def test_eudx_bad_seed():
"""Test passing a bad seed to eudx"""
fimg, fbvals, fbvecs = get_data('small_101D')
img = ni.load(fimg)
affine = img.get_affine()
data = img.get_data()
gtab = gradient_table(fbvals, fbvecs)
tensor_model = TensorModel(gtab)
ten = tensor_model.fit(data)
ind = quantize_evecs(ten.evecs)
seed = [1000000., 1000000., 1000000.]
eu = EuDX(a=ten.fa, ind=ind, seeds=[seed], a_low=.2)
try:
track = list(eu)
except ValueError as ve:
if ve.args[0] == 'Seed outside boundaries':
print(ve)
print(data.shape)
seed = [1., 5., 8.]
eu = EuDX(a=ten.fa, ind=ind, seeds=[seed], a_low=.2)
track = list(eu)
seed = [-1., 1000000., 1000000.]
eu = EuDX(a=ten.fa, ind=ind, seeds=[seed], a_low=.2)
try:
track = list(eu)
except ValueError as ve:
if ve.args[0] == 'Seed outside boundaries':
print(ve)
def test_eudx_bad_seed():
"""Test passing a bad seed to eudx"""
fimg, fbvals, fbvecs = get_data('small_101D')
img = ni.load(fimg)
affine = img.affine
data = img.get_data()
gtab = gradient_table(fbvals, fbvecs)
tensor_model = TensorModel(gtab)
ten = tensor_model.fit(data)
ind = quantize_evecs(ten.evecs)
sphere = get_sphere('symmetric724')
seed = [1000000., 1000000., 1000000.]
eu = EuDX(a=ten.fa, ind=ind, seeds=[seed],
odf_vertices=sphere.vertices, a_low=.2)
assert_raises(ValueError, list, eu)
print(data.shape)
seed = [1., 5., 8.]
eu = EuDX(a=ten.fa, ind=ind, seeds=[seed],
odf_vertices=sphere.vertices, a_low=.2)
track = list(eu)
seed = [-1., 1000000., 1000000.]
eu = EuDX(a=ten.fa, ind=ind, seeds=[seed],
odf_vertices=sphere.vertices, a_low=.2)
assert_raises(ValueError, list, eu)
def compute_tensor_model(dir_src, dir_out, verbose=False):
fbval = pjoin(dir_src, 'bvals_' + par_b_tag)
fbvec = pjoin(dir_src, 'bvecs_' + par_b_tag)
fdwi = pjoin(dir_src, 'data_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
fmask = pjoin(dir_src, 'nodif_brain_mask_' + par_dim_tag + '.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=par_b0_threshold)
data, affine = load_nifti(fdwi, verbose)
mask, _ = load_nifti(fmask, verbose)
ten_model = TensorModel(gtab)
ten_fit = ten_model.fit(data, mask)
FA = ten_fit.fa
MD = ten_fit.md
EV = ten_fit.evecs.astype(np.float32)
fa_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_FA.nii.gz'
save_nifti(pjoin(dir_out, fa_name), FA, affine)
md_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_MD.nii.gz'
save_nifti(pjoin(dir_out, md_name), MD, affine)
ev_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_EV.nii.gz'
save_nifti(pjoin(dir_out, ev_name), EV, affine)
def test_eudx_further():
""" Cause we love testin.. ;-)
"""
fimg,fbvals,fbvecs=get_data('small_101D')
img=ni.load(fimg)
affine=img.get_affine()
data=img.get_data()
gtab = gradient_table(fbvals, fbvecs)
tensor_model = TensorModel(gtab)
ten = tensor_model.fit(data)
x,y,z=data.shape[:3]
seeds=np.zeros((10**4,3))
for i in range(10**4):
rx=(x-1)*np.random.rand()
ry=(y-1)*np.random.rand()
rz=(z-1)*np.random.rand()
seeds[i]=np.ascontiguousarray(np.array([rx,ry,rz]),dtype=np.float64)
ind = quantize_evecs(ten.evecs)
eu=EuDX(a=ten.fa, ind=ind, seeds=seeds, a_low=.2)
T=[e for e in eu]
#check that there are no negative elements
for t in T:
assert_equal(np.sum(t.ravel()<0),0)
def test_response_from_mask():
fdata, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
data = nib.load(fdata).get_data()
gtab = gradient_table(bvals, bvecs)
ten = TensorModel(gtab)
tenfit = ten.fit(data)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
radius = 3
for fa_thr in np.arange(0, 1, 0.1):
response_auto, ratio_auto, nvoxels = auto_response(gtab,
data,
roi_center=None,
roi_radius=radius,
fa_thr=fa_thr,
return_number_of_voxels=True)
ci, cj, ck = np.array(data.shape[:3]) / 2
mask = np.zeros(data.shape[:3])
mask[ci - radius: ci + radius,
cj - radius: cj + radius,
ck - radius: ck + radius] = 1
mask[FA <= fa_thr] = 0
response_mask, ratio_mask = response_from_mask(gtab, data, mask)
assert_equal(int(np.sum(mask)), nvoxels)
assert_array_almost_equal(response_mask[0], response_auto[0])
assert_almost_equal(response_mask[1], response_auto[1])
assert_almost_equal(ratio_mask, ratio_auto)
def test_phantom():
N = 50
vol = orbital_phantom(gtab,
func=f,
t=np.linspace(0, 2 * np.pi, N),
datashape=(10, 10, 10, len(bvals)),
origin=(5, 5, 5),
scale=(3, 3, 3),
angles=np.linspace(0, 2 * np.pi, 16),
radii=np.linspace(0.2, 2, 6),
S0=100)
m = TensorModel(gtab)
t = m.fit(vol)
FA = t.fa
# print vol
FA[np.isnan(FA)] = 0
# 686 -> expected FA given diffusivities of [1500, 400, 400]
l1, l2, l3 = 1500e-6, 400e-6, 400e-6
expected_fa = (np.sqrt(0.5) *
np.sqrt((l1 - l2)**2 + (l2-l3)**2 + (l3-l1)**2) /
np.sqrt(l1**2 + l2**2 + l3**2))
assert_array_almost_equal(FA.max(), expected_fa, decimal=2)
def test_masked_array_with_tensor():
data = np.ones((2, 4, 56))
mask = np.array([[True, False, False, True],
[True, False, True, False]])
bvec, bval = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bval, bvec.T)
tensor_model = TensorModel(gtab)
tensor = tensor_model.fit(data, mask=mask)
assert_equal(tensor.shape, (2, 4))
assert_equal(tensor.fa.shape, (2, 4))
assert_equal(tensor.evals.shape, (2, 4, 3))
assert_equal(tensor.evecs.shape, (2, 4, 3, 3))
tensor = tensor[0]
assert_equal(tensor.shape, (4,))
assert_equal(tensor.fa.shape, (4,))
assert_equal(tensor.evals.shape, (4, 3))
assert_equal(tensor.evecs.shape, (4, 3, 3))
tensor = tensor[0]
assert_equal(tensor.shape, tuple())
assert_equal(tensor.fa.shape, tuple())
assert_equal(tensor.evals.shape, (3,))
assert_equal(tensor.evecs.shape, (3, 3))
assert_equal(type(tensor.model_params), np.ndarray)
def test_WLS_and_LS_fit():
"""
Tests the WLS and LS fitting functions to see if they returns the correct
eigenvalues and eigenvectors.
Uses data/55dir_grad.bvec as the gradient table and 3by3by56.nii
as the data.
"""
### Defining Test Voxel (avoid nibabel dependency) ###
#Recall: D = [Dxx,Dyy,Dzz,Dxy,Dxz,Dyz,log(S_0)] and D ~ 10^-4 mm^2 /s
b0 = 1000.
bvec, bval = read_bvec_file(get_data('55dir_grad.bvec'))
B = bval[1]
#Scale the eigenvalues and tensor by the B value so the units match
D = np.array([1., 1., 1., 0., 0., 1., -np.log(b0) * B]) / B
evals = np.array([2., 1., 0.]) / B
md = evals.mean()
tensor = from_lower_triangular(D)
#Design Matrix
X = dti.design_matrix(bvec, bval)
#Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
gtab = grad.gradient_table(bval, bvec)
### Testing WLS Fit on Single Voxel ###
#Estimate tensor from test signals
model = TensorModel(gtab, min_signal=1e-8, fit_method='WLS')
tensor_est = model.fit(Y)
assert_equal(tensor_est.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_est.evals[0], evals)
assert_array_almost_equal(tensor_est.quadratic_form[0], tensor,
err_msg="Calculation of tensor from Y does not "
"compare to analytical solution")
assert_almost_equal(tensor_est.md[0], md)
# Test that we can fit a single voxel's worth of data (a 1d array)
y = Y[0]
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
# Test using fit_method='LS'
model = TensorModel(gtab, min_signal=1e-8, fit_method='LS')
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
def DIPY_nii2streamlines(imgfile, maskfile, bvals, bvecs, output_prefix):
import numpy as np
import nibabel as nib
import os
from dipy.reconst.dti import TensorModel
print "nii2streamlines"
img = nib.load(imgfile)
bvals = np.genfromtxt(bvals)
bvecs = np.genfromtxt(bvecs)
if bvecs.shape[1] != 3:
bvecs = bvecs.T
print bvecs.shape
from nipype.utils.filemanip import split_filename
_, prefix, _ = split_filename(imgfile)
from dipy.data import gradient_table
gtab = gradient_table(bvals, bvecs)
data = img.get_data()
affine = img.get_affine()
zooms = img.get_header().get_zooms()[:3]
new_zooms = (2., 2., 2.)
data2, affine2 = data, affine
mask = nib.load(maskfile).get_data().astype(np.bool)
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data2, mask)
from dipy.reconst.dti import fractional_anisotropy
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
fa_img = nib.Nifti1Image(FA, img.get_affine())
nib.save(fa_img, experiment_dir + '/' + ('%s_tensor_fa.nii.gz' % prefix))
evecs = tenfit.evecs
evec_img = nib.Nifti1Image(evecs, img.get_affine())
nib.save(evec_img, experiment_dir + '/' + ('%s_tensor_evec.nii.gz' % prefix))
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
from dipy.reconst.dti import quantize_evecs
peak_indices = quantize_evecs(tenfit.evecs, sphere.vertices)
from dipy.tracking.eudx import EuDX
eu = EuDX(FA, peak_indices, odf_vertices = sphere.vertices, a_low=0.2, seeds=10**6, ang_thr=35)
tensor_streamlines = [streamline for streamline in eu]
hdr = nib.trackvis.empty_header()
hdr['voxel_size'] = new_zooms
hdr['voxel_order'] = 'LPS'
hdr['dim'] = data2.shape[:3]
import dipy.tracking.metrics as dmetrics
tensor_streamlines = ((sl, None, None) for sl in tensor_streamlines if dmetrics.length(sl) > 15)
ten_sl_fname = experiment_dir + '/' + ('%s_streamline.trk' % prefix)
nib.trackvis.write(ten_sl_fname, tensor_streamlines, hdr, points_space='voxel')
return ten_sl_fname
def test_eudx_further():
""" Cause we love testin.. ;-)
"""
fimg, fbvals, fbvecs = get_data('small_101D')
img = ni.load(fimg)
affine = img.affine
data = img.get_data()
gtab = gradient_table(fbvals, fbvecs)
tensor_model = TensorModel(gtab)
ten = tensor_model.fit(data)
x, y, z = data.shape[:3]
seeds = np.zeros((10**4, 3))
for i in range(10**4):
rx = (x-1)*np.random.rand()
ry = (y-1)*np.random.rand()
rz = (z-1)*np.random.rand()
seeds[i] = np.ascontiguousarray(np.array([rx, ry, rz]),
dtype=np.float64)
sphere = get_sphere('symmetric724')
ind = quantize_evecs(ten.evecs)
eu = EuDX(a=ten.fa, ind=ind, seeds=seeds,
odf_vertices=sphere.vertices, a_low=.2)
T = [e for e in eu]
# check that there are no negative elements
for t in T:
assert_equal(np.sum(t.ravel() < 0), 0)
# Test eudx with affine
def random_affine(seeds):
affine = np.eye(4)
affine[:3, :] = np.random.random((3, 4))
seeds = np.dot(seeds, affine[:3, :3].T)
seeds += affine[:3, 3]
return affine, seeds
# Make two random affines and move seeds
affine1, seeds1 = random_affine(seeds)
affine2, seeds2 = random_affine(seeds)
# Make tracks using different affines
eu1 = EuDX(a=ten.fa, ind=ind, odf_vertices=sphere.vertices,
seeds=seeds1, a_low=.2, affine=affine1)
eu2 = EuDX(a=ten.fa, ind=ind, odf_vertices=sphere.vertices,
seeds=seeds2, a_low=.2, affine=affine2)
# Move from eu2 affine2 to affine1
eu2_to_eu1 = utils.move_streamlines(eu2, output_space=affine1,
input_space=affine2)
# Check that the tracks are the same
for sl1, sl2 in zip(eu1, eu2_to_eu1):
assert_array_almost_equal(sl1, sl2)
def test_single_tensor():
evals = np.array([1.4, .35, .35]) * 10**(-3)
evecs = np.eye(3)
S = SingleTensor(gtab, 100, evals, evecs, snr=None)
assert_array_almost_equal(S[gtab.b0s_mask], 100)
assert_(np.mean(S[~gtab.b0s_mask]) < 100)
from dipy.reconst.dti import TensorModel
m = TensorModel(gtab)
t = m.fit(S)
assert_array_almost_equal(t.fa, 0.707, decimal=3)
def FA_RGB(data, gtab):
"""
Input : data, gtab taken from the load_data.py script.
Return : FA and RGB as two nd numpy array
"""
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
FA = np.clip(FA, 0, 1)
RGB = color_fa(FA, tenfit.evecs)
return FA, RGB
def estimate_response(gtab, data, affine, mask, fa_thr=0.7):
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
mask[FA <= 0.1] = 0
mask[FA > 1.] = 0
indices = np.where(FA > fa_thr)
lambdas = tenfit.evals[indices][:, :2]
S0s = data[indices][:, 0]
S0 = np.mean(S0s)
l01 = np.mean(lambdas, axis=0)
evals = np.array([l01[0], l01[1], l01[1]])
ratio = evals[1] / evals[0]
print 'Response evals' , evals, ' ratio: ', ratio, '\tMean S0', S0
return (evals, S0), ratio
def prepare(training, category, snr, denoised, odeconv, tv, method):
data, affine, gtab = get_specific_data(training,
category,
snr,
denoised)
prefix = create_file_prefix(training,
category,
snr,
denoised,
odeconv,
tv,
method)
if training:
mask = nib.load('wm_mask_hardi_01.nii.gz').get_data()
else:
#mask = np.ones(data.shape[:-1])
mask = nib.load('test_hardi_30_den=1_fa_0025_dilate2_mask.nii.gz').get_data()
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
mask[FA <= 0.1] = 0
mask[FA > 1.] = 0
indices = np.where(FA > 0.7)
lambdas = tenfit.evals[indices][:, :2]
S0s = data[indices][:, 0]
S0 = np.mean(S0s)
if S0 == 0:
print 'S0 equals to 0 switching to 1'
S0 = 1
l01 = np.mean(lambdas, axis=0)
evals = np.array([l01[0], l01[1], l01[1]])
print evals, S0
return data, affine, gtab, mask, evals, S0, prefix
def reconstruction(dwi,bval_file,bvec_file,mask=None,type='dti',b0=0.,order=4):
""" Uses Dipy to reconstruct an fODF for each voxel.
Parameters
----------
dwi: numpy array (mandatory)
Holds the diffusion weighted image in a 4D-array (see nibabel).
bval_file: string (mandatory)
Path to the b-value file (FSL format).
bvec_file: string (mandatory)
Path to the b-vectors file (FSL format).
mask: numpy array
Holds the mask in a 3D array (see nibabel).
type: string \in {'dti','csd','csa'} (default = 'dti')
The type of the ODF reconstruction.
b0: float (default = 0)
Threshold to use for defining b0 images.
order: int (default = 4)
Order to use for constrained spherical deconvolution (csd) or constant solid angle (csa).
Returns
-----------
model_fit: Dipy Object (depends on the type)
Represents the fitted model for each voxel.
"""
#b-values and b-vectors
bvals, bvecs = read_bvals_bvecs(bval_file,bvec_file)
gtab = gradient_table(bvals, bvecs, b0_threshold=b0)
#reconstruction
if type == 'dti':
model = TensorModel(gtab,fit_method='WLS')
elif type == 'csd':
response, ratio = auto_response(gtab, dwi, roi_radius=10, fa_thr=0.7)
model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=order)
elif type == 'csa':
model = CsaOdfModel(gtab, order)
if mask is not None:
model_fit = model.fit(dwi,mask=mask)
else:
model_fit = model.fit(dwi)
return model_fit
def response_from_mask(gtab, data, mask):
""" Estimate the response function from a given mask.
