def run(self, image):
"Correct for Nyquist ghosting due to field inhomogeneity."
if not verify_scanner_image(self, image): return
if not self.fmap_file:
self.log("No field map file provided, quitting")
return
if not image.isepi:
self.log("Can't apply inhomogeneity correction"\
" to non-epi sequences, quitting")
return
fMap = readImage(self.fmap_file)
# grab the fieldmap, ignore the mask
fMap = fMap.subImage(0)
if fMap.shape[-3:] != image.shape[-3:]:
self.log("This field map's shape does not match"\
" the image shape, quitting")
return
shift = (image.idim * image.T_pe/2/N.pi)
#watch the sign
pixel_pos = -shift*fMap[:] + N.outer(N.arange(fMap.jdim),
N.ones(fMap.jdim))
image[:].real = resample_phase_axis(abs(image[:]), pixel_pos)
image[:].imag = 0.
def test_orientation(self):
rad_xform = np.array([[-1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.],])
neur_xform = np.array([[ 1., 0., 0.],
[ 0., 1., 0.],
[ 0., 0., 1.],])
sag_xform = np.array([[ 0., 0.,-1.],
[ 1., 0., 0.],
[ 0., 1., 0.],])
nif = nifti.readImage(os.path.join(self.pwd, 'avg152T1_LR_nifti'))
assert_array_equal(nif.orientation_xform.tomatrix(), rad_xform)
nif = nifti.readImage(os.path.join(self.pwd, 'avg152T1_RL_nifti'))
assert_array_equal(nif.orientation_xform.tomatrix(), neur_xform)
nif = nifti.readImage(os.path.join(self.pwd, 'gems2'))
assert_array_equal(nif.orientation_xform.tomatrix(), sag_xform)
def run(self, image):
if not verify_scanner_image(self, image):
return
fmap_file = clean_name(self.fmap_file)[0]
## if hasattr(image, 'n_chan'):
## fmap_file += '.c%02d'%image.chan
try:
fmapIm = readImage(fmap_file)
except:
self.log("fieldmap not found: " + fmap_file)
return -1
(nslice, npe, nfe) = image.shape[-3:]
# make sure that the length of the q1 columns of the fmap
# are AT LEAST equal to that of the image
regrid_fac = max(npe, fmapIm.shape[-2])
# fmap and chi-mask are swapped to be of shape (Q1,Q2)
fmap = np.swapaxes(
regrid_bilinear(fmapIm[0], regrid_fac, axis=-2).astype(np.float64),
-1, -2)
chi = np.swapaxes(regrid_bilinear(fmapIm[1], regrid_fac, axis=-2), -1,
-2)
Q1, Q2 = fmap.shape[-2:]
# compute T_n2 vector
Tl = image.T_pe
delT = image.delT
a, b, n2, _ = image.epi_trajectory()
K = get_kernel(Q2, Tl, b, n2, fmap, chi)
for s in range(nslice):
# dchunk is shaped (nvol, npe, nfe)
# inverse transform along nfe (can't do in-place)
dchunk = ifft1(image[:, s, :, :])
# now shape is (nfe, npe, nvol)
dchunk = np.swapaxes(dchunk, 0, 2)
for fe in range(nfe):
# want to solve Kx = y for x
# K is (npe,npe), and y is (npe,nvol)
#
# There seems to be a trade-off here as nvol changes...
# Doing this in two steps is faster for large nvol; I think
# it takes advantage of the faster BLAS matrix-product in dot
# as opposed to LAPACK's linear solver. For smaller values
# of nvol, the overhead seems to outweigh the benefit.
iK = regularized_inverse(K[s, fe], self.lmbda)
dchunk[fe] = np.dot(iK, dchunk[fe])
dchunk = np.swapaxes(dchunk, 0, 2)
# fft x back to kx, can do inplace here
fft1(dchunk, inplace=True)
image[:, s, :, :] = dchunk
def run(self, image):
if not verify_scanner_image(self, image):
return
fmap_file = clean_name(self.fmap_file)[0]
## if hasattr(image, 'n_chan'):
## fmap_file += '.c%02d'%image.chan
try:
fmapIm = readImage(fmap_file)
except:
self.log("fieldmap not found: " + fmap_file)
return -1
(nslice, npe, nfe) = image.shape[-3:]
# make sure that the length of the q1 columns of the fmap
# are AT LEAST equal to that of the image
regrid_fac = max(npe, fmapIm.shape[-2])
# fmap and chi-mask are swapped to be of shape (Q1,Q2)
fmap = np.swapaxes(regrid_bilinear(fmapIm[0], regrid_fac, axis=-2).astype(np.float64), -1, -2)
chi = np.swapaxes(regrid_bilinear(fmapIm[1], regrid_fac, axis=-2), -1, -2)
Q1, Q2 = fmap.shape[-2:]
# compute T_n2 vector
Tl = image.T_pe
delT = image.delT
a, b, n2, _ = image.epi_trajectory()
K = get_kernel(Q2, Tl, b, n2, fmap, chi)
for s in range(nslice):
# dchunk is shaped (nvol, npe, nfe)
# inverse transform along nfe (can't do in-place)
dchunk = ifft1(image[:, s, :, :])
# now shape is (nfe, npe, nvol)
dchunk = np.swapaxes(dchunk, 0, 2)
for fe in range(nfe):
# want to solve Kx = y for x
# K is (npe,npe), and y is (npe,nvol)
#
# There seems to be a trade-off here as nvol changes...
# Doing this in two steps is faster for large nvol; I think
# it takes advantage of the faster BLAS matrix-product in dot
# as opposed to LAPACK's linear solver. For smaller values
# of nvol, the overhead seems to outweigh the benefit.
iK = regularized_inverse(K[s, fe], self.lmbda)
dchunk[fe] = np.dot(iK, dchunk[fe])
dchunk = np.swapaxes(dchunk, 0, 2)
# fft x back to kx, can do inplace here
fft1(dchunk, inplace=True)
image[:, s, :, :] = dchunk
def setUp(self):
self.pwd = os.path.split(__file__)[0]
fname = os.path.join(self.pwd, 'filtered_func_data')
self.image = nifti.readImage(fname, vrange=(0,1))