def test_peaks_shm_coeff():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
from dipy.data import get_sphere
sphere = get_sphere('repulsion724')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab,
mevals,
S0,
angles=[(0, 0), (60, 0)],
fractions=[50, 50],
snr=SNR)
from dipy.reconst.shm import CsaOdfModel
model = CsaOdfModel(gtab, 4)
pam = peaks_from_model(model,
data[None, :],
sphere,
.5,
45,
return_odf=True,
return_sh=True)
# Test that spherical harmonic coefficients return back correctly
odf2 = np.dot(pam.shm_coeff, pam.B)
assert_array_almost_equal(pam.odf, odf2)
assert_equal(pam.shm_coeff.shape[-1], 45)
pam = peaks_from_model(model,
data[None, :],
sphere,
.5,
45,
return_odf=True,
return_sh=False)
assert_equal(pam.shm_coeff, None)
pam = peaks_from_model(model,
data[None, :],
sphere,
.5,
45,
return_odf=True,
return_sh=True,
sh_basis_type='mrtrix')
odf2 = np.dot(pam.shm_coeff, pam.B)
assert_array_almost_equal(pam.odf, odf2)
def test_peaksFromModelParallel():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (60, 0)],
fractions=[50, 50], snr=SNR)
# test equality with/without multiprocessing
model = SimpleOdfModel(gtab)
pam_multi = peaks_from_model(model, data, _sphere, .5, 45,
normalize_peaks=True, return_odf=True,
return_sh=True, parallel=True)
pam_single = peaks_from_model(model, data, _sphere, .5, 45,
normalize_peaks=True, return_odf=True,
return_sh=True, parallel=False)
assert_equal(pam_multi.gfa.dtype, pam_single.gfa.dtype)
assert_equal(pam_multi.gfa.shape, pam_single.gfa.shape)
assert_array_almost_equal(pam_multi.gfa, pam_single.gfa)
assert_equal(pam_multi.qa.dtype, pam_single.qa.dtype)
assert_equal(pam_multi.qa.shape, pam_single.qa.shape)
assert_array_almost_equal(pam_multi.qa, pam_single.qa)
assert_equal(pam_multi.peak_values.dtype, pam_single.peak_values.dtype)
assert_equal(pam_multi.peak_values.shape, pam_single.peak_values.shape)
assert_array_almost_equal(pam_multi.peak_values, pam_single.peak_values)
assert_equal(pam_multi.peak_indices.dtype, pam_single.peak_indices.dtype)
assert_equal(pam_multi.peak_indices.shape, pam_single.peak_indices.shape)
assert_array_equal(pam_multi.peak_indices, pam_single.peak_indices)
assert_equal(pam_multi.peak_dirs.dtype, pam_single.peak_dirs.dtype)
assert_equal(pam_multi.peak_dirs.shape, pam_single.peak_dirs.shape)
assert_array_almost_equal(pam_multi.peak_dirs, pam_single.peak_dirs)
assert_equal(pam_multi.shm_coeff.dtype, pam_single.shm_coeff.dtype)
assert_equal(pam_multi.shm_coeff.shape, pam_single.shm_coeff.shape)
assert_array_almost_equal(pam_multi.shm_coeff, pam_single.shm_coeff)
assert_equal(pam_multi.odf.dtype, pam_single.odf.dtype)
assert_equal(pam_multi.odf.shape, pam_single.odf.shape)
assert_array_almost_equal(pam_multi.odf, pam_single.odf)
def _run_interface(self, runtime):
from dipy.reconst import shm
from dipy.data import get_sphere
from dipy.reconst.peaks import peaks_from_model
gtab = self._get_gradient_table()
img = nb.load(self.inputs.in_file)
data = img.get_data()
affine = img.affine
mask = None
if isdefined(self.inputs.mask_file):
mask = nb.load(self.inputs.mask_file).get_data()
# Fit it
model = shm.QballModel(gtab, 8)
sphere = get_sphere('symmetric724')
peaks = peaks_from_model(
model=model,
data=data,
relative_peak_threshold=.5,
min_separation_angle=25,
sphere=sphere,
mask=mask)
apm = shm.anisotropic_power(peaks.shm_coeff)
out_file = self._gen_filename('apm')
nb.Nifti1Image(apm.astype("float32"), affine).to_filename(out_file)
IFLOGGER.info('APM qball image saved as %s', out_file)
return runtime
def _run_interface(self, runtime):
from dipy.reconst import shm
from dipy.data import get_sphere
from dipy.reconst.peaks import peaks_from_model
gtab = self._get_gradient_table()
img = nb.load(self.inputs.in_file)
data = img.get_data()
affine = img.affine
mask = None
if isdefined(self.inputs.mask_file):
mask = nb.load(self.inputs.mask_file).get_data()
# Fit it
model = shm.QballModel(gtab, 8)
sphere = get_sphere('symmetric724')
peaks = peaks_from_model(model=model,
data=data,
relative_peak_threshold=.5,
min_separation_angle=25,
sphere=sphere,
mask=mask)
apm = shm.anisotropic_power(peaks.shm_coeff)
out_file = self._gen_filename('apm')
nb.Nifti1Image(apm.astype("float32"), affine).to_filename(out_file)
IFLOGGER.info('APM qball image saved as %s', out_file)
return runtime
def test_peaksFromModel():
data = np.zeros((10, 2))
# Test basic case
model = SimpleOdfModel(_gtab)
odf_argmax = _odf.argmax()
pam = peaks_from_model(model, data, _sphere, .5, 45, normalize_peaks=True)
assert_array_equal(pam.gfa, gfa(_odf))
assert_array_equal(pam.peak_values[:, 0], 1.)
assert_array_equal(pam.peak_values[:, 1:], 0.)
mn, mx = _odf.min(), _odf.max()
assert_array_equal(pam.qa[:, 0], (mx - mn) / mx)
assert_array_equal(pam.qa[:, 1:], 0.)
assert_array_equal(pam.peak_indices[:, 0], odf_argmax)
assert_array_equal(pam.peak_indices[:, 1:], -1)
# Test that odf array matches and is right shape
pam = peaks_from_model(model, data, _sphere, .5, 45, return_odf=True)
expected_shape = (len(data), len(_odf))
assert_equal(pam.odf.shape, expected_shape)
assert_((_odf == pam.odf).all())
assert_array_equal(pam.peak_values[:, 0], _odf.max())
# Test mask
mask = (np.arange(10) % 2) == 1
pam = peaks_from_model(model,
data,
_sphere,
.5,
45,
mask=mask,
normalize_peaks=True)
assert_array_equal(pam.gfa[~mask], 0)
assert_array_equal(pam.qa[~mask], 0)
assert_array_equal(pam.peak_values[~mask], 0)
assert_array_equal(pam.peak_indices[~mask], -1)
assert_array_equal(pam.gfa[mask], gfa(_odf))
assert_array_equal(pam.peak_values[mask, 0], 1.)
assert_array_equal(pam.peak_values[mask, 1:], 0.)
mn, mx = _odf.min(), _odf.max()
assert_array_equal(pam.qa[mask, 0], (mx - mn) / mx)
assert_array_equal(pam.qa[mask, 1:], 0.)
assert_array_equal(pam.peak_indices[mask, 0], odf_argmax)
assert_array_equal(pam.peak_indices[mask, 1:], -1)
def test_peaks_shm_coeff():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (60, 0)],
fractions=[50, 50], snr=SNR)
from dipy.reconst.shm import CsaOdfModel
model = CsaOdfModel(gtab, 4)
pam = peaks_from_model(model, data[None, :], sphere, .5, 45,
return_odf=True, return_sh=True)
# Test that spherical harmonic coefficients return back correctly
odf2 = np.dot(pam.shm_coeff, pam.B)
assert_array_almost_equal(pam.odf, odf2)
assert_equal(pam.shm_coeff.shape[-1], 45)
pam = peaks_from_model(model, data[None, :], sphere, .5, 45,
return_odf=True, return_sh=False)
assert_equal(pam.shm_coeff, None)
pam = peaks_from_model(model, data[None, :], sphere, .5, 45,
return_odf=True, return_sh=True,
sh_basis_type='mrtrix')
odf2 = np.dot(pam.shm_coeff, pam.B)
assert_array_almost_equal(pam.odf, odf2)
def test_peaksFromModel():
data = np.zeros((10, 2))
# Test basic case
model = SimpleOdfModel(_gtab)
odf_argmax = _odf.argmax()
pam = peaks_from_model(model, data, _sphere, .5, 45, normalize_peaks=True)
assert_array_equal(pam.gfa, gfa(_odf))
assert_array_equal(pam.peak_values[:, 0], 1.)
assert_array_equal(pam.peak_values[:, 1:], 0.)
mn, mx = _odf.min(), _odf.max()
assert_array_equal(pam.qa[:, 0], (mx - mn) / mx)
assert_array_equal(pam.qa[:, 1:], 0.)
assert_array_equal(pam.peak_indices[:, 0], odf_argmax)
assert_array_equal(pam.peak_indices[:, 1:], -1)
# Test that odf array matches and is right shape
pam = peaks_from_model(model, data, _sphere, .5, 45, return_odf=True)
expected_shape = (len(data), len(_odf))
assert_equal(pam.odf.shape, expected_shape)
assert_true((_odf == pam.odf).all())
assert_array_equal(pam.peak_values[:, 0], _odf.max())
# Test mask
mask = (np.arange(10) % 2) == 1
pam = peaks_from_model(model, data, _sphere, .5, 45, mask=mask,
normalize_peaks=True)
assert_array_equal(pam.gfa[~mask], 0)
assert_array_equal(pam.qa[~mask], 0)
assert_array_equal(pam.peak_values[~mask], 0)
assert_array_equal(pam.peak_indices[~mask], -1)
assert_array_equal(pam.gfa[mask], gfa(_odf))
assert_array_equal(pam.peak_values[mask, 0], 1.)
assert_array_equal(pam.peak_values[mask, 1:], 0.)
mn, mx = _odf.min(), _odf.max()
assert_array_equal(pam.qa[mask, 0], (mx - mn) / mx)
assert_array_equal(pam.qa[mask, 1:], 0.)