Parameters
----------
gtab : GradientTable
data : ndarray
Diffusion data
mask : ndarray
Mask to use for the estimation of the response function. For example a
mask of the white matter voxels with FA values higher than 0.7
(see [1]_).
Returns
-------
response : tuple, (2,)
(`evals`, `S0`)
ratio : float
The ratio between smallest versus largest eigenvalue of the response.
Notes
-----
See csdeconv.auto_response() or csdeconv.recursive_response() if you don't
have a computed mask for the response function estimation.
References
----------
.. [1] Tournier, J.D., et al. NeuroImage 2004. Direct estimation of the
fiber orientation density function from diffusion-weighted MRI
data using spherical deconvolution
"""
ten = TensorModel(gtab)
indices = np.where(mask > 0)
if indices[0].size == 0:
msg = "No voxel in mask with value > 0 were found."
warnings.warn(msg, UserWarning)
return (np.nan, np.nan), np.nan
tenfit = ten.fit(data[indices])
lambdas = tenfit.evals[:, :2]
S0s = data[indices][:, np.nonzero(gtab.b0s_mask)[0]]
return _get_response(S0s, lambdas)
def test_boot_pmf():
"""This tests the local model used for the bootstrapping.
"""
hsph_updated = HemiSphere.from_sphere(unit_octahedron)
vertices = hsph_updated.vertices
bvecs = vertices
bvals = np.ones(len(vertices)) * 1000
bvecs = np.insert(bvecs, 0, np.array([0, 0, 0]), axis=0)
bvals = np.insert(bvals, 0, 0)
gtab = gradient_table(bvals, bvecs)
voxel = single_tensor(gtab)
data = np.tile(voxel, (3, 3, 3, 1))
point = np.array([1., 1., 1.])
tensor_model = TensorModel(gtab)
boot_pmf_gen = BootPmfGen(data, model=tensor_model, sphere=hsph_updated)
no_boot_pmf = boot_pmf_gen.get_pmf_no_boot(point)
model_pmf = tensor_model.fit(voxel).odf(hsph_updated)
npt.assert_equal(len(hsph_updated.vertices), no_boot_pmf.shape[0])
npt.assert_array_almost_equal(no_boot_pmf, model_pmf)
# test model sherical harminic order different than bootstrap order
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
csd_model = ConstrainedSphericalDeconvModel(gtab, None, sh_order=6)
assert_greater(len([lw for lw in w if issubclass(lw.category,
UserWarning)]), 0)
boot_pmf_gen_sh4 = BootPmfGen(data, model=csd_model, sphere=hsph_updated,
sh_order=4)
pmf_sh4 = boot_pmf_gen_sh4.get_pmf(point)
npt.assert_equal(len(hsph_updated.vertices), pmf_sh4.shape[0])
npt.assert_(np.sum(pmf_sh4.shape) > 0)
boot_pmf_gen_sh8 = BootPmfGen(data, model=csd_model, sphere=hsph_updated,
sh_order=8)
pmf_sh8 = boot_pmf_gen_sh8.get_pmf(point)
npt.assert_equal(len(hsph_updated.vertices), pmf_sh8.shape[0])
npt.assert_(np.sum(pmf_sh8.shape) > 0)
def single_fiber_response(diffusionData, mask, gtable, fa_thr = 0.7):
from dipy.reconst.dti import TensorModel, fractional_anisotropy
ten = TensorModel(gtable)
tenfit = ten.fit(diffusionData, mask=mask)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
indices = np.where(FA > fa_thr)
lambdas = tenfit.evals[indices][:, :2]
S0s = diffusionData[indices][:, np.nonzero(gtable.b0s_mask)[0]]
S0 = np.mean(S0s)
l01 = np.mean(lambdas, axis=0)
evals = np.array([l01[0], l01[1], l01[1]])
response = (evals, S0)
ratio = evals[1]/evals[0]
return response, ratio
def tensor_model(
input_filename_data, input_filename_bvecs, input_filename_bvals, output_filename_fa=None, output_filename_evecs=None
):
# print 'Tensor model ...'
# print 'Loading data ...'
img = nib.load(input_filename_data)
data = img.get_data()
affine = img.get_affine()
bvals, bvecs = read_bvals_bvecs(input_filename_bvals, input_filename_bvecs)
gtab = gradient_table(bvals, bvecs)
mask = data[..., 0] > 50
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
if output_filename_fa == None:
filename_save_fa = input_filename_data.split(".")[0] + "_tensor_fa.nii.gz"
else:
filename_save_fa = os.path.abspath(output_filename_fa)
fa_img = nib.Nifti1Image(FA, img.get_affine())
nib.save(fa_img, filename_save_fa)
print "Saving fa to:", filename_save_fa
if output_filename_evecs == None:
filename_save_evecs = input_filename_data.split(".")[0] + "_tensor_evecs.nii.gz"
else:
filename_save_evecs = os.path.abspath(output_filename_evecs)
evecs_img = nib.Nifti1Image(tenfit.evecs, img.get_affine())
nib.save(evecs_img, filename_save_evecs)
print "Saving evecs to:", filename_save_evecs
return filename_save_fa, filename_save_evecs
def eudx_basic(self, dti_file, mask_file, gtab, stop_val=0.1):
"""
Tracking with basic tensors and basic eudx - experimental
We now force seeding at every voxel in the provided mask for
simplicity. Future functionality will extend these options.
**Positional Arguments:**
dti_file:
- File (registered) to use for tensor/fiber tracking
mask_file:
- Brain mask to keep tensors inside the brain
gtab:
- dipy formatted bval/bvec Structure
**Optional Arguments:**
stop_val:
- Value to cutoff fiber track
"""
img = nb.load(dti_file)
data = img.get_data()
img = nb.load(mask_file)
mask = img.get_data()
# use all points in mask
seedIdx = np.where(mask > 0) # seed everywhere not equal to zero
seedIdx = np.transpose(seedIdx)
model = TensorModel(gtab)
ten = model.fit(data, mask)
sphere = get_sphere('symmetric724')
ind = quantize_evecs(ten.evecs, sphere.vertices)
eu = EuDX(a=ten.fa, ind=ind, seeds=seedIdx,
odf_vertices=sphere.vertices, a_low=stop_val)
tracks = [e for e in eu]
return (ten, tracks)
def auto_response(gtab, data, roi_center=None, roi_radius=10, fa_thr=0.7,
fa_callable=fa_superior, return_number_of_voxels=False):
""" Automatic estimation of response function using FA.
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data
roi_center : tuple, (3,)
Center of ROI in data. If center is None, it is assumed that it is
the center of the volume with shape `data.shape[:3]`.
roi_radius : int
radius of cubic ROI
fa_thr : float
FA threshold
fa_callable : callable
A callable that defines an operation that compares FA with the fa_thr. The operator
should have two positional arguments (e.g., `fa_operator(FA, fa_thr)`) and it should
return a bool array.
return_number_of_voxels : bool
If True, returns the number of voxels used for estimating the response
function.
Returns
-------
response : tuple, (2,)
(`evals`, `S0`)
ratio : float
The ratio between smallest versus largest eigenvalue of the response.
number of voxels : int (optional)
The number of voxels used for estimating the response function.
Notes
-----
In CSD there is an important pre-processing step: the estimation of the
fiber response function. In order to do this we look for voxels with very
anisotropic configurations. For example we can use an ROI (20x20x20) at
the center of the volume and store the signal values for the voxels with
FA values higher than 0.7. Of course, if we haven't precalculated FA we
need to fit a Tensor model to the datasets. Which is what we do in this
function.
For the response we also need to find the average S0 in the ROI. This is
possible using `gtab.b0s_mask()` we can find all the S0 volumes (which
correspond to b-values equal 0) in the dataset.
The `response` consists always of a prolate tensor created by averaging
the highest and second highest eigenvalues in the ROI with FA higher than
threshold. We also include the average S0s.
We also return the `ratio` which is used for the SDT models. If requested,
the number of voxels used for estimating the response function is also
returned, which can be used to judge the fidelity of the response function.
As a rule of thumb, at least 300 voxels should be used to estimate a good
response function (see [1]_).
References
----------
.. [1] Tournier, J.D., et al. NeuroImage 2004. Direct estimation of the
fiber orientation density function from diffusion-weighted MRI
data using spherical deconvolution
"""
ten = TensorModel(gtab)
if roi_center is None:
ci, cj, ck = np.array(data.shape[:3]) // 2
else:
ci, cj, ck = roi_center
w = roi_radius
roi = data[int(ci - w): int(ci + w),
int(cj - w): int(cj + w),
int(ck - w): int(ck + w)]
tenfit = ten.fit(roi)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
indices = np.where(fa_callable(FA, fa_thr))
if indices[0].size == 0:
msg = "No voxel with a FA higher than " + str(fa_thr) + " were found."
msg += " Try a larger roi or a lower threshold."
warnings.warn(msg, UserWarning)
lambdas = tenfit.evals[indices][:, :2]
S0s = roi[indices][:, np.nonzero(gtab.b0s_mask)[0]]
response, ratio = _get_response(S0s, lambdas)
if return_number_of_voxels:
return response, ratio, indices[0].size
return response, ratio
def test_boot_pmf():
# This tests the local model used for the bootstrapping.
hsph_updated = HemiSphere.from_sphere(unit_octahedron)
vertices = hsph_updated.vertices
bvecs = vertices
bvals = np.ones(len(vertices)) * 1000
bvecs = np.insert(bvecs, 0, np.array([0, 0, 0]), axis=0)
bvals = np.insert(bvals, 0, 0)
gtab = gradient_table(bvals, bvecs)
voxel = single_tensor(gtab)
data = np.tile(voxel, (3, 3, 3, 1))
point = np.array([1., 1., 1.])
tensor_model = TensorModel(gtab)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
boot_pmf_gen = BootPmfGen(data,
model=tensor_model,
sphere=hsph_updated)
no_boot_pmf = boot_pmf_gen.get_pmf_no_boot(point)
model_pmf = tensor_model.fit(voxel).odf(hsph_updated)
npt.assert_equal(len(hsph_updated.vertices), no_boot_pmf.shape[0])
npt.assert_array_almost_equal(no_boot_pmf, model_pmf)
# test model spherical harmonic order different than bootstrap order
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
warnings.simplefilter("always", category=PendingDeprecationWarning)
csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=6)
# Tests that the first catched warning comes from
# the CSD model constructor
npt.assert_(issubclass(w[0].category, UserWarning))
npt.assert_("Number of parameters required " in str(w[0].message))
# Tests that additional warnings are raised for outdated SH basis
npt.assert_(len(w) > 1)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
boot_pmf_gen_sh4 = BootPmfGen(data,
sphere=hsph_updated,
model=csd_model,
sh_order=4)
pmf_sh4 = boot_pmf_gen_sh4.get_pmf(point)
npt.assert_equal(len(hsph_updated.vertices), pmf_sh4.shape[0])
npt.assert_(np.sum(pmf_sh4.shape) > 0)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
boot_pmf_gen_sh8 = BootPmfGen(data,
model=csd_model,
sphere=hsph_updated,
sh_order=8)
pmf_sh8 = boot_pmf_gen_sh8.get_pmf(point)
npt.assert_equal(len(hsph_updated.vertices), pmf_sh8.shape[0])
npt.assert_(np.sum(pmf_sh8.shape) > 0)
def auto_response(gtab, data, roi_center=None, roi_radius=10, fa_thr=0.7):
""" Automatic estimation of response function using FA
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data
roi_center : tuple, (3,)
Center of ROI in data. If center is None, it is assumed that it is
the center of the volume with shape `data.shape[:3]`.
roi_radius : int
radius of cubic ROI
fa_thr : float
FA threshold
Returns
-------
response : tuple, (2,)
(`evals`, `S0`)
ratio : float
the ratio between smallest versus largest eigenvalue of the response
Notes
-----
In CSD there is an important pre-processing step: the estimation of the
fiber response function. In order to do this we look for voxels with very
anisotropic configurations. For example we can use an ROI (20x20x20) at
the center of the volume and store the signal values for the voxels with
FA values higher than 0.7. Of course, if we haven't precalculated FA we
need to fit a Tensor model to the datasets. Which is what we do in this
function.
For the response we also need to find the average S0 in the ROI. This is
possible using `gtab.b0s_mask()` we can find all the S0 volumes (which
correspond to b-values equal 0) in the dataset.
The `response` consists always of a prolate tensor created by averaging
the highest and second highest eigenvalues in the ROI with FA higher than
threshold. We also include the average S0s.
Finally, we also return the `ratio` which is used for the SDT models.
"""
ten = TensorModel(gtab)
if roi_center is None:
ci, cj, ck = np.array(data.shape[:3]) / 2
else:
ci, cj, ck = roi_center
w = roi_radius
roi = data[ci - w: ci + w, cj - w: cj + w, ck - w: ck + w]
tenfit = ten.fit(roi)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
indices = np.where(FA > fa_thr)
lambdas = tenfit.evals[indices][:, :2]
S0s = roi[indices][:, np.nonzero(gtab.b0s_mask)[0]]
S0 = np.mean(S0s)
l01 = np.mean(lambdas, axis=0)
evals = np.array([l01[0], l01[1], l01[1]])
response = (evals, S0)
ratio = evals[1]/evals[0]
return response, ratio
def test_wls_and_ls_fit():
"""
Tests the WLS and LS fitting functions to see if they returns the correct
eigenvalues and eigenvectors.
Uses data/55dir_grad.bvec as the gradient table and 3by3by56.nii
as the data.
"""
# Defining Test Voxel (avoid nibabel dependency) ###
# Recall: D = [Dxx,Dyy,Dzz,Dxy,Dxz,Dyz,log(S_0)] and D ~ 10^-4 mm^2 /s
b0 = 1000.
bvec, bval = read_bvec_file(get_fnames('55dir_grad.bvec'))
B = bval[1]
# Scale the eigenvalues and tensor by the B value so the units match
D = np.array([1., 1., 1., 0., 0., 1., -np.log(b0) * B]) / B
evals = np.array([2., 1., 0.]) / B
md = evals.mean()
tensor = from_lower_triangular(D)
# Design Matrix
gtab = grad.gradient_table(bval, bvec)
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
npt.assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Testing WLS Fit on Single Voxel
# If you do something wonky (passing min_signal<0), you should get an
# error:
npt.assert_raises(ValueError, TensorModel, gtab, fit_method='WLS',
min_signal=-1)
# Estimate tensor from test signals
model = TensorModel(gtab, fit_method='WLS', return_S0_hat=True)
tensor_est = model.fit(Y)
npt.assert_equal(tensor_est.shape, Y.shape[:-1])
npt.assert_array_almost_equal(tensor_est.evals[0], evals)
npt.assert_array_almost_equal(tensor_est.quadratic_form[0], tensor,
err_msg="Calculation of tensor from Y does "
"not compare to analytical solution")
npt.assert_almost_equal(tensor_est.md[0], md)
npt.assert_array_almost_equal(tensor_est.S0_hat[0], b0, decimal=3)
# Test that we can fit a single voxel's worth of data (a 1d array)
y = Y[0]
tensor_est = model.fit(y)
npt.assert_equal(tensor_est.shape, tuple())
npt.assert_array_almost_equal(tensor_est.evals, evals)
npt.assert_array_almost_equal(tensor_est.quadratic_form, tensor)
npt.assert_almost_equal(tensor_est.md, md)
npt.assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
# Test using fit_method='LS'
model = TensorModel(gtab, fit_method='LS')
tensor_est = model.fit(y)
npt.assert_equal(tensor_est.shape, tuple())
npt.assert_array_almost_equal(tensor_est.evals, evals)
npt.assert_array_almost_equal(tensor_est.quadratic_form, tensor)
npt.assert_almost_equal(tensor_est.md, md)
npt.assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
npt.assert_array_almost_equal(tensor_est.linearity, linearity(evals))
npt.assert_array_almost_equal(tensor_est.planarity, planarity(evals))
npt.assert_array_almost_equal(tensor_est.sphericity, sphericity(evals))
def main():
parser = _build_args_parser()
args = parser.parse_args()
img = nib.load(args.input)
data = img.get_data()
print('\ndata shape ({}, {}, {}, {})'.format(data.shape[0], data.shape[1],
data.shape[2], data.shape[3]))
print('total voxels {}'.format(np.prod(data.shape[:3])))
# remove negatives
print('\ncliping negative ({} voxels, {:.2f} % of total)'.format(
(data < 0).sum(),
100 * (data < 0).sum() / float(np.prod(data.shape[:3]))))
data = np.clip(data, 0, np.inf)
affine = img.affine
if args.mask is None:
mask = None
masksum = np.prod(data.shape[:3])
else:
mask = nib.load(args.mask).get_data().astype(np.bool)
masksum = mask.sum()
print('\nMask has {} voxels, {:.2f} % of total'.format(
masksum, 100 * masksum / float(np.prod(data.shape[:3]))))
# Validate bvals and bvecs
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
if not is_normalized_bvecs(bvecs):
print('Your b-vectors do not seem normalized...')
