def mni305_mni152(voxels):
mni152_header, mni305_header = get_mni152_and_305_headers()
ras = apply_trans(np.linalg.inv(mni305_header.get_vox2ras()), voxels)
mni152 = np.rint(
apply_trans(np.linalg.inv(mni152_header.get_vox2ras()),
ras)).astype(int)
return mni152
def mni_to_tkras(points,
subject,
subjects_dir,
tal_xfm=None,
orig_vox2ras=None,
orig_vox2tkras=None):
# https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html
# MNI305RAS = TalXFM * orig_vox2ras * inv(orig_vox2tkras) * [tkrR tkrA tkrS 1]
if tal_xfm is None:
tal_xfm = get_talxfm(subject, subjects_dir)
if orig_vox2ras is None:
orig_vox2ras = get_vox2ras(
op.join(subjects_dir, subject, 'mri', 'orig.mgz'))
if orig_vox2tkras is None:
orig_vox2tkras = get_vox2ras_tkr(
op.join(subjects_dir, subject, 'mri', 'orig.mgz'))
# Only in python 3.5:
# trans = tal_xfm @ orig_vox2ras @ np.linalg.inv(orig_vox2tkras)
# trans = tal_xfm.dot(orig_vox2ras).dot(np.linalg.inv(orig_vox2tkras))
# trans = np.linalg.inv(trans)
trans = inv(tal_xfm @ orig_vox2ras @ inv(orig_vox2tkras))
# points = apply_trans(orig_vox2tkras, points)
# points = apply_trans(np.linalg.inv(orig_vox2ras), points)
# points = apply_trans(np.linalg.inv(tal_xfm), points)
points = apply_trans(trans, points)
return points
def tkras_to_vox(points,
subject_orig_header=None,
subject='',
subjects_dir=''):
if subject_orig_header is None:
subject_orig_header = get_subject_orig_header(subject, subjects_dir)
vox2ras_tkr = subject_orig_header.get_vox2ras_tkr()
ras_tkr2vox = np.linalg.inv(vox2ras_tkr)
vox = apply_trans(ras_tkr2vox, points)
return vox
def tkras_to_mni(points, subject, subjects_dir):
# https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html
# MNI305RAS = TalXFM * orig_vox2ras * inv(orig_vox2tkras) * [tkrR tkrA tkrS 1]
tal_xfm = get_talxfm(subject, subjects_dir)
orig_vox2ras = get_vox2ras(
op.join(subjects_dir, subject, 'mri', 'orig.mgz'))
orig_vox2tkras = get_vox2ras_tkr(
op.join(subjects_dir, subject, 'mri', 'orig.mgz'))
trans = tal_xfm @ orig_vox2ras @ inv(orig_vox2tkras)
points = apply_trans(trans, points)
# points = apply_trans(tal_xfm, points)
# points = apply_trans(orig_vox2ras, points)
# points = apply_trans(np.linalg.inv(orig_vox2tkras), points)
return points
def vox_to_ras(points, subject_orig_header=None, subject='', subjects_dir=''):
if subject_orig_header is None:
subject_orig_header = get_subject_orig_header(subject, subjects_dir)
vox2ras = subject_orig_header.get_vox2ras()
ras = apply_trans(vox2ras, points)
return ras
def mni152_mni305(points):
return apply_trans(np.linalg.inv(mni305_to_mni152_matrix()), points)
def mni305_to_mni152(points):
return apply_trans(mni305_to_mni152_matrix(), points)