assert_array_equal(pam.peak_indices[mask, 0], odf_argmax)
assert_array_equal(pam.peak_indices[mask, 1:], -1)
def tracking_eudx4csd(dir_src, dir_out, verbose=False):
# Load data
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')
fmask = pjoin(dir_src,
'wm_mask_' + par_b_tag + '_' + 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)
sphere = get_sphere('symmetric724')
response, ratio = auto_response(gtab,
data,
roi_radius=par_ar_radius,
fa_thr=par_ar_fa_th)
# print('Response function', response)
# Model fitting
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
csd_peaks = peaks_from_model(csd_model,
data,
sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
# Computation of streamlines
streamlines = EuDX(csd_peaks.peak_values,
csd_peaks.peak_indices,
seeds=par_eudx_seeds,
odf_vertices=sphere.vertices,
a_low=par_eudx_threshold)
# Saving tractography
voxel_size = (par_dim_vox, ) * 3
dims = mask.shape[:3]
hdr = nib.trackvis.empty_header()
hdr['voxel_size'] = voxel_size
hdr['voxel_order'] = 'LAS'
hdr['dim'] = dims
hdr['vox_to_ras'] = affine
strm = ((sl, None, None) for sl in streamlines)
trk_name = 'tractogram_' + par_b_tag + '_' + par_dim_tag + '_' + par_csd_tag + '_' + par_eudx_tag + '.trk'
trk_out = os.path.join(dir_out, trk_name)
nib.trackvis.write(trk_out, strm, hdr, points_space='voxel')
def tracking_eudx4csd(dir_src, dir_out, verbose=False):
# Load data
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')
fmask = pjoin(dir_src, 'wm_mask_' + par_b_tag + '_' + 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)
sphere = get_sphere('symmetric724')
response, ratio = auto_response(gtab, data, roi_radius=par_ar_radius,
fa_thr=par_ar_fa_th)
# print('Response function', response)
# Model fitting
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
csd_peaks = peaks_from_model(csd_model,
data,
sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
# Computation of streamlines
streamlines = EuDX(csd_peaks.peak_values,
csd_peaks.peak_indices,
seeds=par_eudx_seeds,
odf_vertices= sphere.vertices,
a_low=par_eudx_threshold)
# Saving tractography
voxel_size = (par_dim_vox,) * 3
dims = mask.shape[:3]
hdr = nib.trackvis.empty_header()
hdr['voxel_size'] = voxel_size
hdr['voxel_order'] = 'LAS'
hdr['dim'] = dims
hdr['vox_to_ras'] = affine
strm = ((sl, None, None) for sl in streamlines)
trk_name = 'tractogram_' + par_b_tag + '_' + par_dim_tag + '_' + par_csd_tag + '_' + par_eudx_tag + '.trk'
trk_out = os.path.join(dir_out, trk_name)
nib.trackvis.write(trk_out, strm, hdr, points_space='voxel')
def peaks_from_nifti(fdwi, fbvec=None, fbval=None, mask=None):
if '.' not in fdwi:
fbase = fdwi
fdwi = fdwi+".nii.gz"
if not fbval:
fbval = fbase+".bval"
if not fbvec:
fbvec = fbase+".bvec"
print fdwi
img = nib.load(fdwi)
data = img.get_data()
zooms = img.get_header().get_zooms()[:3]
affine = img.get_affine()
bval, bvec = dio.read_bvals_bvecs(fbval, fbvec)
gtab = dgrad.gradient_table(bval, bvec)
if not mask:
print 'generate mask'
maskdata, mask = median_otsu(data, 3, 1, False, vol_idx=range(10, 50), dilate=2)
else:
mask_img = nib.load(mask)
mask = mask_img.get_data()
from dipy.segment.mask import applymask
maskdata = applymask(data, mask)
print maskdata.shape, mask.shape
from dipy.reconst.shm import QballModel, CsaOdfModel
model = QballModel(gtab, 6)
sphere = get_sphere('symmetric724')
print "fit Qball peaks"
proc_num = multiprocessing.cpu_count()-1
print "peaks_from_model using core# =" + str(proc_num)
peaks = peaks_from_model(model=model, data=maskdata, relative_peak_threshold=.5,
min_separation_angle=25,
sphere=sphere, mask=mask, parallel=True, nbr_processes=proc_num)
return peaks
from dipy.reconst.csdeconv import (ConstrainedSphericalDeconvModel,
auto_response)
response, ratio = auto_response(gtab, data)
response = list(response)
peaks_sphere = get_sphere('symmetric362')
model = ConstrainedSphericalDeconvModel(gtab, response,
sh_order=sh_order)
peaks_csd = peaks_from_model(model=model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
fpeaks = dname + 'peaks.npz'
save_peaks(fpeaks, peaks_csd)
from dipy.io.trackvis import save_trk
from dipy.tracking import utils
from dipy.tracking.local import (ThresholdTissueClassifier,
LocalTracking)
print '\tCreating Mask' data_masked, mask = median_otsu(data, 2, 1) ''' We've loaded an image called `atlas` which is a map of tissue types such that every integer value in the array `labels` represents an anatomical structure or tissue type [#]_. We'll use `peaks_from_model` to apply the `CsaOdfModel` to each white matter voxel and estimate fiber orientations which we can use for tracking. ''' print '\tCalculating peaks' csamodel = shm.CsaOdfModel(gtab, 6) csapeaks = peaks.peaks_from_model(model=csamodel, data=data, sphere=peaks.default_sphere, relative_peak_threshold=.5, min_separation_angle=25, mask=mask) ''' Brief interlude to make sure we don't seed from low-FA voxels. ''' print '\tTensor Fitting' tensor_model = TensorModel(gtab, fit_method='WLS') tensor_fit = tensor_model.fit(data, mask) FA = fractional_anisotropy(tensor_fit.evals) stopping_values = np.zeros(csapeaks.peak_values.shape) stopping_values[:] = FA[..., None]
def run(self, input_files, bvalues, bvectors, mask_files,
b0_threshold=0.0,
bvecs_tol=0.01,
roi_center=None,
roi_radius=10,
fa_thr=0.7,
frf=None, extract_pam_values=False,
sh_order=8,
odf_to_sh_order=8,
out_dir='',
out_pam='peaks.pam5', out_shm='shm.nii.gz',
out_peaks_dir='peaks_dirs.nii.gz',
out_peaks_values='peaks_values.nii.gz',
out_peaks_indices='peaks_indices.nii.gz', out_gfa='gfa.nii.gz'):
""" Constrained spherical deconvolution
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
bvalues : string
Path to the bvalues files. This path may contain wildcards to use
multiple bvalues files at once.
bvectors : string
Path to the bvectors files. This path may contain wildcards to use
multiple bvectors files at once.
mask_files : string
Path to the input masks. This path may contain wildcards to use
multiple masks at once. (default: No mask used)
b0_threshold : float, optional
Threshold used to find b=0 directions
bvecs_tol : float, optional
Bvecs should be unit vectors. (default:0.01)
roi_center : variable int, optional
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]` (default None)
roi_radius : int, optional
radius of cubic ROI in voxels (default 10)
fa_thr : float, optional
FA threshold for calculating the response function (default 0.7)
frf : variable float, optional
Fiber response function can be for example inputed as 15 4 4
(from the command line) or [15, 4, 4] from a Python script to be
converted to float and mutiplied by 10**-4 . If None
the fiber response function will be computed automatically
(default: None).
extract_pam_values : bool, optional
Save or not to save pam volumes as single nifti files.
sh_order : int, optional
Spherical harmonics order (default 6) used in the CSA fit.
odf_to_sh_order : int, optional
Spherical harmonics order used for peak_from_model to compress
the ODF to spherical harmonics coefficients (default 8)
out_dir : string, optional
Output directory (default input file directory)
out_pam : string, optional
Name of the peaks volume to be saved (default 'peaks.pam5')
out_shm : string, optional
Name of the shperical harmonics volume to be saved
(default 'shm.nii.gz')
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved
(default 'peaks_dirs.nii.gz')
out_peaks_values : string, optional
Name of the peaks values volume to be saved
(default 'peaks_values.nii.gz')
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved
(default 'peaks_indices.nii.gz')
out_gfa : string, optional
Name of the generalise fa volume to be saved (default 'gfa.nii.gz')
References
----------
.. [1] Tournier, J.D., et al. NeuroImage 2007. Robust determination of
the fibre orientation distribution in diffusion MRI: Non-negativity
constrained super-resolved spherical deconvolution.
"""
io_it = self.get_io_iterator()
for (dwi, bval, bvec, maskfile, opam, oshm, opeaks_dir, opeaks_values,
opeaks_indices, ogfa) in io_it:
logging.info('Loading {0}'.format(dwi))
img = nib.load(dwi)
data = img.get_data()
affine = img.affine
bvals, bvecs = read_bvals_bvecs(bval, bvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold,
atol=bvecs_tol)
mask_vol = nib.load(maskfile).get_data().astype(np.bool)
sh_order = 8
if data.shape[-1] < 15:
raise ValueError(
'You need at least 15 unique DWI volumes to '
'compute fiber odfs. You currently have: {0}'
' DWI volumes.'.format(data.shape[-1]))
elif data.shape[-1] < 30:
sh_order = 6
if frf is None:
logging.info('Computing response function')
if roi_center is not None:
logging.info('Response ROI center:\n{0}'
.format(roi_center))
logging.info('Response ROI radius:\n{0}'
.format(roi_radius))
response, ratio, nvox = auto_response(
gtab, data,
roi_center=roi_center,
roi_radius=roi_radius,
fa_thr=fa_thr,
return_number_of_voxels=True)
response = list(response)
else:
logging.info('Using response function')
if isinstance(frf, str):
l01 = np.array(literal_eval(frf), dtype=np.float64)
else:
l01 = np.array(frf, dtype=np.float64)
l01 *= 10 ** -4
response = np.array([l01[0], l01[1], l01[1]])
ratio = l01[1] / l01[0]
response = (response, ratio)
logging.info(
'Eigenvalues for the frf of the input data are :{0}'
.format(response[0]))
logging.info('Ratio for smallest to largest eigen value is {0}'
.format(ratio))
peaks_sphere = get_sphere('repulsion724')
logging.info('CSD computation started.')
csd_model = ConstrainedSphericalDeconvModel(gtab, response,
sh_order=sh_order)
peaks_csd = peaks_from_model(model=csd_model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
save_peaks(opam, peaks_csd)
logging.info('CSD computation completed.')
if extract_pam_values:
peaks_to_niftis(peaks_csd, oshm, opeaks_dir, opeaks_values,
opeaks_indices, ogfa, reshape_dirs=True)
dname_ = os.path.dirname(opam)
if dname_ == '':
logging.info('Pam5 file saved in current directory')
else:
logging.info(
'Pam5 file saved in {0}'.format(dname_))
return io_it
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)
sf_model = sfm.SparseFascicleModel(gtab,
sphere=sphere,
l1_ratio=0.5,
alpha=0.001,
response=response[0])
"""
We fit this model to the data in each voxel in the white-matter mask, so that
we can use these directions in tracking:
"""
from dipy.reconst.peaks import peaks_from_model
pnm = peaks_from_model(sf_model,
data,
sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=white_matter,
parallel=True)
"""
A ThresholdTissueClassifier object is used to segment the data to track only
through areas in which the Generalized Fractional Anisotropy (GFA) is
sufficiently high.
"""
from dipy.tracking.local import ThresholdTissueClassifier
classifier = ThresholdTissueClassifier(pnm.gfa, .25)
"""
Tracking will be started from a set of seeds evenly distributed in the white
matter:
"""
sf_odf = sf_fit.odf(sphere)
fodf_spheres = fvtk.sphere_funcs(sf_odf, sphere, scale=1.3, norm=True)
ren = fvtk.ren()
fvtk.add(ren, fodf_spheres)
print('Saving illustration as sf_odfs.png')
fvtk.record(ren, out_path='sf_odfs.png', size=(1000, 1000))
"""
We can extract the peaks from the ODF, and plot these as well
"""
sf_peaks = dpp.peaks_from_model(sf_model,
data_small,
sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
return_sh=False)
fvtk.clear(ren)
fodf_peaks = fvtk.peaks(sf_peaks.peak_dirs, sf_peaks.peak_values, scale=1.3)
fvtk.add(ren, fodf_peaks)
print('Saving illustration as sf_peaks.png')
fvtk.record(ren, out_path='sf_peaks.png', size=(1000, 1000))
"""
Finally, we plot both the peaks and the ODFs, overlayed:
"""
fodf_spheres.GetProperty().SetOpacity(0.4)
fvtk.add(ren, fodf_spheres)
def run(self,
input_files,
bvalues_files,
bvectors_files,
mask_files,
sh_order=6,
odf_to_sh_order=8,
b0_threshold=0.0,
bvecs_tol=0.01,
extract_pam_values=False,
out_dir='',
out_pam='peaks.pam5',
out_shm='shm.nii.gz',
out_peaks_dir='peaks_dirs.nii.gz',
out_peaks_values='peaks_values.nii.gz',
out_peaks_indices='peaks_indices.nii.gz',
out_gfa='gfa.nii.gz'):
""" Constant Solid Angle.
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
bvalues_files : string
Path to the bvalues files. This path may contain wildcards to use
multiple bvalues files at once.
bvectors_files : string
Path to the bvectors files. This path may contain wildcards to use
multiple bvectors files at once.
mask_files : string
Path to the input masks. This path may contain wildcards to use
multiple masks at once. (default: No mask used)
sh_order : int, optional
Spherical harmonics order (default 6) used in the CSA fit.
odf_to_sh_order : int, optional
Spherical harmonics order used for peak_from_model to compress
the ODF to spherical harmonics coefficients (default 8)
b0_threshold : float, optional
Threshold used to find b=0 directions
bvecs_tol : float, optional
Threshold used so that norm(bvec)=1 (default 0.01)
extract_pam_values : bool, optional
Wheter or not to save pam volumes as single nifti files.
out_dir : string, optional
Output directory (default input file directory)
out_pam : string, optional
Name of the peaks volume to be saved (default 'peaks.pam5')
out_shm : string, optional
Name of the shperical harmonics volume to be saved
(default 'shm.nii.gz')
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved
(default 'peaks_dirs.nii.gz')
out_peaks_values : string, optional
Name of the peaks values volume to be saved
(default 'peaks_values.nii.gz')
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved
(default 'peaks_indices.nii.gz')
out_gfa : string, optional
Name of the generalise fa volume to be saved (default 'gfa.nii.gz')
References
----------
.. [1] Aganj, I., et al. 2009. ODF Reconstruction in Q-Ball Imaging
with Solid Angle Consideration.
"""
io_it = self.get_io_iterator()
for (dwi, bval, bvec, maskfile, opam, oshm, opeaks_dir, opeaks_values,
opeaks_indices, ogfa) in io_it:
logging.info('Loading {0}'.format(dwi))
vol = nib.load(dwi)
data = vol.get_data()
affine = vol.affine
bvals, bvecs = read_bvals_bvecs(bval, bvec)
if b0_threshold < bvals.min():
warn("b0_threshold (value: {0}) is too low, increase your "
"b0_threshold. It should higher than the first b0 value "
"({1}).".format(b0_threshold, bvals.min()))
gtab = gradient_table(bvals,
bvecs,
b0_threshold=b0_threshold,
atol=bvecs_tol)
mask_vol = nib.load(maskfile).get_data().astype(np.bool)
peaks_sphere = get_sphere('repulsion724')
logging.info('Starting CSA computations {0}'.format(dwi))
csa_model = CsaOdfModel(gtab, sh_order)
peaks_csa = peaks_from_model(model=csa_model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=odf_to_sh_order,
normalize_peaks=True,
parallel=False)
peaks_csa.affine = affine
save_peaks(opam, peaks_csa)
logging.info('Finished CSA {0}'.format(dwi))
if extract_pam_values:
peaks_to_niftis(peaks_csa,
oshm,
opeaks_dir,
opeaks_values,
opeaks_indices,
ogfa,
reshape_dirs=True)
dname_ = os.path.dirname(opam)
if dname_ == '':
logging.info('Pam5 file saved in current directory')
else:
logging.info('Pam5 file saved in {0}'.format(dname_))
return io_it
def deterministic(diffusion_file, bvecs_file, bvals_file, outdir,
mask_file=None, order=4, nb_seeds_per_voxel=1, step=0.5,
fmt="%.4f"):
""" Compute a deterministic tractography using an ODF model.