bvecs = normalize_bvecs(bvecs)
# detect unique b-shell and assign shell id to each volume
# sort bvals to get monotone increasing bvalue
bvals_argsort = np.argsort(bvals)
bvals_sorted = bvals[bvals_argsort]
b_shell_threshold = 25.
unique_bvalues = []
shell_idx = []
unique_bvalues.append(bvals_sorted[0])
shell_idx.append(0)
for newb in bvals_sorted[1:]:
# check if volume is in existing shell
done = False
for i, b in enumerate(unique_bvalues):
if (newb - b_shell_threshold < b) and (newb + b_shell_threshold >
b):
shell_idx.append(i)
done = True
if not done:
unique_bvalues.append(newb)
shell_idx.append(i + 1)
unique_bvalues = np.array(unique_bvalues)
# un-sort shells
shells = np.zeros_like(bvals)
shells[bvals_argsort] = shell_idx
print('\nWe have {} shells'.format(len(unique_bvalues)))
print('with b-values {}\n'.format(unique_bvalues))
for i in range(len(unique_bvalues)):
shell_b = bvals[shells == i]
print('shell {}: n = {}, min/max {} {}'.format(i, len(shell_b),
shell_b.min(),
shell_b.max()))
# Get tensors
method = 'WLS'
min_signal = 1e-16
print('\nUsing fitting method {}'.format(method))
# print('Using minimum signal = {}'.format(min_signal)
b0_thr = bvals.min() + 10
print('\nassuming existence of b0 (thr = {})\n'.format(b0_thr))
mds = []
for i in range(len(unique_bvalues) - 1):
# max_shell = i+1
print('fitting using first {} shells (bmax = {})'.format(
i + 2, bvals[shells == i + 1].max()))
# restricted gtab
gtab = gradient_table(bvals[shells <= i + 1],
bvecs[shells <= i + 1],
b0_threshold=b0_thr)
tenmodel = TensorModel(gtab, fit_method=method, min_signal=min_signal)
tenfit = tenmodel.fit(data[..., shells <= i + 1], mask)
mds.append(tenfit.md[mask])
peaks = []
fifty = []
th = 0.01
print('\nonly using values inside quantile [{}, {}] for plotting'.format(
th, 1 - th))
for i in range(len(unique_bvalues) - 1):
plt.figure()
tit = 'MD^-1, first {} shells (bmax = {})'.format(
i + 2, bvals[shells == i + 1].max())
print('\nbmax = {}'.format(bvals[shells == i + 1].max()))
# truncate lower and upper MD to remove crazy outliers
minval = np.quantile(mds[i], th)
maxval = np.quantile(mds[i], 1 - th)
tmp = mds[i]
# vv1 = tmp.shape[0]
tmp = tmp[np.logical_and(tmp >= minval, tmp <= maxval)]**-1
# vv2 = tmp.shape[0]
print('quantile threshold removed {} voxels'.format(
np.logical_and(tmp >= minval, tmp <= maxval).sum()))
# remove high diffusivity non physical outlier
idx1 = (tmp <= 1 / 3.0e-3
) # free water diffusivity at in-vivo brain temperature
print(
'{} voxels above free water diffusivity ({:.2f} % of mask)'.format(
idx1.sum(), 100 * idx1.sum() / float(masksum)))
# remove low diffusivity probable outlier
th_diff = 0.05
idx2 = (
tmp >= 1 / (th_diff * 1.0e-3)
) # 1% of mean diffusivity of in-vivo WM at in-vivo brain temperature
print(
'{} voxels below {} of in-vivo WM diffusivity ({:.2f} % of mask)'.
format(idx2.sum(), th_diff, 100 * idx2.sum() / float(masksum)))
tmp = tmp[np.logical_not(np.logical_or(idx1, idx2))]
# fit smoothed curve for peak extraction
gkde = gaussian_kde(tmp)
plt.hist(tmp, bins=100, density=True, color='grey')
bs = np.linspace(tmp.min(), tmp.max(), 1000)
smoothed = gkde.pdf(bs)
plt.plot(bs, smoothed, color='blue', linewidth=2)
# peak extraction
smoothed_peak = bs[smoothed.argmax()]
plt.axvline(smoothed_peak,
color='red',
label='peak ({:.0f})'.format(smoothed_peak))
peaks.append(smoothed_peak)
# useless extra lines
onequart = np.quantile(tmp, 0.25)
threequart = np.quantile(tmp, 0.75)
twoquart = np.quantile(tmp, 0.5)
fifty.append(twoquart)
plt.axvline(onequart,
color='pink',
label='25% ({:.0f})'.format(onequart))
plt.axvline(twoquart,
color='yellow',
label='50% ({:.0f})'.format(twoquart))
plt.axvline(threequart,
color='green',
label='75% ({:.0f})'.format(threequart))
plt.title(tit)
plt.legend(loc=1)
plt.savefig('./bvalEst_bmax_{}.png'.format(unique_bvalues[i + 1]))
print(
'\nHigher-than-required bmax will artifactually decrease MD, increasing 1/MD'
)
print(
'The error on the estimation of 1/MD should be small when the peak is close to bmax'
)
print(
'This is under the assumption that we have a valid WM mask so that the tissues are somewhat uniform'
)
bmaxs = np.array(
[bvals[shells == i + 1].max() for i in range(len(unique_bvalues) - 1)])
plt.figure()
plt.plot(bmaxs, peaks, '-x', label='fit')
plt.plot(bmaxs, bmaxs, label='identity')
plt.xlabel('bmax')
plt.ylabel('MD^-1')
plt.legend()
plt.title('PEAK')
plt.savefig('./bvalEst_peak.png')
plt.figure()
plt.plot(bmaxs, fifty, '-x', label='fit')
plt.plot(bmaxs, bmaxs, label='identity')
plt.xlabel('bmax')
plt.ylabel('MD^-1')
plt.legend()
plt.title('50% quartile')
plt.savefig('./bvalEst_50Q.png')
def segment_from_dwi(image,
bvals_file,
bvecs_file,
ROI,
threshold,
mask=None,
filename=None,
overwrite=True):
"""
Takes a dwi, bvals and bvecs files and computes FA, RGB and a binary mask
estimation of the supplied ROI according to a threshold on the RGB.
"""
# Load raw dwi image
data = image.get_data()
affine = image.get_affine()
# Load bval and bvec files, fit the tensor model
print("Now fitting tensor model")
b_vals, b_vecs = read_bvals_bvecs(bvals_file, bvecs_file)
gtab = gradient_table_from_bvals_bvecs(b_vals, b_vecs)
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
FA = np.clip(
FA, 0,
1) # We clamp the FA between 0 and 1 to remove degenerate tensors
if mask is not None:
FA = apply_mask(FA, mask)
FA_vol = nib.Nifti1Image(FA.astype('float32'), affine)
if filename is None:
FA_path = 'FA.nii.gz'
else:
FA_path = filename + '_FA.nii.gz'
# Check if FA already exists
if os.path.exists(FA_path):
print("FA", FA_path, "already exists!")
if overwrite is True:
nib.save(FA_vol, FA_path)
print("FA", FA_path, "was overwritten")
else:
print("New FA was not saved")
else:
nib.save(FA_vol, FA_path)
print("FA was saved as ", FA_path)
RGB = color_fa(FA, tenfit.evecs)
if filename is None:
RGB_path = 'RGB.nii.gz'
else:
RGB_path = filename + '_RGB.nii.gz'
RGB_vol = nib.Nifti1Image(np.array(255 * RGB, 'uint8'), affine)
# Check if RGB already exists
if os.path.exists(RGB_path):
print("RGB", RGB_path, "already exists!")
if overwrite is True:
nib.save(RGB_vol, RGB_path)
print("RGB", RGB_path, "was overwritten")
else:
print("New RGB was not saved")
else:
nib.save(RGB_vol, RGB_path)
print("RGB was saved as ", RGB_path)
return segment_from_RGB(RGB, ROI, threshold)
def prepare_data_for_actors(dwi_filename, bvals_filename, bvecs_filename,
target_template_filename, slices_choice,
shells=None):
# Load and prepare the data
dwi_img = nib.load(dwi_filename)
dwi_data = dwi_img.get_data()
dwi_affine = dwi_img.get_affine()
bvals, bvecs = read_bvals_bvecs(bvals_filename, bvecs_filename)
target_template_img = nib.load(target_template_filename)
target_template_data = target_template_img.get_data()
target_template_affine = target_template_img.affine
mask_data = np.zeros(target_template_data.shape)
mask_data[target_template_data > 0] = 1
# Prepare mask for tensors fit
x_slice, y_slice, z_slice = slices_choice
mask_data = prepare_slices_mask(mask_data,
x_slice, y_slice, z_slice)
# Extract B0
gtab = gradient_table(bvals, normalize_bvecs(bvecs), b0_threshold=10)
b0_idx = np.where(gtab.b0s_mask)[0]
mean_b0 = np.mean(dwi_data[..., b0_idx], axis=3, dtype=dwi_data.dtype)
if shells:
indices = [get_shell_indices(bvals, shell) for shell in shells]
indices = np.sort(np.hstack(indices))
if len(indices) < 1:
raise ValueError(
'There are no volumes that have the supplied b-values.')
shell_data = np.zeros((dwi_data.shape[:-1] + (len(indices),)),
dtype=dwi_data.dtype)
shell_bvecs = np.zeros((len(indices), 3))
shell_bvals = np.zeros((len(indices),))
for i, indice in enumerate(indices):
shell_data[..., i] = dwi_data[..., indice]
shell_bvals[i] = bvals[indice]
shell_bvecs[i, :] = bvecs[indice, :]
else:
shell_data = dwi_data
shell_bvals = bvals
shell_bvecs = bvecs
# Register the DWI data to the template
transformed_dwi, transformation = register_image(target_template_data,
target_template_affine,
mean_b0,
dwi_affine,
transformation_type='rigid',
dwi=shell_data)
# Rotate gradients
rotated_bvecs = np.dot(shell_bvecs, transformation[0:3, 0:3])
rotated_bvecs = normalize_bvecs(rotated_bvecs)
rotated_gtab = gradient_table(shell_bvals, rotated_bvecs, b0_threshold=10)
# Get tensors
tensor_model = TensorModel(rotated_gtab, fit_method='LS')
tensor_fit = tensor_model.fit(transformed_dwi, mask_data)
# Get FA
fa_map = np.clip(fractional_anisotropy(tensor_fit.evals), 0, 1)
# Get eigen vals/vecs
evals = np.zeros(target_template_data.shape + (1,))
evals[..., 0] = tensor_fit.evals[..., 0] / np.max(tensor_fit.evals[..., 0])
evecs = np.zeros(target_template_data.shape + (1, 3))
evecs[:, :, :, 0, :] = tensor_fit.evecs[..., 0]
return fa_map, evals, evecs
def run(self,
data_files,
bvals_files,
bvecs_files,
mask_file,
bbox_threshold=[0.6, 1, 0, 0.1, 0, 0.1],
out_dir='',
out_file='product.json',
out_mask_cc='cc.nii.gz',
out_mask_noise='mask_noise.nii.gz'):
"""Compute the signal-to-noise ratio in the corpus callosum.
Parameters
----------
data_files : string
Path to the dwi.nii.gz file. This path may contain wildcards to
process multiple inputs at once.
bvals_files : string
Path of bvals.
bvecs_files : string
Path of bvecs.
mask_file : string
Path of a brain mask file.
bbox_threshold : variable float, optional
Threshold for bounding box, values separated with commas for ex.
[0.6,1,0,0.1,0,0.1]. (default (0.6, 1, 0, 0.1, 0, 0.1))
out_dir : string, optional
Where the resulting file will be saved. (default '')
out_file : string, optional
Name of the result file to be saved. (default 'product.json')
out_mask_cc : string, optional
Name of the CC mask volume to be saved (default 'cc.nii.gz')
out_mask_noise : string, optional
Name of the mask noise volume to be saved
(default 'mask_noise.nii.gz')
"""
io_it = self.get_io_iterator()
for dwi_path, bvals_path, bvecs_path, mask_path, out_path, \
cc_mask_path, mask_noise_path in io_it:
data, affine = load_nifti(dwi_path)
bvals, bvecs = read_bvals_bvecs(bvals_path, bvecs_path)
gtab = gradient_table(bvals=bvals, bvecs=bvecs)
mask, affine = load_nifti(mask_path)
logging.info('Computing tensors...')
tenmodel = TensorModel(gtab)
tensorfit = tenmodel.fit(data, mask=mask)
logging.info('Computing worst-case/best-case SNR using the CC...')
if np.ndim(data) == 4:
CC_box = np.zeros_like(data[..., 0])
elif np.ndim(data) == 3:
CC_box = np.zeros_like(data)
else:
raise IOError('DWI data has invalid dimensions')
mins, maxs = bounding_box(mask)
mins = np.array(mins)
maxs = np.array(maxs)
diff = (maxs - mins) // 4
bounds_min = mins + diff
bounds_max = maxs - diff
CC_box[bounds_min[0]:bounds_max[0], bounds_min[1]:bounds_max[1],
bounds_min[2]:bounds_max[2]] = 1
if len(bbox_threshold) != 6:
raise IOError('bbox_threshold should have 6 float values')
mask_cc_part, cfa = segment_from_cfa(tensorfit,
CC_box,
bbox_threshold,
return_cfa=True)
if not np.count_nonzero(mask_cc_part.astype(np.uint8)):
logging.warning("Empty mask: corpus callosum not found."
" Update your data or your threshold")
save_nifti(cc_mask_path, mask_cc_part.astype(np.uint8), affine)
logging.info('CC mask saved as {0}'.format(cc_mask_path))
masked_data = data[mask_cc_part]
mean_signal = 0
if masked_data.size:
mean_signal = np.mean(masked_data, axis=0)
mask_noise = binary_dilation(mask, iterations=10)
mask_noise[..., :mask_noise.shape[-1] // 2] = 1
mask_noise = ~mask_noise
save_nifti(mask_noise_path, mask_noise.astype(np.uint8), affine)
logging.info('Mask noise saved as {0}'.format(mask_noise_path))
noise_std = 0
if np.count_nonzero(mask_noise.astype(np.uint8)):
noise_std = np.std(data[mask_noise, :])
logging.info('Noise standard deviation sigma= ' + str(noise_std))
idx = np.sum(gtab.bvecs, axis=-1) == 0
gtab.bvecs[idx] = np.inf
axis_X = np.argmin(
np.sum((gtab.bvecs - np.array([1, 0, 0]))**2, axis=-1))
axis_Y = np.argmin(
np.sum((gtab.bvecs - np.array([0, 1, 0]))**2, axis=-1))
axis_Z = np.argmin(
np.sum((gtab.bvecs - np.array([0, 0, 1]))**2, axis=-1))
SNR_output = []
SNR_directions = []
for direction in ['b0', axis_X, axis_Y, axis_Z]:
if direction == 'b0':
SNR = mean_signal[0] / noise_std if noise_std else 0
logging.info("SNR for the b=0 image is :" + str(SNR))
else:
logging.info("SNR for direction " + str(direction) + " " +
str(gtab.bvecs[direction]) + "is :" +
str(SNR))
SNR_directions.append(direction)
SNR = mean_signal[direction] / noise_std if noise_std else 0
SNR_output.append(SNR)
data = []
data.append({
'data':
str(SNR_output[0]) + ' ' + str(SNR_output[1]) + ' ' +
str(SNR_output[2]) + ' ' + str(SNR_output[3]),
'directions':
'b0' + ' ' + str(SNR_directions[0]) + ' ' +
str(SNR_directions[1]) + ' ' + str(SNR_directions[2])
})
with open(os.path.join(out_dir, out_path), 'w') as myfile:
json.dump(data, myfile)
ocmask_data = oc_mask.get_fdata()
ocmask_affine = oc_mask.affine
ocmask_good = resample_img(oc_mask,
affine,
img.shape[0:3],
interpolation='continuous')
ocmask_data = ocmask_good.get_fdata()
ocmask_affine = ocmask_good.affine
print('Computing brain mask...')
b0_mask, mask = median_otsu(data, np.arange(1, 138))
print('Computing tensors...')
tenmodel = TensorModel(gtab)
tensorfit = tenmodel.fit(data, mask=mask)
"""Next, we set our red-green-blue thresholds to (0.6, 1) in the x axis
and (0, 0.1) in the y and z axes respectively.
