile(lta_fname):
return None
lta = fu.read_lta_file(lta_fname)
subject_header = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'T1.mgz')).get_header()
template_header = nib.load(
op.join(SUBJECTS_DIR, template_system, 'mri', 'T1.mgz')).get_header()
vox = apply_trans(np.linalg.inv(subject_header.get_vox2ras_tkr()), coords)
template_vox = apply_trans(lta, vox)
template_cords = apply_trans(template_header.get_vox2ras_tkr(),
template_vox)
return template_cords
def lta_transfer_ras2ras(subject, coords, return_trans=False):
lta_fname = op.join(SUBJECTS_DIR, subject, 'mri',
't1_to_{}.lta'.format(template_system))
if not op.isfile(lta_fname):
return None
lta = fu.read_lta_file(lta_fname)
lta[np.isclose(lta, np.zeros(lta.shape))] = 0
subject_header = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'T1.mgz')).get_header()
template_header = nib.load(
op.join(SUBJECTS_DIR, template_system, 'mri', 'T1.mgz')).get_header()
vox = apply_trans(np.linalg.inv(subject_header.get_vox2ras_tkr()), coords)
ras = apply_trans(subject_header.get_vox2ras(), vox)
template_ras = apply_trans(lta, ras)
template_vox = apply_trans(template_header.get_ras2vox(), template_ras)
template_cords = apply_trans(template_header.get_vox2ras_tkr(),
template_vox)
if return_trans:
return template_cords, lta
else:
return template_cords