Parameters
----------
diffusion_file: str (mandatory)
a file containing the preprocessed diffusion data.
bvecs_file: str (mandatory)
a file containing the diffusion gradient directions.
bvals_file: str (mandatory)
a file containing the diffusion b-values.
outdir: str (mandatory)
the output directory.
mask_file: str (optional, default None)
an image used to mask the diffusion data during the tractography. If
not set, all the image voxels are considered.
order: int (optional, default 4)
the order of the ODF model.
nb_seeds_per_voxel: int (optional, default 1)
the number of seeds per voxel used during the propagation.
step: float (optional, default 0.5)
the integration step in voxel fraction used during the propagation.
fmt: str (optional, default '%.4f')
the saved track elements format.
Returns
-------
track_file: str
a determinist model of the white matter organization.
"""
# Read diffusion sequence
bvals, bvecs = read_bvals_bvecs(bvals_file, bvecs_file)
gtab = gradient_table(bvals, bvecs)
diffusion_array = nibabel.load(diffusion_file).get_data()
if mask_file is not None:
mask_array = nibabel.load(mask_file).get_data()
else:
mask_array = numpy.ones(diffusion_array.shape[:3], dtype=numpy.uint8)
# Estimate ODF model
csamodel = shm.CsaOdfModel(gtab, order)
csapeaks = peaks.peaks_from_model(
model=csamodel, data=diffusion_array, sphere=peaks.default_sphere,
relative_peak_threshold=.8, min_separation_angle=45,
mask=mask_array)
# Compute deterministic tractography in voxel space so affine is equal
# to identity
seeds = utils.seeds_from_mask(mask_array, density=nb_seeds_per_voxel)
streamline_generator = EuDX(
csapeaks.peak_values, csapeaks.peak_indices,
odf_vertices=peaks.default_sphere.vertices, a_low=.05, step_sz=step,
seeds=seeds)
affine = streamline_generator.affine
streamlines = list(streamline_generator)
# Save the tracks
track_file = os.path.join(outdir, "fibers.txt")
savetxt(track_file, streamlines, fmt=fmt)
return track_file
# Loading values, vectors, image and mask
sphere = get_sphere('symmetric362')
print "loading bval/bvec files"
bvals, bvecs = read_bvals_bvecs("tp3_data//bvals2000", "tp3_data//bvecs2000")
gtab = gradient_table(bvals, bvecs)
print "loading nifti files"
img = nib.load("tp3_data//dwi2000.nii.gz")
affine = img.get_affine()
data = img.get_data()
mask = nib.load("tp3_data//_binary_mask.nii.gz").get_data()
## Apply mask
data_in_wm = applymask(data, mask)
response, ratio = auto_response(gtab, data_in_wm)
# Computing ODF
print "computing fODF... please wait an hour"
csd_model = ConstrainedSphericalDeconvModel(gtab, response, reg_sphere=sphere)
peaks_csd = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
relative_peak_threshold=.25,
min_separation_angle=25,
mask=mask,
normalize_peaks=True,
parallel=True)
# Saving files
print "saving files"
nib.save(nib.Nifti1Image(peaks_csd.shm_coeff.astype(np.float32), affine), "tp3_data//_fodf.nii.gz")
nib.save(nib.Nifti1Image(reshape_peaks_for_visualization(peaks_csd), affine), "tp3_data//_fodfpeaks.nii.gz")
def recursive_response(gtab,
data,
mask=None,
sh_order=8,
peak_thr=0.01,
init_fa=0.08,
init_trace=0.0021,
iter=8,
convergence=0.001,
parallel=True,
nbr_processes=None,
sphere=default_sphere):
""" Recursive calibration of response function using peak threshold
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data
mask : ndarray, optional
mask for recursive calibration, for example a white matter mask. It has
shape `data.shape[0:3]` and dtype=bool. Default: use the entire data
array.
sh_order : int, optional
maximal spherical harmonics order. Default: 8
peak_thr : float, optional
peak threshold, how large the second peak can be relative to the first
peak in order to call it a single fiber population [1]. Default: 0.01
init_fa : float, optional
FA of the initial 'fat' response function (tensor). Default: 0.08
init_trace : float, optional
trace of the initial 'fat' response function (tensor). Default: 0.0021
iter : int, optional
maximum number of iterations for calibration. Default: 8.
convergence : float, optional
convergence criterion, maximum relative change of SH
coefficients. Default: 0.001.
parallel : bool, optional
Whether to use parallelization in peak-finding during the calibration
procedure. Default: True
nbr_processes: int
If `parallel` is True, the number of subprocesses to use
(default multiprocessing.cpu_count()).
sphere : Sphere, optional.
The sphere used for peak finding. Default: default_sphere.
Returns
-------
response : ndarray
response function in SH coefficients
Notes
-----
In CSD there is an important pre-processing step: the estimation of the
fiber response function. Using an FA threshold is not a very robust method.
It is dependent on the dataset (non-informed used subjectivity), and still
depends on the diffusion tensor (FA and first eigenvector),
which has low accuracy at high b-value. This function recursively
calibrates the response function, for more information see [1].
References
----------
.. [1] Tax, C.M.W., et al. NeuroImage 2014. Recursive calibration of
the fiber response function for spherical deconvolution of
diffusion MRI data.
"""
S0 = 1
evals = fa_trace_to_lambdas(init_fa, init_trace)
res_obj = (evals, S0)
if mask is None:
data = data.reshape(-1, data.shape[-1])
else:
data = data[mask]
n = np.arange(0, sh_order + 1, 2)
where_dwi = lazy_index(~gtab.b0s_mask)
response_p = np.ones(len(n))
for num_it in range(1, iter):
r_sh_all = np.zeros(len(n))
csd_model = ConstrainedSphericalDeconvModel(gtab,
res_obj,
sh_order=sh_order)
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
relative_peak_threshold=peak_thr,
min_separation_angle=25,
parallel=parallel,
nbr_processes=nbr_processes)
dirs = csd_peaks.peak_dirs
vals = csd_peaks.peak_values
single_peak_mask = (vals[:, 1] / vals[:, 0]) < peak_thr
data = data[single_peak_mask]
dirs = dirs[single_peak_mask]
for num_vox in range(0, data.shape[0]):
rotmat = vec2vec_rotmat(dirs[num_vox, 0], np.array([0, 0, 1]))
rot_gradients = np.dot(rotmat, gtab.gradients.T).T
x, y, z = rot_gradients[where_dwi].T
r, theta, phi = cart2sphere(x, y, z)
# for the gradient sphere
B_dwi = real_sph_harm(0, n, theta[:, None], phi[:, None])
r_sh_all += np.linalg.lstsq(B_dwi, data[num_vox, where_dwi])[0]
response = r_sh_all / data.shape[0]
res_obj = AxSymShResponse(data[:, gtab.b0s_mask].mean(), response)
change = abs((response_p - response) / response_p)
if all(change < convergence):
break
response_p = response
return res_obj
def main():
parser = _build_arg_parser()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
if not args.not_all:
args.fodf = args.fodf or 'fodf.nii.gz'
args.peaks = args.peaks or 'peaks.nii.gz'
args.peak_indices = args.peak_indices or 'peak_indices.nii.gz'
arglist = [args.fodf, args.peaks, args.peak_indices]
if args.not_all and not any(arglist):
parser.error('When using --not_all, you need to specify at least '
'one file to output.')
assert_inputs_exist(parser, [args.input, args.bvals, args.bvecs])
assert_outputs_exists(parser, args, arglist)
nbr_processes = args.nbr_processes
parallel = True
if nbr_processes <= 0:
nbr_processes = None
elif nbr_processes == 1:
parallel = False
# Check for FRF filename
base_odf_name, _ = split_name_with_nii(args.fodf)
frf_filename = base_odf_name + '_frf.txt'
if os.path.isfile(frf_filename) and not args.overwrite:
parser.error('Cannot save frf file, "{0}" already exists. '
'Use -f to overwrite.'.format(frf_filename))
vol = nib.load(args.input)
data = vol.get_data()
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
if args.mask_wm is not None:
wm_mask = nib.load(args.mask_wm).get_data().astype('bool')
else:
wm_mask = np.ones_like(data[..., 0], dtype=np.bool)
logging.info(
'No white matter mask specified! mask_data will be used instead, '
'if it has been supplied. \nBe *VERY* careful about the '
'estimation of the fiber response function for the CSD.')
data_in_wm = applymask(data, wm_mask)
if not is_normalized_bvecs(bvecs):
logging.warning('Your b-vectors do not seem normalized...')
bvecs = normalize_bvecs(bvecs)
if bvals.min() != 0:
if bvals.min() > 20:
raise ValueError(
'The minimal bvalue is greater than 20. This is highly '
'suspicious. Please check your data to ensure everything is '
'correct.\nValue found: {}'.format(bvals.min()))
else:
logging.warning(
'Warning: no b=0 image. Setting b0_threshold to '
'bvals.min() = %s', bvals.min())
gtab = gradient_table(bvals, bvecs, b0_threshold=bvals.min())
else:
gtab = gradient_table(bvals, bvecs)
if args.mask is None:
mask = None
else:
mask = nib.load(args.mask).get_data().astype(np.bool)
# Raise warning for sh order if there is not enough DWIs
if data.shape[-1] < (args.sh_order + 1) * (args.sh_order + 2) / 2:
warnings.warn(
'We recommend having at least %s unique DWIs volumes, but you '
'currently have %s volumes. Try lowering the parameter --sh_order '
'in case of non convergence.',
(args.sh_order + 1) * (args.sh_order + 2) / 2), data.shape[-1]
fa_thresh = args.fa_thresh
# If threshold is too high, try lower until enough indices are found
# estimating a response function with fa < 0.5 does not make sense
nvox = 0
while nvox < 300 and fa_thresh > 0.5:
response, ratio, nvox = auto_response(gtab,
data_in_wm,
roi_center=args.roi_center,
roi_radius=args.roi_radius,
fa_thr=fa_thresh,
return_number_of_voxels=True)
logging.info('Number of indices is %s with threshold of %s', nvox,
fa_thresh)
fa_thresh -= 0.05
if fa_thresh <= 0:
raise ValueError(
'Could not find at least 300 voxels for estimating the frf!')
logging.info('Found %s valid voxels for frf estimation.', nvox)
response = list(response)
logging.info('Response function is %s', response)
if args.frf is not None:
l01 = np.array(literal_eval(args.frf), dtype=np.float64)
if not args.no_factor:
l01 *= 10**-4
response[0] = np.array([l01[0], l01[1], l01[1]])
ratio = l01[1] / l01[0]
logging.info("Eigenvalues for the frf of the input data are: %s",
response[0])
logging.info("Ratio for smallest to largest eigen value is %s", ratio)
np.savetxt(frf_filename, response[0])
if not args.frf_only:
reg_sphere = get_sphere('symmetric362')
peaks_sphere = get_sphere('symmetric724')
csd_model = ConstrainedSphericalDeconvModel(gtab,
response,
reg_sphere=reg_sphere,
sh_order=args.sh_order)
peaks_csd = peaks_from_model(model=csd_model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_sh=True,
sh_basis_type=args.basis,
sh_order=args.sh_order,
normalize_peaks=True,
parallel=parallel,
nbr_processes=nbr_processes)
if args.fodf:
nib.save(
nib.Nifti1Image(peaks_csd.shm_coeff.astype(np.float32),
vol.affine), args.fodf)
if args.peaks:
nib.save(
nib.Nifti1Image(reshape_peaks_for_visualization(peaks_csd),
vol.affine), args.peaks)
if args.peak_indices:
nib.save(nib.Nifti1Image(peaks_csd.peak_indices, vol.affine),
args.peak_indices)
sphere, like ``default_sphere`` which has 362 directions on the hemisphere,
without having to worry about memory limitations.
"""
from dipy.data import default_sphere
prob_dg = ProbabilisticDirectionGetter.from_shcoeff(csd_fit.shm_coeff,
max_angle=30.,
sphere=default_sphere)
streamlines = LocalTracking(prob_dg, classifier, seeds, affine, step_size=.5)
save_trk("probabilistic_shm_coeff.trk", streamlines, affine, labels.shape)
"""
Not all model fits have the ``shm_coeff`` attribute because not all models use
this basis to represent the data internally. However we can fit the ODF of any
model to the spherical harmonic basis using the ``peaks_from_model`` function.