These values work well in practice to isolate the very RED voxels of the cfa map.
Then, as assurance, we want just RED voxels in the CC (there could be
noisy red voxels around the brain mask and we don't want those). Unless the brain
acquisition was badly aligned, the CC is always close to the mid-sagittal slice.
The following lines perform these two operations and then saves the computed mask.
"""
print('Computing worst-case/best-case SNR using the corpus callosum...')
#region = 80
def _run_interface(self, runtime):
from scipy.special import gamma
from dipy.reconst.dti import TensorModel
import gc
img = nb.load(self.inputs.in_file)
hdr = img.header.copy()
affine = img.affine
data = img.get_fdata()
gtab = self._get_gradient_table()
if isdefined(self.inputs.in_mask):
msk = np.asanyarray(nb.load(self.inputs.in_mask).dataobj).astype(
np.uint8)
else:
msk = np.ones(data.shape[:3], dtype=np.uint8)
try_b0 = True
if isdefined(self.inputs.noise_mask):
noise_msk = (nb.load(self.inputs.noise_mask).get_fdata(
dtype=np.float32).reshape(-1))
noise_msk[noise_msk > 0.5] = 1
noise_msk[noise_msk < 1.0] = 0
noise_msk = noise_msk.astype(np.uint8)
try_b0 = False
elif np.all(data[msk == 0, 0] == 0):
IFLOGGER.info("Input data are masked.")
noise_msk = msk.reshape(-1).astype(np.uint8)
else:
noise_msk = (1 - msk).reshape(-1).astype(np.uint8)
nb0 = np.sum(gtab.b0s_mask)
dsample = data.reshape(-1, data.shape[-1])
if try_b0 and (nb0 > 1):
noise_data = dsample.take(np.where(gtab.b0s_mask),
axis=-1)[noise_msk == 0, ...]
n = nb0
else:
nodiff = np.where(~gtab.b0s_mask)
nodiffidx = nodiff[0].tolist()
n = 20 if len(nodiffidx) >= 20 else len(nodiffidx)
idxs = np.random.choice(nodiffidx, size=n, replace=False)
noise_data = dsample.take(idxs, axis=-1)[noise_msk == 1, ...]
# Estimate sigma required by RESTORE
mean_std = np.median(noise_data.std(-1))
try:
bias = 1.0 - np.sqrt(2.0 / (n - 1)) * (gamma(n / 2.0) / gamma(
(n - 1) / 2.0))
except:
bias = 0.0
pass
sigma = mean_std * (1 + bias)
if sigma == 0:
IFLOGGER.warning(
"Noise std is 0.0, looks like data was masked and "
"noise cannot be estimated correctly. Using default "
"tensor model instead of RESTORE.")
dti = TensorModel(gtab)
else:
IFLOGGER.info("Performing RESTORE with noise std=%.4f.", sigma)
dti = TensorModel(gtab, fit_method="RESTORE", sigma=sigma)
try:
fit_restore = dti.fit(data, msk)
except TypeError:
dti = TensorModel(gtab)
fit_restore = dti.fit(data, msk)
hdr.set_data_dtype(np.float32)
hdr["data_type"] = 16
for k in self._outputs().get():
scalar = getattr(fit_restore, k)
hdr.set_data_shape(np.shape(scalar))
nb.Nifti1Image(scalar.astype(np.float32), affine,
hdr).to_filename(self._gen_filename(k))
return runtime
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if not args.not_all:
args.fa = args.fa or 'fa.nii.gz'
args.ga = args.ga or 'ga.nii.gz'
args.rgb = args.rgb or 'rgb.nii.gz'
args.md = args.md or 'md.nii.gz'
args.ad = args.ad or 'ad.nii.gz'
args.rd = args.rd or 'rd.nii.gz'
args.mode = args.mode or 'mode.nii.gz'
args.norm = args.norm or 'tensor_norm.nii.gz'
args.tensor = args.tensor or 'tensor.nii.gz'
args.evecs = args.evecs or 'tensor_evecs.nii.gz'
args.evals = args.evals or 'tensor_evals.nii.gz'
args.residual = args.residual or 'dti_residual.nii.gz'
args.p_i_signal =\
args.p_i_signal or 'physically_implausible_signals_mask.nii.gz'
args.pulsation = args.pulsation or 'pulsation_and_misalignment.nii.gz'
outputs = [
args.fa, args.ga, args.rgb, args.md, args.ad, args.rd, args.mode,
args.norm, args.tensor, args.evecs, args.evals, args.residual,
args.p_i_signal, args.pulsation
]
if args.not_all and not any(outputs):
parser.error('When using --not_all, you need to specify at least ' +
'one metric to output.')
assert_inputs_exist(parser, [args.input, args.bvals, args.bvecs],
args.mask)
assert_outputs_exist(parser, args, outputs)
img = nib.load(args.input)
data = img.get_fdata(dtype=np.float32)
affine = img.affine
if args.mask is None:
mask = None
else:
mask = get_data_as_mask(nib.load(args.mask), dtype=bool)
# Validate bvals and bvecs
logging.info('Tensor estimation with the {} method...'.format(args.method))
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
if not is_normalized_bvecs(bvecs):
logging.warning('Your b-vectors do not seem normalized...')
bvecs = normalize_bvecs(bvecs)
check_b0_threshold(args.force_b0_threshold, bvals.min())
gtab = gradient_table(bvals, bvecs, b0_threshold=bvals.min())
# Get tensors
if args.method == 'restore':
sigma = ne.estimate_sigma(data)
tenmodel = TensorModel(gtab,
fit_method=args.method,
sigma=sigma,
min_signal=_get_min_nonzero_signal(data))
else:
tenmodel = TensorModel(gtab,
fit_method=args.method,
min_signal=_get_min_nonzero_signal(data))
tenfit = tenmodel.fit(data, mask)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
FA = np.clip(FA, 0, 1)
if args.tensor:
# Get the Tensor values and format them for visualisation
# in the Fibernavigator.
tensor_vals = lower_triangular(tenfit.quadratic_form)
correct_order = [0, 1, 3, 2, 4, 5]
tensor_vals_reordered = tensor_vals[..., correct_order]
fiber_tensors = nib.Nifti1Image(
tensor_vals_reordered.astype(np.float32), affine)
nib.save(fiber_tensors, args.tensor)
del tensor_vals, fiber_tensors, tensor_vals_reordered
if args.fa:
fa_img = nib.Nifti1Image(FA.astype(np.float32), affine)
nib.save(fa_img, args.fa)
del fa_img
if args.ga:
GA = geodesic_anisotropy(tenfit.evals)
GA[np.isnan(GA)] = 0
ga_img = nib.Nifti1Image(GA.astype(np.float32), affine)
nib.save(ga_img, args.ga)
del GA, ga_img
if args.rgb:
RGB = color_fa(FA, tenfit.evecs)
rgb_img = nib.Nifti1Image(np.array(255 * RGB, 'uint8'), affine)
nib.save(rgb_img, args.rgb)
del RGB, rgb_img
if args.md:
MD = mean_diffusivity(tenfit.evals)
md_img = nib.Nifti1Image(MD.astype(np.float32), affine)
nib.save(md_img, args.md)
del MD, md_img
if args.ad:
AD = axial_diffusivity(tenfit.evals)
ad_img = nib.Nifti1Image(AD.astype(np.float32), affine)
nib.save(ad_img, args.ad)
del AD, ad_img
if args.rd:
RD = radial_diffusivity(tenfit.evals)
rd_img = nib.Nifti1Image(RD.astype(np.float32), affine)
nib.save(rd_img, args.rd)
del RD, rd_img
if args.mode:
# Compute tensor mode
inter_mode = dipy_mode(tenfit.quadratic_form)
# Since the mode computation can generate NANs when not masked,
# we need to remove them.
non_nan_indices = np.isfinite(inter_mode)
mode = np.zeros(inter_mode.shape)
mode[non_nan_indices] = inter_mode[non_nan_indices]
mode_img = nib.Nifti1Image(mode.astype(np.float32), affine)
nib.save(mode_img, args.mode)
del inter_mode, mode_img, mode
if args.norm:
NORM = norm(tenfit.quadratic_form)
norm_img = nib.Nifti1Image(NORM.astype(np.float32), affine)
nib.save(norm_img, args.norm)
del NORM, norm_img
if args.evecs:
evecs = tenfit.evecs.astype(np.float32)
evecs_img = nib.Nifti1Image(evecs, affine)
nib.save(evecs_img, args.evecs)
# save individual e-vectors also
for i in range(3):
e_img = nib.Nifti1Image(evecs[..., i], affine)
nib.save(e_img, add_filename_suffix(args.evecs, '_v' + str(i + 1)))
del e_img
del evecs, evecs_img
if args.evals:
evals = tenfit.evals.astype(np.float32)
evals_img = nib.Nifti1Image(evals, affine)
nib.save(evals_img, args.evals)
# save individual e-values also
for i in range(3):
e_img = nib.Nifti1Image(evals[..., i], affine)
nib.save(e_img, add_filename_suffix(args.evals, '_e' + str(i + 1)))
del e_img
del evals, evals_img
if args.p_i_signal:
S0 = np.mean(data[..., gtab.b0s_mask], axis=-1, keepdims=True)
DWI = data[..., ~gtab.b0s_mask]
pis_mask = np.max(S0 < DWI, axis=-1)
if args.mask is not None:
pis_mask *= mask
pis_img = nib.Nifti1Image(pis_mask.astype(np.int16), affine)
nib.save(pis_img, args.p_i_signal)
del pis_img, S0, DWI
if args.pulsation:
STD = np.std(data[..., ~gtab.b0s_mask], axis=-1)
if args.mask is not None:
STD *= mask
std_img = nib.Nifti1Image(STD.astype(np.float32), affine)
nib.save(std_img, add_filename_suffix(args.pulsation, '_std_dwi'))
if np.sum(gtab.b0s_mask) <= 1:
logger.info('Not enough b=0 images to output standard '
'deviation map')
else:
if len(np.where(gtab.b0s_mask)) == 2:
logger.info('Only two b=0 images. Be careful with the '
'interpretation of this std map')
STD = np.std(data[..., gtab.b0s_mask], axis=-1)
if args.mask is not None:
STD *= mask
std_img = nib.Nifti1Image(STD.astype(np.float32), affine)
nib.save(std_img, add_filename_suffix(args.pulsation, '_std_b0'))
del STD, std_img
if args.residual:
# Mean residual image
S0 = np.mean(data[..., gtab.b0s_mask], axis=-1)
data_diff = np.zeros(data.shape, dtype=np.float32)
for i in range(data.shape[0]):
if args.mask is not None:
tenfit2 = tenmodel.fit(data[i, :, :, :], mask[i, :, :])
else:
tenfit2 = tenmodel.fit(data[i, :, :, :])
data_diff[i, :, :, :] = np.abs(
tenfit2.predict(gtab, S0[i, :, :]).astype(np.float32) -
data[i, :, :])
R = np.mean(data_diff[..., ~gtab.b0s_mask], axis=-1, dtype=np.float32)
if args.mask is not None:
R *= mask
R_img = nib.Nifti1Image(R.astype(np.float32), affine)
nib.save(R_img, args.residual)
del R, R_img, S0
# Each volume's residual statistics
if args.mask is None:
logger.info("Outlier detection will not be performed, since no "
"mask was provided.")
stats = [
dict.fromkeys([
'label', 'mean', 'iqr', 'cilo', 'cihi', 'whishi', 'whislo',
'fliers', 'q1', 'med', 'q3'
], []) for i in range(data.shape[-1])
] # stats with format for boxplots
# Note that stats will be computed manually and plotted using bxp
# but could be computed using stats = cbook.boxplot_stats
# or pyplot.boxplot(x)
R_k = np.zeros(data.shape[-1],
dtype=np.float32) # mean residual per DWI
std = np.zeros(data.shape[-1],
dtype=np.float32) # std residual per DWI
q1 = np.zeros(data.shape[-1],
dtype=np.float32) # first quartile per DWI
q3 = np.zeros(data.shape[-1],
dtype=np.float32) # third quartile per DWI
iqr = np.zeros(data.shape[-1],
dtype=np.float32) # interquartile per DWI
percent_outliers = np.zeros(data.shape[-1], dtype=np.float32)
nb_voxels = np.count_nonzero(mask)
for k in range(data.shape[-1]):
x = data_diff[..., k]
R_k[k] = np.mean(x)
std[k] = np.std(x)
q3[k], q1[k] = np.percentile(x, [75, 25])
iqr[k] = q3[k] - q1[k]
stats[k]['med'] = (q1[k] + q3[k]) / 2
stats[k]['mean'] = R_k[k]
stats[k]['q1'] = q1[k]
stats[k]['q3'] = q3[k]
stats[k]['whislo'] = q1[k] - 1.5 * iqr[k]
stats[k]['whishi'] = q3[k] + 1.5 * iqr[k]
stats[k]['label'] = k
# Outliers are observations that fall below Q1 - 1.5(IQR) or
# above Q3 + 1.5(IQR) We check if a voxel is an outlier only if
# we have a mask, else we are biased.
if args.mask is not None:
outliers = (x < stats[k]['whislo']) | (x > stats[k]['whishi'])
percent_outliers[k] = np.sum(outliers) / nb_voxels * 100
# What would be our definition of too many outliers?
# Maybe mean(all_means)+-3SD?
# Or we let people choose based on the figure.
# if percent_outliers[k] > ???? :
# logger.warning(' Careful! Diffusion-Weighted Image'
# ' i=%s has %s %% outlier voxels',
# k, percent_outliers[k])
# Saving all statistics as npy values
residual_basename, _ = split_name_with_nii(args.residual)
res_stats_basename = residual_basename + ".npy"
np.save(add_filename_suffix(res_stats_basename, "_mean_residuals"),
R_k)
np.save(add_filename_suffix(res_stats_basename, "_q1_residuals"), q1)
np.save(add_filename_suffix(res_stats_basename, "_q3_residuals"), q3)
np.save(add_filename_suffix(res_stats_basename, "_iqr_residuals"), iqr)
np.save(add_filename_suffix(res_stats_basename, "_std_residuals"), std)
# Showing results in graph
if args.mask is None:
fig, axe = plt.subplots(nrows=1, ncols=1, squeeze=False)
else:
fig, axe = plt.subplots(nrows=1,
ncols=2,
squeeze=False,
figsize=[10, 4.8])
