def gen_ras_to_head_trans(head_to_mri_t, t1_img):
# RAS -> VOXEL
ras_to_vox_t = Transform(fro='ras',
to='mri_voxel',
trans=np.linalg.inv(t1_img.header.get_vox2ras()))
# VOXEL -> MRI
vox_to_mri_t = Transform(fro='mri_voxel',
to='mri',
trans=t1_img.header.get_vox2ras_tkr())
# MRI -> HEAD
mri_to_head_t = invert_transform(head_to_mri_t)
# Now we have generated all the required transformations
# to go from RAS to MNE Head coordinates. Let's combine
# the transforms into a single transform. This requires
# two calls to `combine_transforms()`.
# RAS -> MRI
ras_to_mri_t = combine_transforms(ras_to_vox_t,
vox_to_mri_t,
fro='ras',
to='mri')
# RAS -> HEAD
ras_to_head_t = combine_transforms(ras_to_mri_t,
mri_to_head_t,
fro='ras',
to='head')
return ras_to_head_t
def test_combine():
"""Test combining transforms
"""
trans = read_trans(fname)
inv = invert_transform(trans)
combine_transforms(trans, inv, trans["from"], trans["from"])
assert_raises(RuntimeError, combine_transforms, trans, inv, trans["to"], trans["from"])
assert_raises(RuntimeError, combine_transforms, trans, inv, trans["from"], trans["to"])
assert_raises(RuntimeError, combine_transforms, trans, trans, trans["from"], trans["to"])
def test_combine():
"""Test combining transforms."""
trans = read_trans(fname)
inv = invert_transform(trans)
combine_transforms(trans, inv, trans['from'], trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv, trans['to'],
trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv, trans['from'],
trans['to'])
pytest.raises(RuntimeError, combine_transforms, trans, trans,
trans['from'], trans['to'])
def test_combine():
"""Test combining transforms."""
trans = read_trans(fname)
inv = invert_transform(trans)
combine_transforms(trans, inv, trans['from'], trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv,
trans['to'], trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv,
trans['from'], trans['to'])
pytest.raises(RuntimeError, combine_transforms, trans, trans,
trans['from'], trans['to'])
def test_transforms():
""" Test transformations """
bti_trans = (0.0, 0.02, 0.11)
bti_dev_t = Transform("ctf_meg", "meg", _get_bti_dev_t(0.0, bti_trans))
for pdf, config, hs in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs)
dev_ctf_t = raw.info["dev_ctf_t"]
dev_head_t_old = raw.info["dev_head_t"]
ctf_head_t = raw.info["ctf_head_t"]
# 1) get BTI->Neuromag
bti_dev_t = Transform("ctf_meg", "meg", _get_bti_dev_t(0.0, bti_trans))
# 2) get Neuromag->BTI head
t = combine_transforms(invert_transform(bti_dev_t), dev_ctf_t, "meg", "ctf_head")
# 3) get Neuromag->head
dev_head_t_new = combine_transforms(t, ctf_head_t, "meg", "head")
assert_array_equal(dev_head_t_new["trans"], dev_head_t_old["trans"])
def test_transforms():
"""Test transformations."""
bti_trans = (0.0, 0.02, 0.11)
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
for pdf, config, hs, in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs, preload=False)
dev_ctf_t = raw.info['dev_ctf_t']
dev_head_t_old = raw.info['dev_head_t']
ctf_head_t = raw.info['ctf_head_t']
# 1) get BTI->Neuromag
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
# 2) get Neuromag->BTI head
t = combine_transforms(invert_transform(bti_dev_t), dev_ctf_t, 'meg',
'ctf_head')
# 3) get Neuromag->head
dev_head_t_new = combine_transforms(t, ctf_head_t, 'meg', 'head')
assert_array_equal(dev_head_t_new['trans'], dev_head_t_old['trans'])
def test_transforms():
"""Test transformations."""
bti_trans = (0.0, 0.02, 0.11)
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
for pdf, config, hs, in zip(pdf_fnames, config_fnames, hs_fnames):
raw = read_raw_bti(pdf, config, hs, preload=False)
dev_ctf_t = raw.info['dev_ctf_t']
dev_head_t_old = raw.info['dev_head_t']
ctf_head_t = raw.info['ctf_head_t']
# 1) get BTI->Neuromag
bti_dev_t = Transform('ctf_meg', 'meg', _get_bti_dev_t(0.0, bti_trans))
# 2) get Neuromag->BTI head
t = combine_transforms(invert_transform(bti_dev_t), dev_ctf_t,
'meg', 'ctf_head')
# 3) get Neuromag->head
dev_head_t_new = combine_transforms(t, ctf_head_t, 'meg', 'head')
assert_array_equal(dev_head_t_new['trans'], dev_head_t_old['trans'])
def _prepare_trans(info, trans, coord_frame='head'):
head_mri_t = _ensure_trans(trans, 'head', 'mri')
dev_head_t = info['dev_head_t']
del trans
# Figure out our transformations
if coord_frame == 'meg':
head_trans = invert_transform(dev_head_t)
meg_trans = Transform('meg', 'meg')
mri_trans = invert_transform(
combine_transforms(dev_head_t, head_mri_t, 'meg', 'mri'))
elif coord_frame == 'mri':
head_trans = head_mri_t
meg_trans = combine_transforms(dev_head_t, head_mri_t, 'meg', 'mri')
mri_trans = Transform('mri', 'mri')
else: # coord_frame == 'head'
head_trans = Transform('head', 'head')
meg_trans = info['dev_head_t']
mri_trans = invert_transform(head_mri_t)
return head_trans, meg_trans, mri_trans
def gen_ras_to_head_trans(head_to_mri_t, t1_img):
mri_to_head_t = invert_transform(head_to_mri_t)
# RAS <> VOXEL
ras_to_vox_t = Transform(fro='ras', to='mri_voxel',
trans=np.linalg.inv(t1_img.header.get_vox2ras()))
# trans=t1_img.header.get_ras2vox())
vox_to_mri_t = Transform(fro='mri_voxel', to='mri',
trans=t1_img.header.get_vox2ras_tkr())
# RAS <> MRI
ras_to_mri_t = combine_transforms(ras_to_vox_t,
vox_to_mri_t,
fro='ras', to='mri')
ras_to_head_t = combine_transforms(ras_to_mri_t,
mri_to_head_t,
fro='ras', to='head')
return ras_to_head_t