"""
from dipy.reconst.peaks import peaks_from_model
peaks = peaks_from_model(csd_model, data, default_sphere, .5, 25,
mask=white_matter, return_sh=True, parallel=True)
fod_coeff = peaks.shm_coeff
prob_dg = ProbabilisticDirectionGetter.from_shcoeff(fod_coeff, max_angle=30.,
sphere=default_sphere)
streamlines = LocalTracking(prob_dg, classifier, seeds, affine, step_size=.5)
save_trk("probabilistic_peaks_from_model.trk", streamlines, affine,
labels.shape)
def dmri_recon(sid, data_dir, out_dir, resolution, recon='csd', 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'
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)
fbvec = os.path.abspath(glob(os.path.join(data_dir, 'bvecs',
'camino_120_RAS_flipped-xy.bvecs'))[0])
print("bvec file = %s"%fbvec)
fbval = os.path.abspath(glob(os.path.join(data_dir, 'bvecs',
'camino_120_RAS.bvals'))[0])
print("bval file = %s"%fbval)
img = nib.load(fimg)
data = img.get_data()
affine = img.get_affine()
prefix = sid
from dipy.io import read_bvals_bvecs
from dipy.core.gradients import vector_norm
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
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.reconst.csdeconv import auto_response
response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.1) # 0.7
#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_data()
useFA = True
print("creating model")
if recon == 'csd':
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel
model = ConstrainedSphericalDeconvModel(gtab, response)
useFA = True
elif recon == 'csa':
from dipy.reconst.shm import CsaOdfModel, normalize_data
model = CsaOdfModel(gtab, 4)
useFA = False
else:
raise ValueError('only csd, csa supported currently')
from dipy.reconst.dsi import (DiffusionSpectrumDeconvModel,
DiffusionSpectrumModel)
model = DiffusionSpectrumDeconvModel(gtab)
fit = model.fit(data)
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
#odfs = fit.odf(sphere)
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=True,
return_odf=False,
normalize_peaks=True,
npeaks=5,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=num_threads > 1,
nbr_processes=num_threads)
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)
shm_coeff = fit.shm_coeff
shm_coeff_file = os.path.abspath('%s_shm_coeff.nii.gz' % (prefix))
nib.save(nib.Nifti1Image(shm_coeff, img.get_affine()), shm_coeff_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)
fa_img = nib.Nifti1Image(peaks.gfa, img.get_affine())
model_gfa_file = os.path.abspath('%s_%s_gfa.nii.gz' % (prefix, recon))
nib.save(fa_img, model_gfa_file)
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=0.1,
seeds=10**6,
ang_thr=45)
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_streamline.trk' % (prefix, recon))
"""
#import dipy.tracking.metrics as dmetrics
streamlines = ((sl, None, None) for sl in eu) # if dmetrics.length(sl) > 15)
hdr = nib.trackvis.empty_header()
hdr['voxel_size'] = fa_img.get_header().get_zooms()[:3]
hdr['voxel_order'] = 'RAS' #LAS
hdr['dim'] = FA.shape[:3]
nib.trackvis.write(sl_fname, streamlines, hdr, points_space='voxel')
"""
# 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']
assert tensor_fa_file
assert tensor_evec_file
assert model_gfa_file
assert tensor_ad_file
assert tensor_rd_file
assert tensor_md_file
assert shm_coeff_file
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
def track(dname, fdwi, fbval, fbvec, fmask=None, seed_density = 1, show=False):
data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=50)
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
# compute DTI model
from dipy.reconst.dti import TensorModel
tenmodel = TensorModel(gtab)#, fit_method='OLS') #, min_signal=5000)
# fit the dti model
tenfit = tenmodel.fit(data, mask=mask)
# save fa
ffa = dname + 'tensor_fa.nii.gz'
fa_img = nib.Nifti1Image(tenfit.fa.astype(np.float32), affine)
nib.save(fa_img, ffa)
sh_order = 8 #TODO: check what that does
if data.shape[-1] < 15:
raise ValueError('You need at least 15 unique DWI volumes to '
'compute fiber ODFs. You currently have: {0}'
' DWI volumes.'.format(data.shape[-1]))
elif data.shape[-1] < 30:
sh_order = 6
# compute the response equation ?
from dipy.reconst.csdeconv import auto_response
response, ratio = auto_response(gtab, data)
response = list(response)
peaks_sphere = get_sphere('symmetric362')
#TODO: check what that does
peaks_csd = peaks_from_model(model=tenmodel,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5, #.5
min_separation_angle=25,
mask=mask,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
fpeaks = dname + 'peaks.npz'
save_peaks(fpeaks, peaks_csd)
from dipy.io.trackvis import save_trk
from dipy.tracking import utils
from dipy.tracking.local import (ThresholdTissueClassifier,
LocalTracking)
stopping_thr = 0.25 #0.25
pam = load_peaks(fpeaks)
#ffa = dname + 'tensor_fa_nomask.nii.gz'
fa, fa_affine = load_nifti(ffa)
classifier = ThresholdTissueClassifier(fa,
stopping_thr)
# seeds
seed_mask = fa > 0.4 #0.4 #TODO: check this parameter
seeds = utils.seeds_from_mask(
seed_mask,
density=seed_density,
affine=affine)
# tractography, if affine then in world coordinates
streamlines = LocalTracking(pam, classifier,
seeds, affine=affine, step_size=.5)
# Compute streamlines and store as a list.
streamlines = list(streamlines)
ftractogram = dname + 'tractogram.trk'
#save .trk
save_trk_old_style(ftractogram, streamlines, affine, fa.shape)
if show:
#render
show_results(data,streamlines, fa, fa_affine)
fbvec = "original.bvec"
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)
ten_model = TensorModel(gtab)
ten_fit = ten_model.fit(data, mask)
fa = fractional_anisotropy(ten_fit.evals)
cfa = color_fa(fa, ten_fit.evecs)
csamodel = CsaOdfModel(gtab, 6)
sphere = get_sphere('symmetric724')
pmd = peaks_from_model(model=csamodel,
data=data,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False)
#Deterministic tractography
eu = EuDX(a=fa,
ind=pmd.peak_indices[..., 0],
seeds=2000000,
odf_vertices=sphere.vertices,
a_low=0.2)
affine = eu.affine
csd_streamlines = list(eu)
#Remove tracts shorter than 30mm
#print np.shape(csd_streamlines)
from dipy.tracking.utils import length
def recursive_response(gtab, data, mask=None, sh_order=8, peak_thr=0.01,
init_fa=0.08, init_trace=0.0021, iter=8,
convergence=0.001, parallel=True, nbr_processes=None,
sphere=default_sphere):
""" Recursive calibration of response function using peak threshold
Parameters
----------
gtab : GradientTable
data : ndarray
diffusion data
mask : ndarray, optional
mask for recursive calibration, for example a white matter mask. It has
shape `data.shape[0:3]` and dtype=bool. Default: use the entire data
array.
sh_order : int, optional
maximal spherical harmonics order. Default: 8
peak_thr : float, optional
peak threshold, how large the second peak can be relative to the first
peak in order to call it a single fiber population [1]. Default: 0.01
init_fa : float, optional
FA of the initial 'fat' response function (tensor). Default: 0.08
init_trace : float, optional
trace of the initial 'fat' response function (tensor). Default: 0.0021
iter : int, optional
maximum number of iterations for calibration. Default: 8.
convergence : float, optional
convergence criterion, maximum relative change of SH
coefficients. Default: 0.001.
parallel : bool, optional
Whether to use parallelization in peak-finding during the calibration
procedure. Default: True
nbr_processes: int
If `parallel` is True, the number of subprocesses to use
(default multiprocessing.cpu_count()).
sphere : Sphere, optional.
The sphere used for peak finding. Default: default_sphere.
Returns
-------
response : ndarray
response function in SH coefficients
Notes
-----
In CSD there is an important pre-processing step: the estimation of the
fiber response function. Using an FA threshold is not a very robust method.
It is dependent on the dataset (non-informed used subjectivity), and still
depends on the diffusion tensor (FA and first eigenvector),
which has low accuracy at high b-value. This function recursively
calibrates the response function, for more information see [1].
References
----------
.. [1] Tax, C.M.W., et al. NeuroImage 2014. Recursive calibration of
the fiber response function for spherical deconvolution of
diffusion MRI data.
"""
S0 = 1
evals = fa_trace_to_lambdas(init_fa, init_trace)
res_obj = (evals, S0)
if mask is None:
data = data.reshape(-1, data.shape[-1])
else:
data = data[mask]
n = np.arange(0, sh_order + 1, 2)
where_dwi = lazy_index(~gtab.b0s_mask)
response_p = np.ones(len(n))
for num_it in range(1, iter):
r_sh_all = np.zeros(len(n))
csd_model = ConstrainedSphericalDeconvModel(gtab, res_obj,
sh_order=sh_order)
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
relative_peak_threshold=peak_thr,
min_separation_angle=25,
parallel=parallel,
nbr_processes=nbr_processes)
dirs = csd_peaks.peak_dirs
vals = csd_peaks.peak_values
single_peak_mask = (vals[:, 1] / vals[:, 0]) < peak_thr
data = data[single_peak_mask]
dirs = dirs[single_peak_mask]
for num_vox in range(0, data.shape[0]):
rotmat = vec2vec_rotmat(dirs[num_vox, 0], np.array([0, 0, 1]))
rot_gradients = np.dot(rotmat, gtab.gradients.T).T
x, y, z = rot_gradients[where_dwi].T
r, theta, phi = cart2sphere(x, y, z)
# for the gradient sphere
B_dwi = real_sph_harm(0, n, theta[:, None], phi[:, None])
r_sh_all += np.linalg.lstsq(B_dwi, data[num_vox, where_dwi])[0]
response = r_sh_all / data.shape[0]
res_obj = AxSymShResponse(data[:, gtab.b0s_mask].mean(), response)
change = abs((response_p - response) / response_p)
if all(change < convergence):
break
response_p = response
return res_obj
parcellation_data = parcellation_data * mask_data_bin
parcellation_wm_data = parcellation_data * wm_data_bin
parcellation_wm_data = parcellation_wm_data.astype(np.int)
#=============================================================================
# Track all of white matter using EuDX
#=============================================================================
if not os.path.exists(Msym_file) and not os.path.exists(Mdir_file):
print '\tCalculating peaks'
csamodel = shm.CsaOdfModel(gtab, 6)
csapeaks = peaks.peaks_from_model(model=csamodel,
data=dwi_data,
sphere=peaks.default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=wm_data_bin)
print '\tTracking'
seeds = utils.seeds_from_mask(parcellation_wm_data, density=2)
condition_seeds = condition_seeds(seeds, np.eye(4), csapeaks.peak_values.shape[:3])
streamline_generator = EuDX(csapeaks.peak_values, csapeaks.peak_indices,
odf_vertices=peaks.default_sphere.vertices,
a_low=.05, step_sz=.5, seeds=condition_seeds)
affine = streamline_generator.affine
streamlines = list(streamline_generator)
else:
print '\tTracking already complete'
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
GFA = csd_peaks.gfa
"""
sphere = get_sphere('symmetric724')
csamodel = CsaOdfModel(gtab, 4)
#csafit = csamodel.fit(data_small)
csapeaks = peaks_from_model(model=csamodel,
data=maskdata,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True)
GFA = csapeaks.gfa
GFA_img = nib.Nifti1Image(GFA.astype(np.float32), affine)
print GFA.shape
nib.save(GFA_img, os.getcwd()+'/zhibiao/'+f_name+'_GFA.nii.gz')
print('Saving "GFA.nii.gz" sucessful.')
from dipy.reconst.shore import ShoreModel
asm = ShoreModel(gtab)
print('Calculating...SHORE msd')
asmfit = asm.fit(data,mask)
def deterministic(diffusion_file,
bvecs_file,
bvals_file,
trackfile,
mask_file=None,
order=4,
nb_seeds_per_voxel=1,
step=0.5):
""" Compute a deterministic tractography using an ODF model.
Parameters
----------
diffusion_file: str (mandatory)
a file containing the preprocessed diffusion data.
bvecs_file: str (mandatory)
a file containing the diffusion gradient directions.
bvals_file: str (mandatory)
a file containing the diffusion b-values.
trackfile: str (mandatory)
a file path where the fibers will be saved in trackvis format.
mask_file: str (optional, default None)
an image used to mask the diffusion data during the tractography. If
not set, all the image voxels are considered.
order: int (optional, default 4)
the order of the ODF model.
nb_seeds_per_voxel: int (optional, default 1)
the number of seeds per voxel used during the propagation.
step: float (optional, default 0.5)
the integration step in voxel fraction used during the propagation.
Returns
-------
streamlines: tuple of 3-uplet
the computed fiber tracks in trackvis format (points: ndarray shape
(N,3) where N is the number of points, scalars: None or ndarray shape
(N, M) where M is the number of scalars per point, properties: None or
ndarray shape (P,) where P is the number of properties).
hdr: structured array
structured array with trackvis header fields (voxel size, voxel order,
dim).