# Default is [6.4, 4.8]. Increasing width to see better.
medianprops = dict(linestyle='-', linewidth=2.5, color='firebrick')
meanprops = dict(linestyle='-', linewidth=2.5, color='green')
axe[0, 0].bxp(stats,
showmeans=True,
meanline=True,
showfliers=False,
medianprops=medianprops,
meanprops=meanprops)
axe[0, 0].set_xlabel('DW image')
axe[0, 0].set_ylabel('Residuals per DWI volume. Red is median,\n'
'green is mean. Whiskers are 1.5*interquartile')
axe[0, 0].set_title('Residuals')
axe[0, 0].set_xticks(range(0, q1.shape[0], 5))
axe[0, 0].set_xticklabels(range(0, q1.shape[0], 5))
if args.mask is not None:
axe[0, 1].plot(range(data.shape[-1]), percent_outliers)
axe[0, 1].set_xticks(range(0, q1.shape[0], 5))
axe[0, 1].set_xticklabels(range(0, q1.shape[0], 5))
axe[0, 1].set_xlabel('DW image')
axe[0, 1].set_ylabel('Percentage of outlier voxels')
axe[0, 1].set_title('Outliers')
plt.savefig(residual_basename + '_residuals_stats.png')
def dmri_recon(sid,
data_dir,
out_dir,
resolution,
recon='csd',
dirs='',
num_threads=2):
import tempfile
#tempfile.tempdir = '/om/scratch/Fri/ksitek/'
import os
oldval = None
if 'MKL_NUM_THREADS' in os.environ:
oldval = os.environ['MKL_NUM_THREADS']
os.environ['MKL_NUM_THREADS'] = '%d' % num_threads
ompoldval = None
if 'OMP_NUM_THREADS' in os.environ:
ompoldval = os.environ['OMP_NUM_THREADS']
os.environ['OMP_NUM_THREADS'] = '%d' % num_threads
import nibabel as nib
import numpy as np
from glob import glob
if resolution == '0.2mm':
filename = 'Reg_S64550_nii4d.nii'
#filename = 'angular_resample/dwi_%s.nii.gz'%dirs
fimg = os.path.abspath(glob(os.path.join(data_dir, filename))[0])
else:
filename = 'Reg_S64550_nii4d_resamp-%s.nii.gz' % (resolution)
fimg = os.path.abspath(
glob(os.path.join(data_dir, 'resample', filename))[0])
print("dwi file = %s" % fimg)
fbval = os.path.abspath(
glob(os.path.join(data_dir, 'bvecs', 'camino_120_RAS.bvals'))[0])
print("bval file = %s" % fbval)
fbvec = os.path.abspath(
glob(os.path.join(data_dir, 'bvecs',
'camino_120_RAS_flipped-xy.bvecs'))[0])
# 'angular_resample',
# 'dwi_%s.bvecs'%dirs))[0])
print("bvec file = %s" % fbvec)
img = nib.load(fimg)
data = img.get_fdata()
affine = img.get_affine()
prefix = sid
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
'''
from dipy.core.gradients import vector_norm
b0idx = []
for idx, val in enumerate(bvals):
if val < 1:
pass
#bvecs[idx] = [1, 0, 0]
else:
b0idx.append(idx)
#print "b0idx=%d"%idx
#print "input bvecs:"
#print bvecs
bvecs[b0idx, :] = bvecs[b0idx, :]/vector_norm(bvecs[b0idx])[:, None]
#print "bvecs after normalization:"
#print bvecs
'''
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
gtab.bvecs.shape == bvecs.shape
gtab.bvecs
gtab.bvals.shape == bvals.shape
gtab.bvals
#from dipy.segment.mask import median_otsu
#b0_mask, mask = median_otsu(data[:, :, :, b0idx].mean(axis=3).squeeze(), 4, 4)
if resolution == '0.2mm':
mask_name = 'Reg_S64550_nii_b0-slice_mask.nii.gz'
fmask1 = os.path.join(data_dir, mask_name)
else:
mask_name = 'Reg_S64550_nii_b0-slice_mask_resamp-%s.nii.gz' % (
resolution)
fmask1 = os.path.join(data_dir, 'resample', mask_name)
print("fmask file = %s" % fmask1)
mask = nib.load(fmask1).get_fdata()
''' DTI model & save metrics '''
from dipy.reconst.dti import TensorModel
print("running tensor model")
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
from dipy.reconst.dti import fractional_anisotropy
print("running FA")
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
fa_img = nib.Nifti1Image(FA, img.get_affine())
tensor_fa_file = os.path.abspath('%s_tensor_fa.nii.gz' % (prefix))
nib.save(fa_img, tensor_fa_file)
from dipy.reconst.dti import axial_diffusivity
print("running AD")
AD = axial_diffusivity(tenfit.evals)
AD[np.isnan(AD)] = 0
ad_img = nib.Nifti1Image(AD, img.get_affine())
tensor_ad_file = os.path.abspath('%s_tensor_ad.nii.gz' % (prefix))
nib.save(ad_img, tensor_ad_file)
from dipy.reconst.dti import radial_diffusivity
print("running RD")
RD = radial_diffusivity(tenfit.evals)
RD[np.isnan(RD)] = 0
rd_img = nib.Nifti1Image(RD, img.get_affine())
tensor_rd_file = os.path.abspath('%s_tensor_rd.nii.gz' % (prefix))
nib.save(rd_img, tensor_rd_file)
from dipy.reconst.dti import mean_diffusivity
print("running MD")
MD = mean_diffusivity(tenfit.evals)
MD[np.isnan(MD)] = 0
md_img = nib.Nifti1Image(MD, img.get_affine())
tensor_md_file = os.path.abspath('%s_tensor_md.nii.gz' % (prefix))
nib.save(md_img, tensor_md_file)
evecs = tenfit.evecs
evec_img = nib.Nifti1Image(evecs, img.get_affine())
tensor_evec_file = os.path.abspath('%s_tensor_evec.nii.gz' % (prefix))
nib.save(evec_img, tensor_evec_file)
''' ODF model '''
useFA = True
print("creating %s model" % recon)
if recon == 'csd':
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel
from dipy.reconst.csdeconv import auto_response
response, ratio = auto_response(gtab, data, roi_radius=10,
fa_thr=0.5) # 0.7
model = ConstrainedSphericalDeconvModel(gtab, response)
useFA = True
return_sh = True
elif recon == 'csa':
from dipy.reconst.shm import CsaOdfModel, normalize_data
model = CsaOdfModel(gtab, sh_order=8)
useFA = True
return_sh = True
elif recon == 'gqi':
from dipy.reconst.gqi import GeneralizedQSamplingModel
model = GeneralizedQSamplingModel(gtab)
return_sh = False
else:
raise ValueError('only csd, csa supported currently')
from dipy.reconst.dsi import (DiffusionSpectrumDeconvModel,
DiffusionSpectrumModel)
model = DiffusionSpectrumDeconvModel(gtab)
'''reconstruct ODFs'''
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
#odfs = fit.odf(sphere)
# with CSD/GQI, uses > 50GB per core; don't get greedy with cores!
from dipy.reconst.peaks import peaks_from_model
print("running peaks_from_model")
peaks = peaks_from_model(
model=model,
data=data,
sphere=sphere,
mask=mask,
return_sh=return_sh,
return_odf=False,
normalize_peaks=True,
npeaks=5,
relative_peak_threshold=.5,
min_separation_angle=10, #25,
parallel=num_threads > 1,
nbr_processes=num_threads)
# save the peaks
from dipy.io.peaks import save_peaks
peaks_file = os.path.abspath('%s_peaks.pam5' % (prefix))
save_peaks(peaks_file, peaks)
# save the spherical harmonics
shm_coeff_file = os.path.abspath('%s_shm_coeff.nii.gz' % (prefix))
if return_sh:
shm_coeff = peaks.shm_coeff
nib.save(nib.Nifti1Image(shm_coeff, img.get_affine()), shm_coeff_file)
else:
# if it's not a spherical model, output it as an essentially null file
np.savetxt(shm_coeff_file, [0])
# save the generalized fractional anisotropy image
gfa_img = nib.Nifti1Image(peaks.gfa, img.get_affine())
model_gfa_file = os.path.abspath('%s_%s_gfa.nii.gz' % (prefix, recon))
nib.save(gfa_img, model_gfa_file)
#from dipy.reconst.dti import quantize_evecs
#peak_indices = quantize_evecs(tenfit.evecs, sphere.vertices)
#eu = EuDX(FA, peak_indices, odf_vertices = sphere.vertices,
#a_low=0.2, seeds=10**6, ang_thr=35)
''' probabilistic tracking '''
'''
from dipy.direction import ProbabilisticDirectionGetter
from dipy.tracking.local import LocalTracking
from dipy.tracking.streamline import Streamlines
from dipy.io.streamline import save_trk
prob_dg = ProbabilisticDirectionGetter.from_shcoeff(shm_coeff,
max_angle=45.,
sphere=sphere)
streamlines_generator = LocalTracking(prob_dg,
affine,
step_size=.5,
max_cross=1)
# Generate streamlines object
streamlines = Streamlines(streamlines_generator)
affine = img.get_affine()
vox_size=fa_img.get_header().get_zooms()[:3]
fname = os.path.abspath('%s_%s_prob_streamline.trk' % (prefix, recon))
save_trk(fname, streamlines, affine, vox_size=vox_size)
'''
''' deterministic tracking with EuDX method'''
from dipy.tracking.eudx import EuDX
print("reconstructing with EuDX")
if useFA:
eu = EuDX(
FA,
peaks.peak_indices[..., 0],
odf_vertices=sphere.vertices,
a_low=0.001, # default is 0.0239
seeds=10**6,
ang_thr=75)
else:
eu = EuDX(
peaks.gfa,
peaks.peak_indices[..., 0],
odf_vertices=sphere.vertices,
#a_low=0.1,
seeds=10**6,
ang_thr=45)
sl_fname = os.path.abspath('%s_%s_det_streamline.trk' % (prefix, recon))
# trying new dipy.io.streamline module, per email to neuroimaging list
# 2018.04.05
from nibabel.streamlines import Field
from nibabel.orientations import aff2axcodes
affine = img.get_affine()
vox_size = fa_img.get_header().get_zooms()[:3]
fov_shape = FA.shape[:3]
if vox_size is not None and fov_shape is not None:
hdr = {}
hdr[Field.VOXEL_TO_RASMM] = affine.copy()
hdr[Field.VOXEL_SIZES] = vox_size
hdr[Field.DIMENSIONS] = fov_shape
hdr[Field.VOXEL_ORDER] = "".join(aff2axcodes(affine))
tractogram = nib.streamlines.Tractogram(eu)
tractogram.affine_to_rasmm = affine
trk_file = nib.streamlines.TrkFile(tractogram, header=hdr)
nib.streamlines.save(trk_file, sl_fname)
if oldval:
os.environ['MKL_NUM_THREADS'] = oldval
else:
del os.environ['MKL_NUM_THREADS']
if ompoldval:
os.environ['OMP_NUM_THREADS'] = ompoldval
else:
del os.environ['OMP_NUM_THREADS']
print('all output files created')
return (tensor_fa_file, tensor_evec_file, model_gfa_file, sl_fname, affine,
tensor_ad_file, tensor_rd_file, tensor_md_file, shm_coeff_file,
peaks_file)
def tracking(folder):
print('Tracking in ' + folder)
output_folder = folder + 'dipy_out/'
# make a folder to save new data into
try:
Path(output_folder).mkdir(parents=True, exist_ok=True)
except OSError:
print('Could not create output dir. Aborting...')
return
# load data
print('Loading data...')
img = nib.load(folder + 'data.nii.gz')
dmri = np.asarray(img.dataobj)
affine = img.affine
mask, _ = load_nifti(folder + 'nodif_brain_mask.nii.gz')
bvals, bvecs = read_bvals_bvecs(folder + 'bvals', folder + 'bvecs')
gtab = gradient_table(bvals, bvecs)
# extract peaksoutput_folder + 'peak_vals.nii.gz'
if Path(output_folder + 'peaks.pam5').exists():
peaks = load_peaks(output_folder + 'peaks.pam5')
else:
print('Extracting peaks...')
response, ration = auto_response(gtab, dmri, roi_radius=10, fa_thr=.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
peaks = peaks_from_model(model=csd_model,
data=dmri,
sphere=default_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
save_peaks(output_folder + 'peaks.pam5', peaks, affine)
scaled = peaks.peak_dirs * np.repeat(
np.expand_dims(peaks.peak_values, -1), 3, -1)
cropped = scaled[:, :, :, :3, :].reshape(dmri.shape[:3] + (9, ))
save_nifti(output_folder + 'peaks.nii.gz', cropped, affine)
#save_nifti(output_folder + 'peak_dirs.nii.gz', peaks.peak_dirs, affine)
#save_nifti(output_folder + 'peak_vals.nii.gz', peaks.peak_values, affine)
# tracking
print('Tracking...')
maskdata, mask = median_otsu(dmri,
vol_idx=range(0, dmri.shape[3]),
median_radius=3,
numpass=1,
autocrop=True,
dilate=2)
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(maskdata)
fa = fractional_anisotropy(tensor_fit.evals)
fa[np.isnan(fa)] = 0
bla = np.average(fa)
tissue_classifier = ThresholdStoppingCriterion(fa, .1)
seeds = random_seeds_from_mask(fa > 1e-5, affine, seeds_count=1)
streamline_generator = LocalTracking(direction_getter=peaks,
stopping_criterion=tissue_classifier,
seeds=seeds,
affine=affine,
step_size=.5)
streamlines = Streamlines(streamline_generator)
save_trk(StatefulTractogram(streamlines, img, Space.RASMM),
output_folder + 'whole_brain.trk')
def tens_mod_fa_est(gtab_file, dwi_file, B0_mask):
"""
Estimate a tensor FA image to use for registrations.
Parameters
----------
gtab_file : str
File path to pickled DiPy gradient table object.
dwi_file : str
File path to diffusion weighted image.
B0_mask : str
File path to B0 brain mask.
Returns
-------
fa_path : str
File path to FA Nifti1Image.
B0_mask : str
File path to B0 brain mask Nifti1Image.
gtab_file : str
File path to pickled DiPy gradient table object.
dwi_file : str
File path to diffusion weighted Nifti1Image.
fa_md_path : str
File path to FA/MD mask Nifti1Image.
"""
import os
from dipy.io import load_pickle
from dipy.reconst.dti import TensorModel
from dipy.reconst.dti import fractional_anisotropy, mean_diffusivity
gtab = load_pickle(gtab_file)
data = nib.load(dwi_file, mmap=False).get_fdata()
print("Generating tensor FA image to use for registrations...")
nodif_B0_img = nib.load(B0_mask, mmap=False)
nodif_B0_mask_data = nodif_B0_img.get_fdata().astype("bool")
model = TensorModel(gtab)
mod = model.fit(data, nodif_B0_mask_data)
FA = fractional_anisotropy(mod.evals)
# MD = mean_diffusivity(mod.evals)
# FA_MD = np.logical_or(
# FA >= 0.2, (np.logical_and(
# FA >= 0.08, MD >= 0.0011)))
# FA_MD[np.isnan(FA_MD)] = 0
FA = np.nan_to_num(np.asarray(FA.astype('float32')))
fa_path = f"{os.path.dirname(B0_mask)}{'/tensor_fa.nii.gz'}"
nib.save(
nib.Nifti1Image(
FA,
nodif_B0_img.affine),
fa_path)
# md_path = f"{os.path.dirname(B0_mask)}{'/tensor_md.nii.gz'}"
# nib.save(
# nib.Nifti1Image(
# MD.astype(
# np.float32),
# nodif_B0_img.affine),
# md_path)
nodif_B0_img.uncache()
del FA
return fa_path, B0_mask, gtab_file, dwi_file
del data, affine, zooms
print(data2.shape)
print(affine2)
print(nib.aff2axcodes(affine2))
print('>>> Save resampled data, masks and S0...')