"""
# Read diffusion sequence
bvals, bvecs = read_bvals_bvecs(bvals_file, bvecs_file)
gtab = gradient_table(bvals, bvecs)
diffusion_image = nibabel.load(diffusion_file)
diffusion_array = diffusion_image.get_data()
if mask_file is not None:
mask_array = nibabel.load(mask_file).get_data()
else:
mask_array = numpy.ones(diffusion_array.shape[:3], dtype=numpy.uint8)
# Estimate ODF model
csamodel = shm.CsaOdfModel(gtab, order)
csapeaks = peaks.peaks_from_model(model=csamodel,
data=diffusion_array,
sphere=peaks.default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=mask_array)
# Compute deterministic tractography in voxel space so affine is equal
# to identity
seeds = utils.seeds_from_mask(mask_array, density=nb_seeds_per_voxel)
streamline_generator = EuDX(csapeaks.peak_values,
csapeaks.peak_indices,
odf_vertices=peaks.default_sphere.vertices,
a_low=.05,
step_sz=step,
seeds=seeds)
# affine = streamline_generator.affine
# Save the tracks in trackvis format
hdr = nibabel.trackvis.empty_header()
hdr["voxel_size"] = diffusion_image.get_header().get_zooms()[:3]
hdr["voxel_order"] = "LAS"
hdr["dim"] = diffusion_array.shape[:3]
streamlines = [track for track in streamline_generator]
random.shuffle(streamlines)
streamlines = ((track, None, None) for track in streamlines)
nibabel.trackvis.write(trackfile, streamlines, hdr, points_space="voxel")
return streamlines, hdr
def dodata(f_name,data_path):
dipy_home = pjoin(os.path.expanduser('~'), 'dipy_data')
folder = pjoin(dipy_home, data_path)
fraw = pjoin(folder, f_name+'.nii.gz')
fbval = pjoin(folder, f_name+'.bval')
fbvec = pjoin(folder, f_name+'.bvec')
flabels = pjoin(folder, f_name+'.nii-label.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)
img = nib.load(fraw)
data = img.get_data()
affine = img.get_affine()
label_img = nib.load(flabels)
labels=label_img.get_data()
lap=through_label_sl.label_position(labels, labelValue=1)
dataslice = data[40:80, 20:80, lap[2][2] / 2]
#print lap[2][2]/2
#get_csd_gfa(f_name,data,gtab,dataslice)
maskdata, mask = median_otsu(data, 2, 1, False, vol_idx=range(10, 50), dilate=2) #不去背景
""" get fa and tensor evecs and ODF"""
from dipy.reconst.dti import TensorModel,mean_diffusivity
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
sphere = get_sphere('symmetric724')
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
np.save(os.getcwd()+'\zhibiao'+f_name+'_FA.npy',FA)
fa_img = nib.Nifti1Image(FA.astype(np.float32), affine)
nib.save(fa_img,os.getcwd()+'\zhibiao'+f_name+'_FA.nii.gz')
print('Saving "DTI_tensor_fa.nii.gz" sucessful.')
evecs_img = nib.Nifti1Image(tenfit.evecs.astype(np.float32), affine)
nib.save(evecs_img, os.getcwd()+'\zhibiao'+f_name+'_DTI_tensor_evecs.nii.gz')
print('Saving "DTI_tensor_evecs.nii.gz" sucessful.')
MD1 = mean_diffusivity(tenfit.evals)
nib.save(nib.Nifti1Image(MD1.astype(np.float32), img.get_affine()), os.getcwd()+'\zhibiao'+f_name+'_MD.nii.gz')
#tensor_odfs = tenmodel.fit(data[20:50, 55:85, 38:39]).odf(sphere)
#from dipy.reconst.odf import gfa
#dti_gfa=gfa(tensor_odfs)
wm_mask = (np.logical_or(FA >= 0.4, (np.logical_and(FA >= 0.15, MD >= 0.0011))))
response = recursive_response(gtab, data, mask=wm_mask, sh_order=8,
peak_thr=0.01, init_fa=0.08,
init_trace=0.0021, iter=8, convergence=0.001,
parallel=False)
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
#csd_fit = csd_model.fit(data)
from dipy.direction import peaks_from_model
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
GFA = csd_peaks.gfa
nib.save(GFA, os.getcwd()+'\zhibiao'+f_name+'_MSD.nii.gz')
print('Saving "GFA.nii.gz" sucessful.')
from dipy.reconst.shore import ShoreModel
asm = ShoreModel(gtab)
print('Calculating...SHORE msd')
asmfit = asm.fit(data,mask)
msd = asmfit.msd()
msd[np.isnan(msd)] = 0
#print GFA[:,:,slice].T
print('Saving msd_img.png')
nib.save(msd, os.getcwd()+'\zhibiao'+f_name+'_GFA.nii.gz')
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if not args.not_all:
args.gfa = args.gfa or 'gfa.nii.gz'
args.peaks = args.peaks or 'peaks.nii.gz'
args.peak_indices = args.peak_indices or 'peaks_indices.nii.gz'
args.sh = args.sh or 'sh.nii.gz'
args.nufo = args.nufo or 'nufo.nii.gz'
args.a_power = args.a_power or 'anisotropic_power.nii.gz'
arglist = [
args.gfa, args.peaks, args.peak_indices, args.sh, args.nufo,
args.a_power
]
if args.not_all and not any(arglist):
parser.error('When using --not_all, you need to specify at least ' +
'one file to output.')
assert_inputs_exist(parser, [args.input, args.bvals, args.bvecs])
assert_outputs_exists(parser, args, arglist)
nbr_processes = args.nbr_processes
parallel = True
if nbr_processes <= 0:
nbr_processes = None
elif nbr_processes == 1:
parallel = False
# Load data
img = nib.load(args.input)
data = img.get_data()
affine = img.get_affine()
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)
if bvals.min() != 0:
if bvals.min() > 20:
raise ValueError(
'The minimal bvalue is greater than 20. This is highly '
'suspicious. Please check your data to ensure everything is '
'correct.\nValue found: {0}'.format(bvals.min()))
else:
logging.warning(
'Warning: no b=0 image. Setting b0_threshold to '
'bvals.min() = %s', bvals.min())
gtab = gradient_table(bvals, bvecs, b0_threshold=bvals.min())
else:
gtab = gradient_table(bvals, bvecs)
sphere = get_sphere('symmetric724')
if args.mask is None:
mask = None
else:
mask = nib.load(args.mask).get_data().astype(np.bool)
if args.use_qball:
model = QballModel(gtab, sh_order=int(args.sh_order), smooth=0.006)
else:
model = CsaOdfModel(gtab, sh_order=int(args.sh_order), smooth=0.006)
odfpeaks = peaks_from_model(model=model,
data=data,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True,
return_sh=True,
sh_order=int(args.sh_order),
sh_basis_type=args.basis,
npeaks=5,
parallel=parallel,
nbr_processes=nbr_processes)
if args.gfa:
nib.save(nib.Nifti1Image(odfpeaks.gfa.astype(np.float32), affine),
args.gfa)
if args.peaks:
nib.save(
nib.Nifti1Image(reshape_peaks_for_visualization(odfpeaks), affine),
args.peaks)
if args.peak_indices:
nib.save(nib.Nifti1Image(odfpeaks.peak_indices, affine),
args.peak_indices)
if args.sh:
nib.save(
nib.Nifti1Image(odfpeaks.shm_coeff.astype(np.float32), affine),
args.sh)
if args.nufo:
peaks_count = (odfpeaks.peak_indices > -1).sum(3)
nib.save(nib.Nifti1Image(peaks_count.astype(np.int32), affine),
args.nufo)
if args.a_power:
odf_a_power = anisotropic_power(odfpeaks.shm_coeff)
nib.save(nib.Nifti1Image(odf_a_power.astype(np.float32), affine),
args.a_power)
"""
.. figure:: csd_odfs.png
:align: center
**CSD ODFs**.
In Dipy we also provide tools for finding the peak directions (maxima) of the
ODFs. For this purpose we strongly recommend using ``peaks_from_model``.
"""
from dipy.reconst.peaks import peaks_from_model
csd_peaks = peaks_from_model(model=csd_model,
data=data_small,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
fvtk.clear(ren)
fodf_peaks = fvtk.peaks(csd_peaks.peak_dirs, csd_peaks.peak_values, scale=1.3)
fvtk.add(ren, fodf_peaks)
print('Saving illustration as csd_peaks.png')
fvtk.record(ren, out_path='csd_peaks.png', size=(600, 600))
"""
.. figure:: csd_peaks.png
:align: center
# # white matter mask
# logic1 = np.logical_and(labels_>117, labels_<148)
# logic2 = np.logical_and(labels_>283, labels_<314)
# logic = np.logical_or(logic1, logic2)
# logic_ = np.logical_or(labels_==150, labels_==316)
# wm = np.where(logic, True, np.where(logic_, True, False))
print 'fitting CSA model'
st2 = time.time()
csamodel = shm.CsaOdfModel(gtab, 6)
csapeaks = peaks.peaks_from_model(model=csamodel,
data=data,
sphere=peaks.default_sphere,
relative_peak_threshold=.1,
min_separation_angle=25,
mask=wm,
sh_order=8,
npeaks=5,
parallel=True)
et2 = time.time() - st2
print 'fitting CSA model finished, running time is {}'.format(et2)
# plot peaks
# interactive = False
# ren = window.Renderer()
# slice_actor = actor.peak_slicer(csd_peaks.peak_dirs,
# csd_peaks.peak_values,
# colors=None)
# slice_actor.RotateX(90)
fodf_spheres = fvtk.sphere_funcs(sf_odf, sphere, scale=1.3, norm=True)
ren = fvtk.ren()
fvtk.add(ren, fodf_spheres)
print('Saving illustration as sf_odfs.png')
fvtk.record(ren, out_path='sf_odfs.png', size=(1000, 1000))
"""
We can extract the peaks from the ODF, and plot these as well
"""
sf_peaks = dpp.peaks_from_model(sf_model,
data_small,
sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
return_sh=False)
fvtk.clear(ren)
fodf_peaks = fvtk.peaks(sf_peaks.peak_dirs, sf_peaks.peak_values, scale=1.3)
fvtk.add(ren, fodf_peaks)
print('Saving illustration as sf_peaks.png')
fvtk.record(ren, out_path='sf_peaks.png', size=(1000, 1000))
"""
Finally, we plot both the peaks and the ODFs, overlayed:
"""
def test_peaksFromModelParallel():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab,
mevals,
S0,
angles=[(0, 0), (60, 0)],
fractions=[50, 50],
snr=SNR)
# test equality with/without multiprocessing
model = SimpleOdfModel(gtab)
pam_multi = peaks_from_model(model,
data,
_sphere,
.5,
45,
normalize_peaks=True,
return_odf=True,
return_sh=True,
parallel=True)
pam_single = peaks_from_model(model,
data,
_sphere,
.5,
45,
normalize_peaks=True,
return_odf=True,
return_sh=True,
parallel=False)
assert_equal(pam_multi.gfa.dtype, pam_single.gfa.dtype)
assert_equal(pam_multi.gfa.shape, pam_single.gfa.shape)
assert_array_almost_equal(pam_multi.gfa, pam_single.gfa)
assert_equal(pam_multi.qa.dtype, pam_single.qa.dtype)
assert_equal(pam_multi.qa.shape, pam_single.qa.shape)
assert_array_almost_equal(pam_multi.qa, pam_single.qa)
assert_equal(pam_multi.peak_values.dtype, pam_single.peak_values.dtype)
assert_equal(pam_multi.peak_values.shape, pam_single.peak_values.shape)
assert_array_almost_equal(pam_multi.peak_values, pam_single.peak_values)
assert_equal(pam_multi.peak_indices.dtype, pam_single.peak_indices.dtype)
assert_equal(pam_multi.peak_indices.shape, pam_single.peak_indices.shape)
assert_array_equal(pam_multi.peak_indices, pam_single.peak_indices)
assert_equal(pam_multi.peak_dirs.dtype, pam_single.peak_dirs.dtype)
assert_equal(pam_multi.peak_dirs.shape, pam_single.peak_dirs.shape)
assert_array_almost_equal(pam_multi.peak_dirs, pam_single.peak_dirs)
assert_equal(pam_multi.shm_coeff.dtype, pam_single.shm_coeff.dtype)
assert_equal(pam_multi.shm_coeff.shape, pam_single.shm_coeff.shape)
assert_array_almost_equal(pam_multi.shm_coeff, pam_single.shm_coeff)
assert_equal(pam_multi.odf.dtype, pam_single.odf.dtype)
assert_equal(pam_multi.odf.shape, pam_single.odf.shape)
assert_array_almost_equal(pam_multi.odf, pam_single.odf)
def _run_interface(self, runtime):
from dipy.reconst.peaks import peaks_from_model
from dipy.tracking.eudx import EuDX
from dipy.data import get_sphere
# import marshal as pickle
import pickle as pickle
import gzip
if (not (isdefined(self.inputs.in_model)
or isdefined(self.inputs.in_peaks))):
raise RuntimeError(('At least one of in_model or in_peaks should '
'be supplied'))
img = nb.load(self.inputs.in_file)
imref = nb.four_to_three(img)[0]
affine = img.affine
data = img.get_data().astype(np.float32)
hdr = imref.header.copy()
hdr.set_data_dtype(np.float32)
hdr['data_type'] = 16
sphere = get_sphere('symmetric724')
self._save_peaks = False
if isdefined(self.inputs.in_peaks):
IFLOGGER.info('Peaks file found, skipping ODF peaks search...')