# Save as nii (not nii.gz) to reduce saving and loading time
fname2 = join(dname, 'dwi_1x1x1.nii')
nib.save(nib.Nifti1Image(data2, affine2), fname2)
fname2_mask = join(dname, 'dwi_mask_1x1x1.nii.gz')
nib.save(nib.Nifti1Image(mask2.astype(np.uint8), affine2), fname2_mask)
fname2_S0 = join(dname, 'dwi_S0_1x1x1.nii.gz')
S0s = data2[..., b0_index]
S0 = np.mean(S0s, axis=-1)
nib.save(nib.Nifti1Image(S0, affine2), fname2_S0)
print('>>> Calculate FA...')
ten = TensorModel(gtab)
tenfit = ten.fit(data2, mask2)
fname2_fa = join(dname, 'dwi_fa_1x1x1.nii.gz')
nib.save(nib.Nifti1Image(tenfit.fa, affine2), fname2_fa)
del data2, mask2
class IvimTensorModel(ReconstModel):
def __init__(self, gtab, split_b_D=200.0, n_threads=1):
"""
Model to reconstruct an IVIM tensor
Parameters
----------
gtab : GradientTable class instance
split_b_D : float
The value of b that separates perfusion from diffusion
"""
ReconstModel.__init__(self, gtab)
self.split_b_D = split_b_D
# Use two separate tensors for initial estimation:
self.diffusion_idx = np.hstack(
[np.where(gtab.bvals > self.split_b_D),
np.where(gtab.b0s_mask)]).squeeze()
# The first tensor represents diffusion
self.diffusion_gtab = gradient_table(
self.gtab.bvals[self.diffusion_idx],
self.gtab.bvecs[self.diffusion_idx])
self.diffusion_model = TensorModel(self.diffusion_gtab)
# The second tensor represents perfusion:
self.perfusion_idx = np.array(
np.where(gtab.bvals <= self.split_b_D)).squeeze()
self.perfusion_gtab = gradient_table(
self.gtab.bvals[self.perfusion_idx],
self.gtab.bvecs[self.perfusion_idx])
self.perfusion_model = TensorModel(self.perfusion_gtab)
# We'll need a "vanilla" IVIM model:
self.ivim_model = IvimModel(self.gtab)
# How many threads in parallel execution:
self.n_threads = n_threads
def model_eq1(self, b, *params):
"""
The model with a fixed perfusion fraction
"""
bvecs = self.gtab.bvecs
beta = self._ivim_pf
Q, Q_star = _reconstruct_tensors(params)
return _ivim_tensor_equation(beta, b, bvecs, Q_star, Q)
def model_eq2(self, b, *params):
"""
The full model, including perfusion fraction as free parameter
"""
beta = params[0]
bvecs = self.gtab.bvecs
Q, Q_star = _reconstruct_tensors(params[1:])
return _ivim_tensor_equation(beta, b, bvecs, Q_star, Q)
def _inner_loop(self, vox_chunk):
model_params = np.zeros((vox_chunk.shape[0], 13))
for ii, vox in enumerate(vox_chunk):
# Extract initial guess of Euler angles for the diffusion fit:
dt_evecs = self.diffusion_fit.evecs[vox]
angles_dti = calc_euler(dt_evecs)
# Extract initial guess of Euler angles for the perfusion fit:
perfusion_evecs = self.perfusion_fit.evecs[vox]
angles_perfusion = calc_euler(perfusion_evecs)
# Initial guess of perfusion fraction based on "vanilla" IVIM:
self._ivim_pf = np.clip(
np.min([
self.ivim_fit.perfusion_fraction[vox],
1 - self.ivim_fit.perfusion_fraction[vox]
]), 0, 1)
# If diffusivity is lower than this, it's not perfusion!
min_D_star = 0.003
# Put together initial guess for 13 parameters of full model:
initial = [
self._ivim_pf,
np.min([self.diffusion_fit.evals[vox, 0], min_D_star]),
np.min([self.diffusion_fit.evals[vox, 1], min_D_star]),
np.min([self.diffusion_fit.evals[vox, 2], min_D_star]),
angles_dti[0], angles_dti[1], angles_dti[2],
np.max([self.perfusion_fit.evals[vox, 0], min_D_star]),
np.max([self.perfusion_fit.evals[vox, 1], min_D_star]),
np.max([self.perfusion_fit.evals[vox, 2], min_D_star]),
angles_perfusion[0], angles_perfusion[1], angles_perfusion[2]
]
# Bounds on the parameters:
lb = (0, 0, 0, 0, -np.pi, -np.pi, -np.pi, 0.003, 0.003, 0.003,
-np.pi, -np.pi, -np.pi)
ub = (0.5, 0.003, 0.003, 0.003, np.pi, np.pi, np.pi, np.inf,
np.inf, np.inf, np.pi, np.pi, np.pi)
# Fit the full model to the data with initial guess and bounds
try:
popt, pcov = curve_fit(
self.model_eq2,
self.gtab.bvals,
self.mask_data[vox] /
np.mean(self.mask_data[vox, self.gtab.b0s_mask]),
p0=initial,
bounds=(lb, ub),
xtol=0.05,
ftol=0.05,
maxfev=10000)
# Sometimes it can't fit the data:
except RuntimeError:
popt = np.ones(len(initial)) * np.nan
model_params[ii] = popt
return model_params
def fit(self, data, mask=None):
"""
Fit the IVIM tensor model
"""
if mask is None:
mask = np.ones(data.shape[:-1], dtype=bool)
self.mask_data = data[mask]
# Fit diffusion tensor to diffusion-weighted data:
diffusion_data = self.mask_data[:, self.diffusion_idx]
self.diffusion_fit = self.diffusion_model.fit(diffusion_data)
# Fit "vanilla" IVIM to all of the data:
self.ivim_fit = self.ivim_model.fit(self.mask_data)
# Fit perfusion tensor to perfusion-weighted data:
perfusion_data = self.mask_data[:, self.perfusion_idx]
self.perfusion_fit = self.perfusion_model.fit(perfusion_data)
# Pre-allocate parameters
#model_params = np.zeros((self.mask_data.shape[0], 13))
voxel_indices = np.arange(self.mask_data.shape[0])
if self.n_threads > 1:
# Loop over voxels:
vox_chunks = np.array_split(voxel_indices, self.n_threads)
with ThreadPoolExecutor(max_workers=self.n_threads) as executor:
loop = asyncio.new_event_loop()
tasks = [
loop.run_in_executor(
executor,
self._inner_loop,
vox_chunk,
) for vox_chunk in vox_chunks
]
try:
model_params = np.concatenate(
list(
tqdm(
loop.run_until_complete(
asyncio.gather(*tasks)))))
finally:
loop.close()
else:
model_params = self._inner_loop(voxel_indices)
return IvimTensorFit(self, model_params)
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
mask=mask,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
"""
For the tracking part, we will use the fiber directions from the ``csd_model``
but stop tracking in areas where fractional anisotropy (FA) is low (< 0.1).
To derive the FA, used here as a stopping criterion, we would need to fit a
tensor model first. Here, we fit the Tensor using weighted least squares (WLS).
"""
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(data, mask)
FA = fractional_anisotropy(tensor_fit.evals)
"""
In order for the stopping values to be used with our tracking algorithm we need
to have the same dimensions as the ``csd_peaks.peak_values``. For this reason,
we can assign the same FA value to every peak direction in the same voxel in
the following way.
"""
stopping_values = np.zeros(csd_peaks.peak_values.shape)
stopping_values[:] = FA[..., None]
"""
def auto_response(gtab,
data,
roi_center=None,
roi_radius=10,
fa_thr=0.7,
fa_callable=fa_superior,
return_number_of_voxels=False):
""" Automatic estimation of response function using FA.
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data
roi_center : tuple, (3,)
Center of ROI in data. If center is None, it is assumed that it is
the center of the volume with shape `data.shape[:3]`.
roi_radius : int
radius of cubic ROI
fa_thr : float
FA threshold
fa_callable : callable
A callable that defines an operation that compares FA with the fa_thr.
The operator should have two positional arguments
(e.g., `fa_operator(FA, fa_thr)`) and it should return a bool array.
return_number_of_voxels : bool
If True, returns the number of voxels used for estimating the response
function.
Returns
-------
response : tuple, (2,)
(`evals`, `S0`)
ratio : float
The ratio between smallest versus largest eigenvalue of the response.
number of voxels : int (optional)
The number of voxels used for estimating the response function.
Notes
-----
In CSD there is an important pre-processing step: the estimation of the
fiber response function. In order to do this we look for voxels with very
anisotropic configurations. For example we can use an ROI (20x20x20) at
the center of the volume and store the signal values for the voxels with
FA values higher than 0.7. Of course, if we haven't precalculated FA we
need to fit a Tensor model to the datasets. Which is what we do in this
function.
For the response we also need to find the average S0 in the ROI. This is
possible using `gtab.b0s_mask()` we can find all the S0 volumes (which
correspond to b-values equal 0) in the dataset.
The `response` consists always of a prolate tensor created by averaging
the highest and second highest eigenvalues in the ROI with FA higher than
threshold. We also include the average S0s.
We also return the `ratio` which is used for the SDT models. If requested,
the number of voxels used for estimating the response function is also
returned, which can be used to judge the fidelity of the response function.
As a rule of thumb, at least 300 voxels should be used to estimate a good
response function (see [1]_).
References
----------
.. [1] Tournier, J.D., et al. NeuroImage 2004. Direct estimation of the
fiber orientation density function from diffusion-weighted MRI
data using spherical deconvolution
"""
ten = TensorModel(gtab)
if roi_center is None:
ci, cj, ck = np.array(data.shape[:3]) // 2
else:
ci, cj, ck = roi_center
w = roi_radius
roi = data[int(ci - w):int(ci + w),
int(cj - w):int(cj + w),
int(ck - w):int(ck + w)]
tenfit = ten.fit(roi)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
indices = np.where(fa_callable(FA, fa_thr))
if indices[0].size == 0:
msg = "No voxel with a FA higher than " + str(fa_thr) + " were found."
msg += " Try a larger roi or a lower threshold."
warnings.warn(msg, UserWarning)
lambdas = tenfit.evals[indices][:, :2]
S0s = roi[indices][:, np.nonzero(gtab.b0s_mask)[0]]
response, ratio = _get_response(S0s, lambdas)
if return_number_of_voxels:
return response, ratio, indices[0].size
return response, ratio
# Brent look at Aman's PR and call here
pass
if rec_model == 'CSD':
# Elef add CSD version and add MTMSCSD when is ready.
pass
pam = peaks_from_model(model,
data,
sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=mask,
parallel=parallel)
ten_model = TensorModel(gtab)
fa = ten_model.fit(data, mask).fa
save_nifti(ffa, fa, affine)
save_peaks(fpam5, pam, affine)
show_odfs_and_fa(fa, pam, mask, None, sphere, ftmp='odf.mmap', basis_type=None)
pve_csf, pve_gm, pve_wm = pve[..., 0], pve[..., 1], pve[..., 2]
cmc_classifier = CmcTissueClassifier.from_pve(
pve_wm,
pve_gm,
pve_csf,
step_size=step_size,
average_voxel_size=np.average(vox_size))
def _run_interface(self, runtime):
from scipy.special import gamma
from dipy.reconst.dti import TensorModel
import gc
img = nb.load(self.inputs.in_file)
hdr = img.get_header().copy()
affine = img.get_affine()
data = img.get_data()
gtab = self._get_gradient_table()
if isdefined(self.inputs.in_mask):
msk = nb.load(self.inputs.in_mask).get_data().astype(np.uint8)
else:
msk = np.ones(data.shape[:3], dtype=np.uint8)
try_b0 = True
if isdefined(self.inputs.noise_mask):
noise_msk = nb.load(self.inputs.noise_mask).get_data().reshape(-1)
noise_msk[noise_msk > 0.5] = 1
noise_msk[noise_msk < 1.0] = 0
noise_msk = noise_msk.astype(np.uint8)
try_b0 = False
elif np.all(data[msk == 0, 0] == 0):
IFLOGGER.info('Input data are masked.')
noise_msk = msk.reshape(-1).astype(np.uint8)
else:
noise_msk = (1 - msk).reshape(-1).astype(np.uint8)
nb0 = np.sum(gtab.b0s_mask)
dsample = data.reshape(-1, data.shape[-1])
if try_b0 and (nb0 > 1):
noise_data = dsample.take(np.where(gtab.b0s_mask),
axis=-1)[noise_msk == 0, ...]
n = nb0
else:
nodiff = np.where(~gtab.b0s_mask)
nodiffidx = nodiff[0].tolist()
n = 20 if len(nodiffidx) >= 20 else len(nodiffidx)
idxs = np.random.choice(nodiffidx, size=n, replace=False)
noise_data = dsample.take(idxs, axis=-1)[noise_msk == 1, ...]
# Estimate sigma required by RESTORE
mean_std = np.median(noise_data.std(-1))
try:
bias = (1. - np.sqrt(2. / (n - 1)) *
(gamma(n / 2.) / gamma((n - 1) / 2.)))
except:
bias = .0
pass
sigma = mean_std * (1 + bias)
if sigma == 0:
IFLOGGER.warn(
('Noise std is 0.0, looks like data was masked and noise'
' cannot be estimated correctly. Using default tensor '
'model instead of RESTORE.'))
dti = TensorModel(gtab)
else:
IFLOGGER.info(('Performing RESTORE with noise std=%.4f.') % sigma)
dti = TensorModel(gtab, fit_method='RESTORE', sigma=sigma)
try:
fit_restore = dti.fit(data, msk)
except TypeError:
dti = TensorModel(gtab)
fit_restore = dti.fit(data, msk)
hdr.set_data_dtype(np.float32)
hdr['data_type'] = 16
for k in self._outputs().get():
scalar = getattr(fit_restore, k)
hdr.set_data_shape(np.shape(scalar))
nb.Nifti1Image(scalar.astype(np.float32),
affine, hdr).to_filename(self._gen_filename(k))
return runtime
def compute_tensors(self, dti_vol, atlas_file, gtab):
# WGR:TODO figure out how to organize tensor options and formats
# WGR:TODO figure out how to deal with files on disk vs. in workspace
"""
Takes registered DTI image and produces tensors
**Positional Arguments:**
dti_vol:
- Registered DTI volume, from workspace.
atlas_file:
- File containing an atlas (or brain mask).
gtab:
- Structure containing dipy formatted bval/bvec information
"""
labeldata = nib.load(atlas_file)
label = labeldata.get_data()
"""
Create a brain mask. Here we just threshold labels.
"""
mask = (label > 0)
gtab.info
print data.shape
"""
For the constrained spherical deconvolution we need to estimate the
response function (see :ref:`example_reconst_csd`) and create a model.
"""
response, ratio = auto_response(gtab, dti_vol, roi_radius=10,
fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
"""
Next, we use ``peaks_from_model`` to fit the data and calculated
the fiber directions in all voxels.
"""
sphere = get_sphere('symmetric724')
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
mask=mask,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
"""
For the tracking part, we will use ``csd_model`` fiber directions
but stop tracking where fractional anisotropy (FA) is low (< 0.1).
To derive the FA, used as a stopping criterion, we need to fit a
tensor model first. Here, we use weighted least squares (WLS).
"""
print 'tensors...'
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(data, mask)
FA = fractional_anisotropy(tensor_fit.evals)
"""
In order for the stopping values to be used with our tracking
algorithm we need to have the same dimensions as the
``csd_peaks.peak_values``. For this reason, we can assign the
same FA value to every peak direction in the same voxel in
the following way.
"""
stopping_values = np.zeros(csd_peaks.peak_values.shape)
stopping_values[:] = FA[..., None]
print datetime.now() - startTime
pass
def compute_tensors(self, dti_vol, atlas_file, gtab):
# WGR:TODO figure out how to organize tensor options and formats
# WGR:TODO figure out how to deal with files on disk vs. in workspace
"""
Takes registered DTI image and produces tensors
**Positional Arguments:**
dti_vol:
- Registered DTI volume, from workspace.
atlas_file:
- File containing an atlas (or brain mask).
gtab:
- Structure containing dipy formatted bval/bvec information
"""
labeldata = nib.load(atlas_file)
label = labeldata.get_data()
"""
Create a brain mask. Here we just threshold labels.
"""
mask = (label > 0)
gtab.info
print data.shape
"""
For the constrained spherical deconvolution we need to estimate the
response function (see :ref:`example_reconst_csd`) and create a model.
"""
response, ratio = auto_response(gtab,
dti_vol,
roi_radius=10,
fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
"""
Next, we use ``peaks_from_model`` to fit the data and calculated
the fiber directions in all voxels.
"""
sphere = get_sphere('symmetric724')
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
mask=mask,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
"""
For the tracking part, we will use ``csd_model`` fiber directions
but stop tracking where fractional anisotropy (FA) is low (< 0.1).
To derive the FA, used as a stopping criterion, we need to fit a
tensor model first. Here, we use weighted least squares (WLS).
"""
print 'tensors...'
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(data, mask)
FA = fractional_anisotropy(tensor_fit.evals)
"""
In order for the stopping values to be used with our tracking
algorithm we need to have the same dimensions as the
``csd_peaks.peak_values``. For this reason, we can assign the
same FA value to every peak direction in the same voxel in
the following way.
"""
stopping_values = np.zeros(csd_peaks.peak_values.shape)
stopping_values[:] = FA[..., None]
print datetime.now() - startTime
pass
def eudx_advanced(self, dti_file, mask_file, gtab,
seed_num=100000, stop_val=0.1):
"""
Tracking with more complex tensors - experimental
Initializes the graph with nodes corresponding to the number of ROIs
**Positional Arguments:**
dti_file:
- File (registered) to use for tensor/fiber tracking
mask_file:
- Brain mask to keep tensors inside the brain
gtab:
- dipy formatted bval/bvec Structure
**Optional Arguments:**
seed_num:
- Number of seeds to use for fiber tracking
stop_val:
- Value to cutoff fiber track
"""
img = nb.load(dti_file)
data = img.get_data()
img = nb.load(mask_file)
mask = img.get_data()
mask = mask > 0 # to ensure binary mask
"""
For the constrained spherical deconvolution we need to estimate the
response function (see :ref:`example_reconst_csd`) and create a model.
"""
response, ratio = auto_response(gtab, data, roi_radius=10,
fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
"""
Next, we use ``peaks_from_model`` to fit the data and calculated
the fiber directions in all voxels.
"""
sphere = get_sphere('symmetric724')
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
mask=mask,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
"""
For the tracking part, we will use ``csd_model`` fiber directions
but stop tracking where fractional anisotropy (FA) is low (< 0.1).
To derive the FA, used as a stopping criterion, we need to fit a
tensor model first. Here, we use weighted least squares (WLS).
"""
print 'tensors...'
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(data, mask)
FA = fractional_anisotropy(tensor_fit.evals)
"""
In order for the stopping values to be used with our tracking
algorithm we need to have the same dimensions as the
``csd_peaks.peak_values``. For this reason, we can assign the
same FA value to every peak direction in the same voxel in
the following way.
"""
stopping_values = np.zeros(csd_peaks.peak_values.shape)
stopping_values[:] = FA[..., None]
streamline_generator = EuDX(stopping_values,
csd_peaks.peak_indices,
seeds=seed_num,
odf_vertices=sphere.vertices,
a_low=stop_val)
streamlines = [streamline for streamline in streamline_generator]
return streamlines
# Correct flipping issue
bvecs = np.c_[bvecs[:, 0], bvecs[:, 1], -bvecs[:, 2]]
gtab = gradient_table(bvals, bvecs)
data, affine, vox_size = load_nifti(fdwi, return_voxsize=True)
# Build Brain Mask
bm = np.where(labels == 0, False, True)
mask = bm
sphere = get_sphere('repulsion724')
from dipy.reconst.dti import TensorModel
tensor_model = TensorModel(gtab)
t1 = time()
tensor_fit = tensor_model.fit(data, mask)
# save_nifti('bmfa.nii.gz', tensor_fit.fa, affine)
# wenlin make this change-adress name to each animal
save_nifti(outpath + 'bmfa' + runno + '.nii.gz', tensor_fit.fa, affine)
fa = tensor_fit.fa
duration1 = time() - t1
#wenlin make this change-adress name to each animal
# print('DTI duration %.3f' % (duration1,))
print(runno + ' DTI duration %.3f' % (duration1, ))
# Compute odfs in Brain Mask
t2 = time()
import nibabel as nib
img = nib.load('t0.nii.gz')
data = img.get_data()
print('data.shape (%d, %d, %d, %d)' % data.shape)
mask = data[..., 0] > 50
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
from dipy.reconst.dti import TensorModel
ten = TensorModel(gtab)
tenfit = ten.fit(data,mask)
from dipy.reconst.dti import fractional_anisotropy
fa = fractional_anisotropy(tenfit.evals)
fa[np.isnan(fa)] = 0
from dipy.reconst.dti import color_fa
Rgbv = color_fa(fa, tenfit.evecs)
fa = np.clip(fa, 0,1)
#save FA to image
nib.save(nib.Nifti1Image(np.array(255*Rgbv,'uint8'),img.get_affine()),'tensor_rgb.nii.gz')
def mask_for_response_ssst(gtab,
data,
roi_center=None,
roi_radii=10,
fa_thr=0.7):
""" Computation of mask for single-shell single-tissue (ssst) response
function using FA.
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data (4D)
roi_center : array-like, (3,)
Center of ROI in data. If center is None, it is assumed that it is
the center of the volume with shape `data.shape[:3]`.
roi_radii : int or array-like, (3,)
radii of cuboid ROI
fa_thr : float
FA threshold
Returns
-------
mask : ndarray
Mask of voxels within the ROI and with FA above the FA threshold.
Notes
-----
In CSD there is an important pre-processing step: the estimation of the
fiber response function. In order to do this, we look for voxels with very
anisotropic configurations. This function aims to accomplish that by
returning a mask of voxels within a ROI, that have a FA value above a
given threshold. For example we can use a ROI (20x20x20) at
the center of the volume and store the signal values for the voxels with
FA values higher than 0.7 (see [1]_).
References
----------
.. [1] Tournier, J.D., et al. NeuroImage 2004. Direct estimation of the
fiber orientation density function from diffusion-weighted MRI
data using spherical deconvolution
"""
if len(data.shape) < 4:
msg = """Data must be 4D (3D image + directions). To use a 2D image,
please reshape it into a (N, N, 1, ndirs) array."""
raise ValueError(msg)
if isinstance(roi_radii, numbers.Number):
roi_radii = (roi_radii, roi_radii, roi_radii)
if roi_center is None:
roi_center = np.array(data.shape[:3]) // 2
roi_radii = _roi_in_volume(data.shape, np.asarray(roi_center),
np.asarray(roi_radii))
roi_mask = _mask_from_roi(data.shape[:3], roi_center, roi_radii)
ten = TensorModel(gtab)
tenfit = ten.fit(data, mask=roi_mask)
fa = fractional_anisotropy(tenfit.evals)
fa[np.isnan(fa)] = 0
mask = np.zeros(fa.shape, dtype=np.int64)
mask[fa > fa_thr] = 1
if np.sum(mask) == 0:
msg = """No voxel with a FA higher than {} were found.
Try a larger roi or a lower threshold.""".format(str(fa_thr))
warnings.warn(msg, UserWarning)
return mask
def processDiffusion(file, ds=False, ec=False, bvs=None):
'''
Process a diffusion-weighted dataset.
file=filename of Analyze or Nifti file (without extension)
bvs = list of b-values (optional)
ec = Whether or not eddy current correction should be applied (takes a while,
and does not work inside Spyder IDE but only from command line)
ds = Whether or not the image should be downsampled to an isotropic voxel size
2D images should be formatted as (x,y,t,z) and 3D images as (x,y,z,t)
which is standard for Bruker files.
This protocol automatically determines how many diffusion
dirs there are and how many b-values according to what is saved in the
accompanying text file. You can provide a list of exact b-values, but if
you do not the program will calculate mean b-values for each cluster of
diffusion directions based on the text file.
'''
dims = list_values(read_line('VisuCoreSize=', file))
ext = checkFileType(file)
img = nib.load(file + ext)
data = img.get_data()
affine = img.get_affine()
bvals, avbvals, dwgrad, dwdir, nA0, nbvals, ndirs = getDiffusionPars(file)
if len(dims) == 2:
#2D arrays are arranged differently. scipy.swapaxes is not sufficient for
#Paravision's Fortran-style column-major ordering as the t-axis is ordered differently.
newshape = (data.shape[0], data.shape[1], data.shape[3], data.shape[2])
print '2D array with shape %r. Reshaping to %r in Fortran-style column major.' % (
data.shape, newshape)
data = np.reshape(data, newshape, order='F')
rescaleImage(file, data, nbvals, dims)
img = nib.Nifti1Image(data, affine)
if ds:
print "Voxel size nonisotropic. Downsampling..."
data, affine = downsampleImage(img)
img = nib.Nifti1Image(data, affine)
else:
affine = img.get_affine()
data = img.get_data()
thresh = np.mean(data[:5, :5, :, 0])
mask = data[..., 0] > 2.5 * thresh
for i in range(data.shape[3]):
data[:, :, :, i] *= mask
if ec:
starttime = datetime.now()
print "Applying eddy current correction."
img = eddyCorrection(img, file + '_Eddy.nii')
data = img.get_data()
affine = img.get_affine()
time = datetime.now() - starttime
print "Eddy current correction completed in %r seconds." % time.seconds
if bvs == None:
bvalmat = np.array(avbvals)
bvalmat[bvalmat < 10] = 0
else:
bvalmat = np.zeros([nA0 + (ndirs * len(bvs))]) #entered pars
for i, b in enumerate(
bvs
): #unfortunately the ideal b-vals(not effective b-vals) are not in the text file. Have to enter manually and convert to appropriate matrix
bvalmat[nA0 + ndirs * i:] = b
bvecmat = np.zeros([nA0 + ndirs * nbvals, 3])
for i in range(nbvals):
bvecmat[nA0 + ndirs * i:nA0 + ndirs * (
i + 1
), :] = dwdir #fills b-vector matrix with the different diffusion dirs
if len(bvecmat) != len(bvals):
print "Error. Cannot process this image."
print bvalmat.shape
print dwgrad.shape
gtab = gradient_table(
bvalmat, bvecmat
) #creates a gradient table with b-vals and diffusion dirs for processing
from dipy.reconst.dti import TensorModel
starttime = datetime.now()
print "Fitting tensor model."
ten = TensorModel(gtab)
tenfit = ten.fit(data, mask)
time = datetime.now() - starttime
print "Tensor fit completed in %r seconds." % time.seconds
from dipy.reconst.dti import fractional_anisotropy
evecs = tenfit.evecs #eigenvectors
fa = fractional_anisotropy(tenfit.evals)
fa = np.clip(
fa, 0, 1) #removes voxels where fit failed by thresholding at 0 and 1
md = tenfit.md
md[np.isnan(md)] = 0 #removes voxels where fit failed
print "Calculated eigenvectors, MD and FA."
from dipy.reconst.dti import color_fa
cfa = color_fa(fa, tenfit.evecs)
return tenfit, cfa, bvalmat, dwgrad, bvecmat
def test_eudx_further():
""" Cause we love testin.. ;-)
"""
fimg, fbvals, fbvecs = get_data('small_101D')
img = ni.load(fimg)
data = img.get_data()
gtab = gradient_table(fbvals, fbvecs)
tensor_model = TensorModel(gtab)
ten = tensor_model.fit(data)
x, y, z = data.shape[:3]
seeds = np.zeros((10**4, 3))
for i in range(10**4):
rx = (x - 1) * np.random.rand()
ry = (y - 1) * np.random.rand()
rz = (z - 1) * np.random.rand()
seeds[i] = np.ascontiguousarray(np.array([rx, ry, rz]),
dtype=np.float64)
sphere = get_sphere('symmetric724')
ind = quantize_evecs(ten.evecs)
eu = EuDX(a=ten.fa,
ind=ind,
seeds=seeds,
odf_vertices=sphere.vertices,
a_low=.2)
T = [e for e in eu]
# check that there are no negative elements
for t in T:
assert_equal(np.sum(t.ravel() < 0), 0)
# Test eudx with affine
def random_affine(seeds):
affine = np.eye(4)
affine[:3, :] = np.random.random((3, 4))
seeds = np.dot(seeds, affine[:3, :3].T)
seeds += affine[:3, 3]
return affine, seeds
# Make two random affines and move seeds
affine1, seeds1 = random_affine(seeds)
affine2, seeds2 = random_affine(seeds)
# Make tracks using different affines
eu1 = EuDX(a=ten.fa,
ind=ind,
odf_vertices=sphere.vertices,
seeds=seeds1,
a_low=.2,
affine=affine1)
eu2 = EuDX(a=ten.fa,
ind=ind,
odf_vertices=sphere.vertices,
seeds=seeds2,
a_low=.2,
affine=affine2)
# Move from eu2 affine2 to affine1
eu2_to_eu1 = utils.move_streamlines(eu2,
output_space=affine1,
input_space=affine2)
# Check that the tracks are the same
for sl1, sl2 in zip(eu1, eu2_to_eu1):
assert_array_almost_equal(sl1, sl2)
def test_wls_and_ls_fit():
"""
Tests the WLS and LS fitting functions to see if they returns the correct
eigenvalues and eigenvectors.
Uses data/55dir_grad.bvec as the gradient table and 3by3by56.nii
as the data.
"""
# Defining Test Voxel (avoid nibabel dependency) ###
# Recall: D = [Dxx,Dyy,Dzz,Dxy,Dxz,Dyz,log(S_0)] and D ~ 10^-4 mm^2 /s
b0 = 1000.
bvec, bval = read_bvec_file(get_data('55dir_grad.bvec'))
B = bval[1]
# Scale the eigenvalues and tensor by the B value so the units match
D = np.array([1., 1., 1., 0., 0., 1., -np.log(b0) * B]) / B
evals = np.array([2., 1., 0.]) / B
md = evals.mean()
tensor = from_lower_triangular(D)
# Design Matrix
gtab = grad.gradient_table(bval, bvec)
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1, ) + Y.shape
# Testing WLS Fit on Single Voxel
# If you do something wonky (passing min_signal<0), you should get an
# error:
npt.assert_raises(ValueError,
TensorModel,
gtab,
fit_method='WLS',
min_signal=-1)
# Estimate tensor from test signals
model = TensorModel(gtab, fit_method='WLS', return_S0_hat=True)
tensor_est = model.fit(Y)
assert_equal(tensor_est.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_est.evals[0], evals)
assert_array_almost_equal(tensor_est.quadratic_form[0],
tensor,
err_msg="Calculation of tensor from Y does not "
"compare to analytical solution")
assert_almost_equal(tensor_est.md[0], md)
assert_array_almost_equal(tensor_est.S0_hat[0], b0, decimal=3)
# Test that we can fit a single voxel's worth of data (a 1d array)
y = Y[0]
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
# Test using fit_method='LS'
model = TensorModel(gtab, fit_method='LS')
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
assert_array_almost_equal(tensor_est.linearity, linearity(evals))
assert_array_almost_equal(tensor_est.planarity, planarity(evals))
assert_array_almost_equal(tensor_est.sphericity, sphericity(evals))
if fmask is None:
from dipy.segment.mask import median_otsu
b0_mask, mask = median_otsu(
data) # TODO: check parameters to improve the mask
else:
mask, mask_affine = load_nifti(fmask)
mask = np.squeeze(mask) #fix mask dimensions
# ### DTI Model computation and fitting (further for CSD--not tested)
# In[33]:
# compute DTI model
from dipy.reconst.dti import TensorModel
tenmodel = TensorModel(gtab) #, fit_method='OLS') #, min_signal=5000)
# In[34]:
# fit the dti model
tenfit = tenmodel.fit(data, mask=mask)
# ### DWI indicators computation and saving in nifti files (FA, first eigen vector, rgb tensor)
# In[35]:
# save fa
ffa = dname + 'tensor_fa.nii.gz'
fa_img = nib.Nifti1Image(tenfit.fa.astype(np.float32), affine)
nib.save(fa_img, ffa)
print 'fitting with dti' data, affine, gtab = get_train_dti(30) elif datat == 1: print 'fitting with hardi' data, affine, gtab = get_train_hardi(30) elif datat == 2: print 'fitting with dsi' data, affine, gtab = get_train_dsi(30) mask, affine = get_train_mask() data.shape mask.shape model = TensorModel(gtab) fit = model.fit(data, mask) print 'done!' fa = fit.fa slice_z = 25 Th = [0.05, 0.075, 0.1,0.15] figure(2*datat+1) imshow(fa[:, :, slice_z], interpolation='nearest') colorbar() title(mask.sum()) figure(2*datat + 2)
from dipy.io.image import load_nifti, save_nifti
from dipy.io import read_bvals_bvecs
from dipy.core.gradients import gradient_table
from dipy.reconst.dti import TensorModel
fdwi = 'dwidata.nii.gz'
fbval = 'bvals'
fbvec = 'bvecs'
mask = load_nifti('mask.nii.gz')
data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data)
fwhm = 1.25
gauss_std = fwhm / np.sqrt(8 * np.log(2)) # converting fwhm to Gaussian std
data_smooth = np.zeros(data.shape)
for v in range(data.shape[-1]):
data_smooth[..., v] = gaussian_filter(data[..., v], sigma=gauss_std)
dkimodel = dki.DiffusionKurtosisModel(gtab)
dkifit = dkimodel.fit(data_smooth, mask=mask[0])
FA = dkifit.fa
MD = dkifit.md
AD = dkifit.ad
import nibabel as nib
img = nib.load('t0.nii.gz')
data = img.get_data()
print('data.shape (%d, %d, %d, %d)' % data.shape)
mask = data[..., 0] > 50
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
from dipy.reconst.dti import TensorModel
ten = TensorModel(gtab)
tenfit = ten.fit(data, mask)
from dipy.reconst.dti import fractional_anisotropy
fa = fractional_anisotropy(tenfit.evals)
fa[np.isnan(fa)] = 0
from dipy.reconst.dti import color_fa
Rgbv = color_fa(fa, tenfit.evecs)
fa = np.clip(fa, 0, 1)
#save FA to image
nib.save(nib.Nifti1Image(np.array(255 * Rgbv, 'uint8'), img.get_affine()),
'tensor_rgb.nii.gz')
def get_tensor_model(self, gtab):
return TensorModel(gtab, fit_method="WLS")
def dwi_dipy_run(dwi_dir,
node_size,
dir_path,
conn_model,
parc,
atlas_select,
network,
wm_mask=None):
from dipy.reconst.dti import TensorModel, quantize_evecs
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel, recursive_response
from dipy.tracking.local import LocalTracking, ActTissueClassifier
from dipy.tracking import utils
from dipy.direction import peaks_from_model
from dipy.tracking.eudx import EuDX
from dipy.data import get_sphere, default_sphere
from dipy.core.gradients import gradient_table
from dipy.io import read_bvals_bvecs
from dipy.tracking.streamline import Streamlines
from dipy.direction import ProbabilisticDirectionGetter, ClosestPeakDirectionGetter, BootDirectionGetter
from nibabel.streamlines import save as save_trk
from nibabel.streamlines import Tractogram
##
dwi_dir = '/Users/PSYC-dap3463/Downloads/bedpostx_s002'
img_pve_csf = nib.load(
'/Users/PSYC-dap3463/Downloads/002_all/tmp/reg_a/t1w_vent_csf_diff_dwi.nii.gz'
)
img_pve_wm = nib.load(
'/Users/PSYC-dap3463/Downloads/002_all/tmp/reg_a/t1w_wm_in_dwi_bin.nii.gz'
)
img_pve_gm = nib.load(
'/Users/PSYC-dap3463/Downloads/002_all/tmp/reg_a/t1w_gm_mask_dwi.nii.gz'
)
labels_img = nib.load(
'/Users/PSYC-dap3463/Downloads/002_all/tmp/reg_a/dwi_aligned_atlas.nii.gz'
)
num_total_samples = 10000
tracking_method = 'boot' # Options are 'boot', 'prob', 'peaks', 'closest'
procmem = [2, 4]
##
if parc is True:
node_size = 'parc'
dwi_img = "%s%s" % (dwi_dir, '/dwi.nii.gz')
nodif_brain_mask_path = "%s%s" % (dwi_dir, '/nodif_brain_mask.nii.gz')
bvals = "%s%s" % (dwi_dir, '/bval')
bvecs = "%s%s" % (dwi_dir, '/bvec')
dwi_img = nib.load(dwi_img)
data = dwi_img.get_data()
[bvals, bvecs] = read_bvals_bvecs(bvals, bvecs)
gtab = gradient_table(bvals, bvecs)
gtab.b0_threshold = min(bvals)
sphere = get_sphere('symmetric724')
# Loads mask and ensures it's a true binary mask
mask_img = nib.load(nodif_brain_mask_path)
mask = mask_img.get_data()
mask = mask > 0
# Fit a basic tensor model first
model = TensorModel(gtab)
ten = model.fit(data, mask)
fa = ten.fa
# Tractography
if conn_model == 'csd':
print('Tracking with csd model...')
elif conn_model == 'tensor':
print('Tracking with tensor model...')
else:
raise RuntimeError("%s%s" % (conn_model, ' is not a valid model.'))