f = gzip.open(self.inputs.in_peaks, 'rb')
peaks = pickle.load(f)
f.close()
else:
self._save_peaks = True
IFLOGGER.info('Loading model and computing ODF peaks')
f = gzip.open(self.inputs.in_model, 'rb')
odf_model = pickle.load(f)
f.close()
peaks = peaks_from_model(
model=odf_model,
data=data,
sphere=sphere,
relative_peak_threshold=self.inputs.peak_threshold,
min_separation_angle=self.inputs.min_angle,
parallel=self.inputs.multiprocess)
f = gzip.open(self._gen_filename('peaks', ext='.pklz'), 'wb')
pickle.dump(peaks, f, -1)
f.close()
hdr.set_data_shape(peaks.gfa.shape)
nb.Nifti1Image(peaks.gfa.astype(np.float32), affine, hdr).to_filename(
self._gen_filename('gfa'))
IFLOGGER.info('Performing tractography')
if isdefined(self.inputs.tracking_mask):
msk = nb.load(self.inputs.tracking_mask).get_data()
msk[msk > 0] = 1
msk[msk < 0] = 0
else:
msk = np.ones(imref.shape)
gfa = peaks.gfa * msk
seeds = self.inputs.num_seeds
if isdefined(self.inputs.seed_coord):
seeds = np.loadtxt(self.inputs.seed_coord)
elif isdefined(self.inputs.seed_mask):
seedmsk = nb.load(self.inputs.seed_mask).get_data()
assert (seedmsk.shape == data.shape[:3])
seedmsk[seedmsk > 0] = 1
seedmsk[seedmsk < 1] = 0
seedps = np.array(np.where(seedmsk == 1), dtype=np.float32).T
vseeds = seedps.shape[0]
nsperv = (seeds // vseeds) + 1
IFLOGGER.info('Seed mask is provided (%d voxels inside '
'mask), computing seeds (%d seeds/voxel).', vseeds,
nsperv)
if nsperv > 1:
IFLOGGER.info('Needed %d seeds per selected voxel (total %d).',
nsperv, vseeds)
seedps = np.vstack(np.array([seedps] * nsperv))
voxcoord = seedps + np.random.uniform(-1, 1, size=seedps.shape)
nseeds = voxcoord.shape[0]
seeds = affine.dot(
np.vstack((voxcoord.T, np.ones((1, nseeds)))))[:3, :].T
if self.inputs.save_seeds:
np.savetxt(self._gen_filename('seeds', ext='.txt'), seeds)
if isdefined(self.inputs.tracking_mask):
tmask = msk
a_low = 0.1
else:
tmask = gfa
a_low = self.inputs.gfa_thresh
eu = EuDX(
tmask,
peaks.peak_indices[..., 0],
seeds=seeds,
affine=affine,
odf_vertices=sphere.vertices,
a_low=a_low)
ss_mm = [np.array(s) for s in eu]
trkfilev = nb.trackvis.TrackvisFile(
[(s, None, None) for s in ss_mm],
points_space='rasmm',
affine=np.eye(4))
trkfilev.to_file(self._gen_filename('tracked', ext='.trk'))
return runtime
if __name__ == '__main__':
freeze_support()
img, gtab = read_stanford_hardi()
data = img.get_data()
maskdata, mask = median_otsu(data, 3, 1, False,
vol_idx=range(10, 50), dilate=2)
response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
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)
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(data, mask)
FA = fractional_anisotropy(tensor_fit.evals)
stopping_values = np.zeros(csd_peaks.peak_values.shape)
stopping_values[:] = FA[..., None]
ren = fvtk.ren()
slice_no = data.shape[2] / 2
fvtk.add(ren, fvtk.peaks(csd_peaks.peak_dirs[:, :, slice_no:slice_no + 1],
stopping_values[:, :, slice_no:slice_no + 1]))
def deterministic(diffusion_file, bvecs_file, bvals_file, trackfile,
mask_file=None, order=4, nb_seeds_per_voxel=1, step=0.5):
""" Compute a deterministic tractography using an ODF model.
Parameters
----------
diffusion_file: str (mandatory)
a file containing the preprocessed diffusion data.
bvecs_file: str (mandatory)
a file containing the diffusion gradient directions.
bvals_file: str (mandatory)
a file containing the diffusion b-values.
trackfile: str (mandatory)
a file path where the fibers will be saved in trackvis format.
mask_file: str (optional, default None)
an image used to mask the diffusion data during the tractography. If
not set, all the image voxels are considered.
order: int (optional, default 4)
the order of the ODF model.
nb_seeds_per_voxel: int (optional, default 1)
the number of seeds per voxel used during the propagation.
step: float (optional, default 0.5)
the integration step in voxel fraction used during the propagation.
Returns
-------
streamlines: tuple of 3-uplet
the computed fiber tracks in trackvis format (points: ndarray shape
(N,3) where N is the number of points, scalars: None or ndarray shape
(N, M) where M is the number of scalars per point, properties: None or
ndarray shape (P,) where P is the number of properties).
hdr: structured array
structured array with trackvis header fields (voxel size, voxel order,
dim).
"""
# Read diffusion sequence
bvals, bvecs = read_bvals_bvecs(bvals_file, bvecs_file)
gtab = gradient_table(bvals, bvecs)
diffusion_image = nibabel.load(diffusion_file)
diffusion_array = diffusion_image.get_data()
if mask_file is not None:
mask_array = nibabel.load(mask_file).get_data()
else:
mask_array = numpy.ones(diffusion_array.shape[:3], dtype=numpy.uint8)
# Estimate ODF model
csamodel = shm.CsaOdfModel(gtab, order)
csapeaks = peaks.peaks_from_model(
model=csamodel, data=diffusion_array, sphere=peaks.default_sphere,
relative_peak_threshold=.8, min_separation_angle=45,
mask=mask_array)
# Compute deterministic tractography in voxel space so affine is equal
# to identity
seeds = utils.seeds_from_mask(mask_array, density=nb_seeds_per_voxel)
streamline_generator = EuDX(
csapeaks.peak_values, csapeaks.peak_indices,
odf_vertices=peaks.default_sphere.vertices, a_low=.05, step_sz=step,
seeds=seeds)
affine = streamline_generator.affine
# Save the tracks in trackvis format
hdr = nibabel.trackvis.empty_header()
hdr["voxel_size"] = diffusion_image.get_header().get_zooms()[:3]
hdr["voxel_order"] = "LAS"
hdr["dim"] = diffusion_array.shape[:3]
streamlines = [track for track in streamline_generator]
random.shuffle(streamlines)
streamlines = ((track, None, None) for track in streamlines)
nibabel.trackvis.write(trackfile, streamlines, hdr, points_space="voxel")
return streamlines, hdr
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel, auto_response
response, ratio = auto_response(gtab, data)
response = list(response)
peaks_sphere = get_sphere("symmetric362")
model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=sh_order)
peaks_csd = peaks_from_model(
model=model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=0.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False,
)
peaks_csd.affine = affine
fpeaks = dname + "peaks.npz"
save_peaks(fpeaks, peaks_csd)
from dipy.io.trackvis import save_trk
from dipy.tracking import utils
from dipy.tracking.local import ThresholdTissueClassifier, LocalTracking
"""
1. The first thing we need to begin fiber tracking is a way of getting
directions from this diffusion data set. In order to do that, we can fit the
data to a Constant Solid Angle ODF Model. This model will estimate the
orientation distribution function (ODF) at each voxel. The ODF is the
distribution of water diffusion as a function of direction. The peaks of an ODF
are good estimates for the orientation of tract segments at a point in the
image.
"""
from dipy.reconst.shm import CsaOdfModel
from dipy.reconst.peaks import peaks_from_model, default_sphere
csa_model = CsaOdfModel(gtab, sh_order=6)
csa_peaks = peaks_from_model(csa_model, data, default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=white_matter)
"""
2. Next we need some way of restricting the fiber tracking to areas with good
directionality information. We've already created the white matter mask,
but we can go a step further and restrict fiber tracking to those areas where
the ODF shows significant restricted diffusion by thresholding on
the general fractional anisotropy (GFA).
"""
from dipy.tracking.local import ThresholdTissueClassifier
classifier = ThresholdTissueClassifier(csa_peaks.gfa, .25)
"""
def test_PeaksAndMetricsDirectionGetter():
class SillyModel(object):
def fit(self, data, mask=None):
return SillyFit(self)
class SillyFit(object):
def __init__(self, model):
self.model = model
def odf(self, sphere):
odf = np.zeros(sphere.theta.shape)
r = np.random.randint(0, len(odf))
odf[r] = 1
return odf
def get_direction(dg, point, dir):
newdir = dir.copy()
state = dg.get_direction(point, newdir)
return (state, np.array(newdir))
data = np.random.random((3, 4, 5, 2))
peaks = peaks_from_model(SillyModel(), data, default_sphere,
relative_peak_threshold=.5,
min_separation_angle=25)
peaks._initialize()
up = np.zeros(3)
up[2] = 1.
down = -up
for i in range(3-1):
for j in range(4-1):
for k in range(5-1):
point = np.array([i, j, k], dtype=float)
# Test that the angle threshold rejects points
peaks.ang_thr = 0.
state, nd = get_direction(peaks, point, up)
npt.assert_equal(state, 1)
# Here we leverage the fact that we know Hemispheres project
# all their vertices into the z >= 0 half of the sphere.
peaks.ang_thr = 90.
state, nd = get_direction(peaks, point, up)
npt.assert_equal(state, 0)
expected_dir = peaks.peak_dirs[i, j, k, 0]
npt.assert_array_almost_equal(nd, expected_dir)
state, nd = get_direction(peaks, point, down)
npt.assert_array_almost_equal(nd, -expected_dir)
# Check that we can get directions at non-integer points
point += np.random.random(3)
state, nd = get_direction(peaks, point, up)
npt.assert_equal(state, 0)
# Check that points are rounded to get initial direction
point -= .5
id = peaks.initial_direction(point)
# id should be a (1, 3) array
npt.assert_array_almost_equal(id, [expected_dir])
def run(self, input_files, bvalues, bvectors, mask_files, sh_order=6,
odf_to_sh_order=8, b0_threshold=0.0, bvecs_tol=0.01,
extract_pam_values=False,
out_dir='',
out_pam='peaks.pam5', out_shm='shm.nii.gz',
out_peaks_dir='peaks_dirs.nii.gz',
out_peaks_values='peaks_values.nii.gz',
out_peaks_indices='peaks_indices.nii.gz',
out_gfa='gfa.nii.gz'):
""" Constant Solid Angle.
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
bvalues : string
Path to the bvalues files. This path may contain wildcards to use
multiple bvalues files at once.
bvectors : string
Path to the bvectors files. This path may contain wildcards to use
multiple bvectors files at once.
mask_files : string
Path to the input masks. This path may contain wildcards to use
multiple masks at once. (default: No mask used)
sh_order : int, optional
Spherical harmonics order (default 6) used in the CSA fit.
odf_to_sh_order : int, optional
Spherical harmonics order used for peak_from_model to compress
the ODF to spherical harmonics coefficients (default 8)
b0_threshold : float, optional
Threshold used to find b=0 directions
bvecs_tol : float, optional
Threshold used so that norm(bvec)=1 (default 0.01)
extract_pam_values : bool, optional
Wheter or not to save pam volumes as single nifti files.
out_dir : string, optional
Output directory (default input file directory)
out_pam : string, optional
Name of the peaks volume to be saved (default 'peaks.pam5')
out_shm : string, optional
Name of the shperical harmonics volume to be saved
(default 'shm.nii.gz')
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved
(default 'peaks_dirs.nii.gz')
out_peaks_values : string, optional
Name of the peaks values volume to be saved
(default 'peaks_values.nii.gz')
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved
(default 'peaks_indices.nii.gz')
out_gfa : string, optional
Name of the generalise fa volume to be saved (default 'gfa.nii.gz')
References
----------
.. [1] Aganj, I., et al. 2009. ODF Reconstruction in Q-Ball Imaging
with Solid Angle Consideration.