# Combine seed counts from voxel with seed counts total
wm_mask_data = img_pve_wm.get_data()
wm_mask_data[0, :, :] = False
wm_mask_data[:, 0, :] = False
wm_mask_data[:, :, 0] = False
seeds = utils.seeds_from_mask(wm_mask_data,
density=1,
affine=dwi_img.get_affine())
seeds_rnd = utils.random_seeds_from_mask(ten.fa > 0.02,
seeds_count=num_total_samples,
seed_count_per_voxel=True)
seeds_all = np.vstack([seeds, seeds_rnd])
# Load tissue maps and prepare tissue classifier (Anatomically-Constrained Tractography (ACT))
background = np.ones(img_pve_gm.shape)
background[(img_pve_gm.get_data() + img_pve_wm.get_data() +
img_pve_csf.get_data()) > 0] = 0
include_map = img_pve_gm.get_data()
include_map[background > 0] = 1
exclude_map = img_pve_csf.get_data()
act_classifier = ActTissueClassifier(include_map, exclude_map)
if conn_model == 'tensor':
ind = quantize_evecs(ten.evecs, sphere.vertices)
streamline_generator = EuDX(a=fa,
ind=ind,
seeds=seeds_all,
odf_vertices=sphere.vertices,
a_low=0.05,
step_sz=.5)
elif conn_model == 'csd':
print('Tracking with CSD model...')
response = recursive_response(
gtab,
data,
mask=img_pve_wm.get_data().astype('bool'),
sh_order=8,
peak_thr=0.01,
init_fa=0.05,
init_trace=0.0021,
iter=8,
convergence=0.001,
parallel=True)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
if tracking_method == 'boot':
dg = BootDirectionGetter.from_data(data,
csd_model,
max_angle=30.,
sphere=default_sphere)
elif tracking_method == 'prob':
try:
print(
'First attempting to build the direction getter directly from the spherical harmonic representation of the FOD...'
)
csd_fit = csd_model.fit(
data, mask=img_pve_wm.get_data().astype('bool'))
dg = ProbabilisticDirectionGetter.from_shcoeff(
csd_fit.shm_coeff, max_angle=30., sphere=default_sphere)
except:
print(
'Sphereical harmonic not available for this model. Using peaks_from_model to represent the ODF of the model on a spherical harmonic basis instead...'
)
peaks = peaks_from_model(
csd_model,
data,
default_sphere,
.5,
25,
mask=img_pve_wm.get_data().astype('bool'),
return_sh=True,
parallel=True,
nbr_processes=procmem[0])
dg = ProbabilisticDirectionGetter.from_shcoeff(
peaks.shm_coeff, max_angle=30., sphere=default_sphere)
elif tracking_method == 'peaks':
dg = peaks_from_model(model=csd_model,
data=data,
sphere=default_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=img_pve_wm.get_data().astype('bool'),
parallel=True,
nbr_processes=procmem[0])
elif tracking_method == 'closest':
csd_fit = csd_model.fit(data,
mask=img_pve_wm.get_data().astype('bool'))
pmf = csd_fit.odf(default_sphere).clip(min=0)
dg = ClosestPeakDirectionGetter.from_pmf(pmf,
max_angle=30.,
sphere=default_sphere)
streamline_generator = LocalTracking(dg,
act_classifier,
seeds_all,
affine=dwi_img.affine,
step_size=0.5)
del dg
try:
del csd_fit
except:
pass
try:
del response
except:
pass
try:
del csd_model
except:
pass
streamlines = Streamlines(streamline_generator, buffer_size=512)
save_trk(Tractogram(streamlines, affine_to_rasmm=dwi_img.affine),
'prob_streamlines.trk')
tracks = [sl for sl in streamlines if len(sl) > 1]
labels_data = labels_img.get_data().astype('int')
labels_affine = labels_img.affine
conn_matrix, grouping = utils.connectivity_matrix(
tracks,
labels_data,
affine=labels_affine,
return_mapping=True,
mapping_as_streamlines=True,
symmetric=True)
conn_matrix[:3, :] = 0
conn_matrix[:, :3] = 0
return conn_matrix
def mask_for_response_msmt(gtab, data, roi_center=None, roi_radii=10,
wm_fa_thr=0.7, gm_fa_thr=0.2, csf_fa_thr=0.1,
gm_md_thr=0.0007, csf_md_thr=0.002):
""" Computation of masks for multi-shell multi-tissue (msmt) response
function using FA and MD.
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data (4D)
roi_center : array-like, (3,)
Center of ROI in data. If center is None, it is assumed that it is
the center of the volume with shape `data.shape[:3]`.
roi_radii : int or array-like, (3,)
radii of cuboid ROI
wm_fa_thr : float
FA threshold for WM.
gm_fa_thr : float
FA threshold for GM.
csf_fa_thr : float
FA threshold for CSF.
gm_md_thr : float
MD threshold for GM.
csf_md_thr : float
MD threshold for CSF.
Returns
-------
mask_wm : ndarray
Mask of voxels within the ROI and with FA above the FA threshold
for WM.
mask_gm : ndarray
Mask of voxels within the ROI and with FA below the FA threshold
for GM and with MD below the MD threshold for GM.
mask_csf : ndarray
Mask of voxels within the ROI and with FA below the FA threshold
for CSF and with MD below the MD threshold for CSF.
Notes
-----
In msmt-CSD there is an important pre-processing step: the estimation of
every tissue's response function. In order to do this, we look for voxels
corresponding to WM, GM and CSF. This function aims to accomplish that by
returning a mask of voxels within a ROI and who respect some threshold
constraints, for each tissue. More precisely, the WM mask must have a FA
value above a given threshold. The GM mask and CSF mask must have a FA
below given thresholds and a MD below other thresholds. To get the FA and
MD, we need to fit a Tensor model to the datasets.
"""
if len(data.shape) < 4:
msg = """Data must be 4D (3D image + directions). To use a 2D image,
please reshape it into a (N, N, 1, ndirs) array."""
raise ValueError(msg)
if isinstance(roi_radii, numbers.Number):
roi_radii = (roi_radii, roi_radii, roi_radii)
if roi_center is None:
roi_center = np.array(data.shape[:3]) // 2
roi_radii = _roi_in_volume(data.shape, np.asarray(roi_center),
np.asarray(roi_radii))
roi_mask = _mask_from_roi(data.shape[:3], roi_center, roi_radii)
list_bvals = unique_bvals_tolerance(gtab.bvals)
if not np.all(list_bvals <= 1200):
msg_bvals = """Some b-values are higher than 1200.
The DTI fit might be affected."""
warnings.warn(msg_bvals, UserWarning)
ten = TensorModel(gtab)
tenfit = ten.fit(data, mask=roi_mask)
fa = fractional_anisotropy(tenfit.evals)
fa[np.isnan(fa)] = 0
md = mean_diffusivity(tenfit.evals)
md[np.isnan(md)] = 0
mask_wm = np.zeros(fa.shape, dtype=np.int64)
mask_wm[fa > wm_fa_thr] = 1
mask_wm *= roi_mask
md_mask_gm = np.zeros(md.shape, dtype=np.int64)
md_mask_gm[(md < gm_md_thr)] = 1
fa_mask_gm = np.zeros(fa.shape, dtype=np.int64)
fa_mask_gm[(fa < gm_fa_thr) & (fa > 0)] = 1
mask_gm = md_mask_gm * fa_mask_gm
mask_gm *= roi_mask
md_mask_csf = np.zeros(md.shape, dtype=np.int64)
md_mask_csf[(md < csf_md_thr) & (md > 0)] = 1
fa_mask_csf = np.zeros(fa.shape, dtype=np.int64)
fa_mask_csf[(fa < csf_fa_thr) & (fa > 0)] = 1
mask_csf = md_mask_csf * fa_mask_csf
mask_csf *= roi_mask
msg = """No voxel with a {0} than {1} were found.
Try a larger roi or a {2} threshold for {3}."""
if np.sum(mask_wm) == 0:
msg_fa = msg.format('FA higher', str(wm_fa_thr), 'lower FA', 'WM')
warnings.warn(msg_fa, UserWarning)
if np.sum(mask_gm) == 0:
msg_fa = msg.format('FA lower', str(gm_fa_thr), 'higher FA', 'GM')
msg_md = msg.format('MD lower', str(gm_md_thr), 'higher MD', 'GM')
warnings.warn(msg_fa, UserWarning)
warnings.warn(msg_md, UserWarning)
if np.sum(mask_csf) == 0:
msg_fa = msg.format('FA lower', str(csf_fa_thr), 'higher FA', 'CSF')
msg_md = msg.format('MD lower', str(csf_md_thr), 'higher MD', 'CSF')
warnings.warn(msg_fa, UserWarning)
warnings.warn(msg_md, UserWarning)
return mask_wm, mask_gm, mask_csf
def test_recursive_response_calibration():
"""
Test the recursive response calibration method.
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
sphere = default_sphere
gtab = gradient_table(bvals, bvecs)
evals = np.array([0.0015, 0.0003, 0.0003])
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
where_dwi = lazy_index(~gtab.b0s_mask)
S_cross, _ = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
S_single = single_tensor(gtab, S0, evals, evecs, snr=SNR)
data = np.concatenate((np.tile(S_cross, (8, 1)),
np.tile(S_single, (2, 1))),
axis=0)
odf_gt_cross = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odf_gt_single = single_tensor_odf(sphere.vertices, evals, evecs)
response = recursive_response(gtab, data, mask=None, sh_order=8,
peak_thr=0.01, init_fa=0.05,
init_trace=0.0021, iter=8, convergence=0.001,
parallel=False)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(data)
assert_equal(np.all(csd_fit.shm_coeff[:, 0] >= 0), True)
fodf = csd_fit.odf(sphere)
directions_gt_single, _, _ = peak_directions(odf_gt_single, sphere)
directions_gt_cross, _, _ = peak_directions(odf_gt_cross, sphere)
directions_single, _, _ = peak_directions(fodf[8, :], sphere)
directions_cross, _, _ = peak_directions(fodf[0, :], sphere)
ang_sim = angular_similarity(directions_cross, directions_gt_cross)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions_cross.shape[0], 2)
assert_equal(directions_gt_cross.shape[0], 2)
ang_sim = angular_similarity(directions_single, directions_gt_single)
assert_equal(ang_sim > 0.9, True)
assert_equal(directions_single.shape[0], 1)
assert_equal(directions_gt_single.shape[0], 1)
with warnings.catch_warnings(record=True) as w:
sphere = Sphere(xyz=gtab.gradients[where_dwi])
npt.assert_equal(len(w), 1)
npt.assert_(issubclass(w[0].category, UserWarning))
npt.assert_("Vertices are not on the unit sphere" in str(w[0].message))
sf = response.on_sphere(sphere)
S = np.concatenate(([response.S0], sf))
tenmodel = TensorModel(gtab, min_signal=0.001)
tenfit = tenmodel.fit(S)
FA = fractional_anisotropy(tenfit.evals)
FA_gt = fractional_anisotropy(evals)
assert_almost_equal(FA, FA_gt, 1)
def eudx_advanced(self,
dti_file,
mask_file,
gtab,
seed_num=100000,
stop_val=0.1):
"""
Tracking with more complex tensors - experimental
Initializes the graph with nodes corresponding to the number of ROIs
**Positional Arguments:**
dti_file:
- File (registered) to use for tensor/fiber tracking
mask_file:
- Brain mask to keep tensors inside the brain
gtab:
- dipy formatted bval/bvec Structure
**Optional Arguments:**
seed_num:
- Number of seeds to use for fiber tracking
stop_val:
- Value to cutoff fiber track
"""
img = nb.load(dti_file)
data = img.get_data()
img = nb.load(mask_file)
mask = img.get_data()
mask = mask > 0 # to ensure binary mask
"""
For the constrained spherical deconvolution we need to estimate the
response function (see :ref:`example_reconst_csd`) and create a model.
"""
response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
"""
Next, we use ``peaks_from_model`` to fit the data and calculated
the fiber directions in all voxels.
"""
sphere = get_sphere('symmetric724')
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
mask=mask,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
"""
For the tracking part, we will use ``csd_model`` fiber directions
but stop tracking where fractional anisotropy (FA) is low (< 0.1).
To derive the FA, used as a stopping criterion, we need to fit a
tensor model first. Here, we use weighted least squares (WLS).
"""
print 'tensors...'
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(data, mask)
FA = fractional_anisotropy(tensor_fit.evals)
"""
In order for the stopping values to be used with our tracking
algorithm we need to have the same dimensions as the
``csd_peaks.peak_values``. For this reason, we can assign the
same FA value to every peak direction in the same voxel in
the following way.
"""
stopping_values = np.zeros(csd_peaks.peak_values.shape)
stopping_values[:] = FA[..., None]
streamline_generator = EuDX(stopping_values,
csd_peaks.peak_indices,
seeds=seed_num,
odf_vertices=sphere.vertices,
a_low=stop_val)
streamlines = [streamline for streamline in streamline_generator]
return streamlines
from show_streamlines import show_streamlines
from conn_mat import connectivity_matrix
from dipy.io.pickles import save_pickle, load_pickle
from time import time
threshold = 0.75
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
dname = 'SNR20/'
if __name__ == '__main__':
data, affine, gtab = get_test_hardi(snr=20, denoised=0)
mask = get_test_mask()
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
nib.save(nib.Nifti1Image(FA.astype('float32'), affine),
'FA.nii.gz')
for i in range(27) :
print 'White matter bundle: ', i
wm_mask = get_test_wm_mask(i)
print(FA[wm_mask].max())
indicesAniso = np.where(np.logical_and(FA > threshold, wm_mask))
print ' Response function'
S0s = data[indicesAniso][:, np.nonzero(gtab.b0s_mask)[0]]
S0 = np.mean(S0s)
- threshold: float
**Stopping States**
- 'ENDPOINT': stops at a position where metric_map < threshold; the streamline
reached the target stopping area.
- 'OUTSIDEIMAGE': stops at a position outside of metric_map; the streamline
reached an area outside the image where no direction data is available.
- 'TRACKPOINT': stops at a position because no direction is available; the
streamline is stopping where metric_map >= threshold, but there is no valid
direction to follow.
- 'INVALIDPOINT': N/A.
"""
tensor_model = TensorModel(gtab)
tenfit = tensor_model.fit(data, mask=labels > 0)
FA = fractional_anisotropy(tenfit.evals)
threshold_criterion = ThresholdStoppingCriterion(FA, .2)
fig = plt.figure()
mask_fa = FA.copy()
mask_fa[mask_fa < 0.2] = 0
plt.xticks([])
plt.yticks([])
plt.imshow(mask_fa[:, :, data.shape[2] // 2].T, cmap='gray', origin='lower',
interpolation='nearest')
fig.tight_layout()
fig.savefig('threshold_fa.png')