"""
io_it = self.get_io_iterator()
for (dwi, bval, bvec, maskfile, opam, oshm, opeaks_dir,
opeaks_values, opeaks_indices, ogfa) in io_it:
logging.info('Loading {0}'.format(dwi))
vol = nib.load(dwi)
data = vol.get_data()
affine = vol.affine
bvals, bvecs = read_bvals_bvecs(bval, bvec)
gtab = gradient_table(bvals, bvecs,
b0_threshold=b0_threshold, atol=bvecs_tol)
mask_vol = nib.load(maskfile).get_data().astype(np.bool)
peaks_sphere = get_sphere('repulsion724')
logging.info('Starting CSA computations {0}'.format(dwi))
csa_model = CsaOdfModel(gtab, sh_order)
peaks_csa = peaks_from_model(model=csa_model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=odf_to_sh_order,
normalize_peaks=True,
parallel=False)
peaks_csa.affine = affine
save_peaks(opam, peaks_csa)
logging.info('Finished CSA {0}'.format(dwi))
if extract_pam_values:
peaks_to_niftis(peaks_csa, oshm, opeaks_dir,
opeaks_values,
opeaks_indices, ogfa, reshape_dirs=True)
dname_ = os.path.dirname(opam)
if dname_ == '':
logging.info('Pam5 file saved in current directory')
else:
logging.info(
'Pam5 file saved in {0}'.format(dname_))
return io_it
def deterministic(diffusion_file,
bvecs_file,
bvals_file,
outdir,
mask_file=None,
order=4,
nb_seeds_per_voxel=1,
step=0.5,
fmt="%.4f"):
""" Compute a deterministic tractography using an ODF model.
Parameters
----------
diffusion_file: str (mandatory)
a file containing the preprocessed diffusion data.
bvecs_file: str (mandatory)
a file containing the diffusion gradient directions.
bvals_file: str (mandatory)
a file containing the diffusion b-values.
outdir: str (mandatory)
the output directory.
mask_file: str (optional, default None)
an image used to mask the diffusion data during the tractography. If
not set, all the image voxels are considered.
order: int (optional, default 4)
the order of the ODF model.
nb_seeds_per_voxel: int (optional, default 1)
the number of seeds per voxel used during the propagation.
step: float (optional, default 0.5)
the integration step in voxel fraction used during the propagation.
fmt: str (optional, default '%.4f')
the saved track elements format.
Returns
-------
track_file: str
a determinist model of the white matter organization.
"""
# Read diffusion sequence
bvals, bvecs = read_bvals_bvecs(bvals_file, bvecs_file)
gtab = gradient_table(bvals, bvecs)
diffusion_array = nibabel.load(diffusion_file).get_data()
if mask_file is not None:
mask_array = nibabel.load(mask_file).get_data()
else:
mask_array = numpy.ones(diffusion_array.shape[:3], dtype=numpy.uint8)
# Estimate ODF model
csamodel = shm.CsaOdfModel(gtab, order)
csapeaks = peaks.peaks_from_model(model=csamodel,
data=diffusion_array,
sphere=peaks.default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=mask_array)
# Compute deterministic tractography in voxel space so affine is equal
# to identity
seeds = utils.seeds_from_mask(mask_array, density=nb_seeds_per_voxel)
streamline_generator = EuDX(csapeaks.peak_values,
csapeaks.peak_indices,
odf_vertices=peaks.default_sphere.vertices,
a_low=.05,
step_sz=step,
seeds=seeds)
affine = streamline_generator.affine
streamlines = list(streamline_generator)
# Save the tracks
track_file = os.path.join(outdir, "fibers.txt")
savetxt(track_file, streamlines, fmt=fmt)
return track_file
def track(dname, fdwi, fbval, fbvec, fmask=None, seed_density=1, show=False):
data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=50)
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
# compute DTI model
from dipy.reconst.dti import TensorModel
tenmodel = TensorModel(gtab) #, fit_method='OLS') #, min_signal=5000)
# fit the dti model
tenfit = tenmodel.fit(data, mask=mask)
# save fa
ffa = dname + 'tensor_fa.nii.gz'
fa_img = nib.Nifti1Image(tenfit.fa.astype(np.float32), affine)
nib.save(fa_img, ffa)
sh_order = 8 #TODO: check what that does
if data.shape[-1] < 15:
raise ValueError('You need at least 15 unique DWI volumes to '
'compute fiber ODFs. You currently have: {0}'
' DWI volumes.'.format(data.shape[-1]))
elif data.shape[-1] < 30:
sh_order = 6
# compute the response equation ?
from dipy.reconst.csdeconv import auto_response
response, ratio = auto_response(gtab, data)
response = list(response)
peaks_sphere = get_sphere('symmetric362')
#TODO: check what that does
peaks_csd = peaks_from_model(
model=tenmodel,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5, #.5
min_separation_angle=25,
mask=mask,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
fpeaks = dname + 'peaks.npz'
save_peaks(fpeaks, peaks_csd)
from dipy.io.trackvis import save_trk
from dipy.tracking import utils
from dipy.tracking.local import (ThresholdTissueClassifier, LocalTracking)
stopping_thr = 0.25 #0.25
pam = load_peaks(fpeaks)
#ffa = dname + 'tensor_fa_nomask.nii.gz'
fa, fa_affine = load_nifti(ffa)
classifier = ThresholdTissueClassifier(fa, stopping_thr)
# seeds
seed_mask = fa > 0.4 #0.4 #TODO: check this parameter
seeds = utils.seeds_from_mask(seed_mask,
density=seed_density,
affine=affine)
# tractography, if affine then in world coordinates
streamlines = LocalTracking(pam,
classifier,
seeds,
affine=affine,
step_size=.5)
# Compute streamlines and store as a list.
streamlines = list(streamlines)
ftractogram = dname + 'tractogram.trk'
#save .trk
save_trk_old_style(ftractogram, streamlines, affine, fa.shape)
if show:
#render
show_results(data, streamlines, fa, fa_affine)
def run(self,
input_files,
bvalues_files,
bvectors_files,
mask_files,
b0_threshold=0.0,
bvecs_tol=0.01,
roi_center=None,
roi_radius=10,
fa_thr=0.7,
frf=None,
extract_pam_values=False,
sh_order=8,
odf_to_sh_order=8,
out_dir='',
out_pam='peaks.pam5',
out_shm='shm.nii.gz',
out_peaks_dir='peaks_dirs.nii.gz',
out_peaks_values='peaks_values.nii.gz',
out_peaks_indices='peaks_indices.nii.gz',
out_gfa='gfa.nii.gz'):
""" Constrained spherical deconvolution
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
bvalues_files : string
Path to the bvalues files. This path may contain wildcards to use
multiple bvalues files at once.
bvectors_files : string
Path to the bvectors files. This path may contain wildcards to use
multiple bvectors files at once.
mask_files : string
Path to the input masks. This path may contain wildcards to use
multiple masks at once. (default: No mask used)
b0_threshold : float, optional
Threshold used to find b=0 directions
bvecs_tol : float, optional
Bvecs should be unit vectors. (default:0.01)
roi_center : variable int, optional
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]` (default None)
roi_radius : int, optional
radius of cubic ROI in voxels (default 10)
fa_thr : float, optional
FA threshold for calculating the response function (default 0.7)
frf : variable float, optional
Fiber response function can be for example inputed as 15 4 4
(from the command line) or [15, 4, 4] from a Python script to be
converted to float and mutiplied by 10**-4 . If None
the fiber response function will be computed automatically
(default: None).
extract_pam_values : bool, optional
Save or not to save pam volumes as single nifti files.
sh_order : int, optional
Spherical harmonics order (default 6) used in the CSA fit.
odf_to_sh_order : int, optional
Spherical harmonics order used for peak_from_model to compress
the ODF to spherical harmonics coefficients (default 8)
out_dir : string, optional
Output directory (default input file directory)
out_pam : string, optional
Name of the peaks volume to be saved (default 'peaks.pam5')
out_shm : string, optional
Name of the shperical harmonics volume to be saved
(default 'shm.nii.gz')
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved
(default 'peaks_dirs.nii.gz')
out_peaks_values : string, optional
Name of the peaks values volume to be saved
(default 'peaks_values.nii.gz')
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved
(default 'peaks_indices.nii.gz')
out_gfa : string, optional
Name of the generalise fa volume to be saved (default 'gfa.nii.gz')
References
----------
.. [1] Tournier, J.D., et al. NeuroImage 2007. Robust determination of
the fibre orientation distribution in diffusion MRI: Non-negativity
constrained super-resolved spherical deconvolution.
"""
io_it = self.get_io_iterator()
for (dwi, bval, bvec, maskfile, opam, oshm, opeaks_dir, opeaks_values,
opeaks_indices, ogfa) in io_it:
logging.info('Loading {0}'.format(dwi))
img = nib.load(dwi)
data = img.get_data()
affine = img.affine
bvals, bvecs = read_bvals_bvecs(bval, bvec)
print(b0_threshold, bvals.min())
if b0_threshold < bvals.min():
warn("b0_threshold (value: {0}) is too low, increase your "
"b0_threshold. It should higher than the first b0 value "
"({1}).".format(b0_threshold, bvals.min()))
gtab = gradient_table(bvals,
bvecs,
b0_threshold=b0_threshold,
atol=bvecs_tol)
mask_vol = nib.load(maskfile).get_data().astype(np.bool)
n_params = ((sh_order + 1) * (sh_order + 2)) / 2
if data.shape[-1] < n_params:
raise ValueError('You need at least {0} unique DWI volumes to '
'compute fiber odfs. You currently have: {1}'
' DWI volumes.'.format(
n_params, data.shape[-1]))
if frf is None:
logging.info('Computing response function')
if roi_center is not None:
logging.info(
'Response ROI center:\n{0}'.format(roi_center))
logging.info(
'Response ROI radius:\n{0}'.format(roi_radius))
response, ratio, nvox = auto_response(
gtab,
data,
roi_center=roi_center,
roi_radius=roi_radius,
fa_thr=fa_thr,
return_number_of_voxels=True)
response = list(response)
else:
logging.info('Using response function')
if isinstance(frf, str):
l01 = np.array(literal_eval(frf), dtype=np.float64)
else:
l01 = np.array(frf, dtype=np.float64)
l01 *= 10**-4
response = np.array([l01[0], l01[1], l01[1]])
ratio = l01[1] / l01[0]
response = (response, ratio)
logging.info(
'Eigenvalues for the frf of the input data are :{0}'.format(
response[0]))
logging.info(
'Ratio for smallest to largest eigen value is {0}'.format(
ratio))
peaks_sphere = get_sphere('repulsion724')
logging.info('CSD computation started.')
csd_model = ConstrainedSphericalDeconvModel(gtab,
response,
sh_order=sh_order)
peaks_csd = peaks_from_model(model=csd_model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
save_peaks(opam, peaks_csd)
logging.info('CSD computation completed.')
if extract_pam_values:
peaks_to_niftis(peaks_csd,
oshm,
opeaks_dir,
opeaks_values,
opeaks_indices,
ogfa,
reshape_dirs=True)
dname_ = os.path.dirname(opam)
if dname_ == '':
logging.info('Pam5 file saved in current directory')
else:
logging.info('Pam5 file saved in {0}'.format(dname_))
return io_it
t1 = read_stanford_t1()
t1_data = t1.get_data()
"""
We've loaded an image called ``labels_img`` which is a map of tissue types such
that every integer value in the array ``labels`` represents an anatomical
structure or tissue type [#]_. For this example, the image was created so that
white matter voxels have values of either 1 or 2. We'll use
``peaks_from_model`` to apply the ``CsaOdfModel`` to each white matter voxel
and estimate fiber orientations which we can use for tracking.
"""
white_matter = (labels == 1) | (labels == 2)
csamodel = shm.CsaOdfModel(gtab, 6)
csapeaks = peaks.peaks_from_model(model=csamodel,
data=data,
sphere=peaks.default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=white_matter)
"""
Now we can use EuDX to track all of the white matter. To keep things reasonably
fast we use ``density=2`` which will result in 8 seeds per voxel. We'll set
``a_low`` (the parameter which determines the threshold of FA/QA under which
tracking stops) to be very low because we've already applied a white matter
mask.
"""
seeds = utils.seeds_from_mask(white_matter, density=2)
streamline_generator = EuDX(csapeaks.peak_values,
csapeaks.peak_indices,
odf_vertices=peaks.default_sphere.vertices,
a_low=.05,
"""
We will first run `peaks_from_model` using parallelism with 2 processes. If
`nbr_processes` is None (default option) then this function will find the total
number of processors from the operating system and use this number as
`nbr_processes`. Sometimes it makes sense to use only a few of the processes in
order to allow resources for other applications. However, most of the times
using the default option will be sufficient.
"""
csapeaks_parallel = peaks_from_model(model=csamodel,
data=maskdata,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True,
npeaks=5,
parallel=True,
nbr_processes=2)
time_parallel = time.time() - start_time
print("peaks_from_model using 2 processes ran in : " +
str(time_parallel) + " seconds")
"""
peaks_from_model using 2 process ran in : 114.333221912 seconds, using 2 process
If we don't use parallelism then we need to set `parallel=False`:
"""
def compCsdPeaks(basename, output, mask=None):
home = os.getcwd()
fbase = basename
fdwi = fbase+".nii.gz"
fbval = fbase+".bval"
fbvec = fbase+".bvec"
print fdwi,fbval,fbvec
img = nib.load(fdwi)
data = img.get_data()
zooms = img.get_header().get_zooms()[:3]
affine = img.get_affine()
# reslice image into 1x1x1 iso voxel
# new_zooms = (1., 1., 1.)
# data, affine = resample(data, affine, zooms, new_zooms)
# img = nib.Nifti1Image(data, affine)
#
# print data.shape
# print img.get_header().get_zooms()
# print "###"
#
# nib.save(img, 'C5_iso.nii.gz')
bval, bvec = dio.read_bvals_bvecs(fbval, fbvec)
# invert bvec z for GE scanner
bvec[:,1]*= -1
gtab = dgrad.gradient_table(bval, bvec)
if mask is None:
print 'generate mask'
maskdata, mask = median_otsu(data, 3, 1, False, vol_idx=range(10, 50), dilate=2)
else:
mask = nib.load(mask).get_data()
maskdata = applymask(data, mask)
# tenmodel = dti.TensorModel(gtab)
# tenfit = tenmodel.fit(data)
# print('Computing anisotropy measures (FA, MD, RGB)')
#
#
# FA = fractional_anisotropy(tenfit.evals)
# FA[np.isnan(FA)] = 0
#
# fa_img = nib.Nifti1Image(FA.astype(np.float32), img.get_affine())
# nib.save(fa_img, 'FA.nii.gz')
#
# return
# estimate response function, ratio should be ~0.2
response, ratio = auto_response(gtab, maskdata, roi_radius=10, fa_thr=0.7)
print response, ratio
# reconstruct csd model
print "estimate csd_model"
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
#a_data = maskdata[40:80, 40:80, 60:61]
#c_data = maskdata[40:80, 59:60, 50:80]
#s_data = maskdata[59:60, 40:70, 30:80]
#data_small = a_data
#
# evals = response[0]
# evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
#sphere = get_sphere('symmetric362')
#csd_fit = csd_model.fit(data_small)
#csd_odf = csd_fit.odf(sphere)
#
#
#fodf_spheres = fvtk.sphere_funcs(csd_odf, sphere, scale=1, norm=False)
##fodf_spheres.GetProperty().SetOpacity(0.4)
##
#fvtk.add(ren, fodf_spheres)
##fvtk.add(ren, fodf_peaks)
#fvtk.show(ren)
#
#sys.exit()
# fit csd peaks
print "fit csd peaks"
print "peaks_from_model using core# =" + str(multiprocessing.cpu_count())
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, nbr_processes=10)
#fodf_peaks = fvtk.peaks(csd_peaks.peak_dirs, csd_peaks.peak_values, scale=1)
# fd, fname = mkstemp()
# pickle.save_pickle(fname, csd_peaks)
#
# os.close(fd)
#pickle.dump(csd_peaks, open("csd.p", "wb"))
with open(output, 'wb') as fout:
cPickle.dump(csd_peaks, fout, -1)
print "done writing to file %s"% (output)
return csd_peaks
from dipy.data import get_sphere
sphere = get_sphere()
from dipy.reconst import sfm
sf_model = sfm.SparseFascicleModel(gtab, sphere=sphere, l1_ratio=0.5, alpha=0.001, response=response[0])
"""
We fit this model to the data in each voxel in the white-matter mask, so that
we can use these directions in tracking:
"""
from dipy.reconst.peaks import peaks_from_model
pnm = peaks_from_model(
sf_model, data, sphere, relative_peak_threshold=0.5, min_separation_angle=25, mask=white_matter, parallel=True
)
"""
A ThresholdTissueClassifier object is used to segment the data to track only
through areas in which the Generalized Fractional Anisotropy (GFA) is
sufficiently high.
"""
from dipy.tracking.local import ThresholdTissueClassifier
classifier = ThresholdTissueClassifier(pnm.gfa, 0.25)
"""
Tracking will be started from a set of seeds evenly distributed in the white
matter:
def dodata(f_name, data_path):
dipy_home = pjoin(os.path.expanduser('~'), 'dipy_data')
folder = pjoin(dipy_home, data_path)
fraw = pjoin(folder, f_name + '.nii.gz')
fbval = pjoin(folder, f_name + '.bval')
fbvec = pjoin(folder, f_name + '.bvec')
flabels = pjoin(folder, f_name + '.nii-label.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)
img = nib.load(fraw)
data = img.get_data()
affine = img.get_affine()
label_img = nib.load(flabels)
labels = label_img.get_data()
lap = through_label_sl.label_position(labels, labelValue=1)
dataslice = data[40:80, 20:80, lap[2][2] / 2]
#print lap[2][2]/2
#get_csd_gfa(f_name,data,gtab,dataslice)
maskdata, mask = median_otsu(data,
2,
1,
False,
vol_idx=range(10, 50),
dilate=2) #不去背景
""" get fa and tensor evecs and ODF"""
from dipy.reconst.dti import TensorModel, mean_diffusivity
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
sphere = get_sphere('symmetric724')
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
np.save(os.getcwd() + '\zhibiao' + f_name + '_FA.npy', FA)
fa_img = nib.Nifti1Image(FA.astype(np.float32), affine)
nib.save(fa_img, os.getcwd() + '\zhibiao' + f_name + '_FA.nii.gz')
print('Saving "DTI_tensor_fa.nii.gz" sucessful.')
evecs_img = nib.Nifti1Image(tenfit.evecs.astype(np.float32), affine)
nib.save(evecs_img,
os.getcwd() + '\zhibiao' + f_name + '_DTI_tensor_evecs.nii.gz')
print('Saving "DTI_tensor_evecs.nii.gz" sucessful.')
MD1 = mean_diffusivity(tenfit.evals)
nib.save(nib.Nifti1Image(MD1.astype(np.float32), img.get_affine()),
os.getcwd() + '\zhibiao' + f_name + '_MD.nii.gz')
#tensor_odfs = tenmodel.fit(data[20:50, 55:85, 38:39]).odf(sphere)
#from dipy.reconst.odf import gfa
#dti_gfa=gfa(tensor_odfs)
wm_mask = (np.logical_or(FA >= 0.4,
(np.logical_and(FA >= 0.15, MD >= 0.0011))))
response = recursive_response(gtab,
data,
mask=wm_mask,
sh_order=8,
peak_thr=0.01,
init_fa=0.08,
init_trace=0.0021,
iter=8,
convergence=0.001,
parallel=False)
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
#csd_fit = csd_model.fit(data)
from dipy.direction import peaks_from_model
csd_peaks = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
GFA = csd_peaks.gfa
nib.save(GFA, os.getcwd() + '\zhibiao' + f_name + '_MSD.nii.gz')
print('Saving "GFA.nii.gz" sucessful.')
from dipy.reconst.shore import ShoreModel
asm = ShoreModel(gtab)
print('Calculating...SHORE msd')
asmfit = asm.fit(data, mask)
msd = asmfit.msd()
msd[np.isnan(msd)] = 0
#print GFA[:,:,slice].T
print('Saving msd_img.png')
nib.save(msd, os.getcwd() + '\zhibiao' + f_name + '_GFA.nii.gz')
"""
`Peaks_from_model` is used to calculate properties of the ODFs (Orientation
Distribution Function) and return for
example the peaks and their indices, or GFA which is similar to FA but for ODF
based models. This function mainly needs a reconstruction model, the data and a
sphere as input. The sphere is an object that represents the spherical discrete
grid where the ODF values will be evaluated.
"""
sphere = get_sphere('symmetric724')
csapeaks = peaks_from_model(model=csamodel,
data=maskdata,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True)
GFA = csapeaks.gfa
print('GFA.shape (%d, %d, %d)' % GFA.shape)
"""
GFA.shape ``(81, 106, 76)``
Apart from GFA, csapeaks also has the attributes peak_values, peak_indices and
ODF. peak_values shows the maxima values of the ODF and peak_indices gives us
their position on the discrete sphere that was used to do the reconstruction of
the ODF. In order to obtain the full ODF, return_odf should be True. Before
ODF = gqfit.odf(sphere)
print('ODF.shape (%d, %d, %d)' % ODF.shape)
"""
ODF.shape ``(96, 96, 724)``
Using peaks_from_model we can find the main peaks of the ODFs and other
properties.
"""
gqpeaks = peaks_from_model(model=gqmodel,
data=dataslice,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True)
gqpeak_values = gqpeaks.peak_values
"""
gqpeak_indices show which sphere points have the maximum values.
"""
gqpeak_indices = gqpeaks.peak_indices
"""
It is also possible to calculate GFA.
"""
def _run_interface(self, runtime):
from dipy.reconst.peaks import peaks_from_model
from dipy.tracking.eudx import EuDX
from dipy.data import get_sphere
# import marshal as pickle
import pickle as pickle
import gzip
if (not (isdefined(self.inputs.in_model)
or isdefined(self.inputs.in_peaks))):
raise RuntimeError(('At least one of in_model or in_peaks should '
'be supplied'))
img = nb.load(self.inputs.in_file)
imref = nb.four_to_three(img)[0]
affine = img.affine
data = img.get_data().astype(np.float32)
hdr = imref.header.copy()
hdr.set_data_dtype(np.float32)
hdr['data_type'] = 16
sphere = get_sphere('symmetric724')
self._save_peaks = False
if isdefined(self.inputs.in_peaks):
IFLOGGER.info('Peaks file found, skipping ODF peaks search...')
f = gzip.open(self.inputs.in_peaks, 'rb')
peaks = pickle.load(f)
f.close()
else:
self._save_peaks = True
IFLOGGER.info('Loading model and computing ODF peaks')
f = gzip.open(self.inputs.in_model, 'rb')
odf_model = pickle.load(f)
f.close()
peaks = peaks_from_model(
model=odf_model,
data=data,
sphere=sphere,
relative_peak_threshold=self.inputs.peak_threshold,
min_separation_angle=self.inputs.min_angle,
parallel=self.inputs.multiprocess)
f = gzip.open(self._gen_filename('peaks', ext='.pklz'), 'wb')
pickle.dump(peaks, f, -1)
f.close()
hdr.set_data_shape(peaks.gfa.shape)
nb.Nifti1Image(peaks.gfa.astype(np.float32), affine,
hdr).to_filename(self._gen_filename('gfa'))
IFLOGGER.info('Performing tractography')
if isdefined(self.inputs.tracking_mask):
msk = nb.load(self.inputs.tracking_mask).get_data()
msk[msk > 0] = 1
msk[msk < 0] = 0
else:
msk = np.ones(imref.shape)
gfa = peaks.gfa * msk
seeds = self.inputs.num_seeds
if isdefined(self.inputs.seed_coord):
seeds = np.loadtxt(self.inputs.seed_coord)
elif isdefined(self.inputs.seed_mask):
seedmsk = nb.load(self.inputs.seed_mask).get_data()
assert (seedmsk.shape == data.shape[:3])
seedmsk[seedmsk > 0] = 1
seedmsk[seedmsk < 1] = 0
seedps = np.array(np.where(seedmsk == 1), dtype=np.float32).T
vseeds = seedps.shape[0]
nsperv = (seeds // vseeds) + 1
IFLOGGER.info(
'Seed mask is provided (%d voxels inside '
'mask), computing seeds (%d seeds/voxel).', vseeds, nsperv)
if nsperv > 1:
IFLOGGER.info('Needed %d seeds per selected voxel (total %d).',
nsperv, vseeds)
seedps = np.vstack(np.array([seedps] * nsperv))
voxcoord = seedps + np.random.uniform(-1, 1, size=seedps.shape)
nseeds = voxcoord.shape[0]
seeds = affine.dot(
np.vstack((voxcoord.T, np.ones((1, nseeds)))))[:3, :].T
if self.inputs.save_seeds:
np.savetxt(self._gen_filename('seeds', ext='.txt'), seeds)
if isdefined(self.inputs.tracking_mask):
tmask = msk
a_low = 0.1
else:
tmask = gfa
a_low = self.inputs.gfa_thresh
eu = EuDX(tmask,
peaks.peak_indices[..., 0],
seeds=seeds,
affine=affine,
odf_vertices=sphere.vertices,
a_low=a_low)
ss_mm = [np.array(s) for s in eu]
trkfilev = nb.trackvis.TrackvisFile([(s, None, None) for s in ss_mm],
points_space='rasmm',
affine=np.eye(4))
trkfilev.to_file(self._gen_filename('tracked', ext='.trk'))
return runtime
parallel. If ``nbr_processes`` is None it will figure out automatically the
number of CPUs available in your system. Alternatively, you can set
``nbr_processes`` manually. Here, we show an example were we compare the
duration of execution with or without parallelism.
"""
import time
from dipy.reconst.peaks import peaks_from_model
start_time = time.time()
csd_peaks_parallel = peaks_from_model(model=csd_model,
data=data,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_sh=True,
return_odf=False,
normalize_peaks=True,
npeaks=5,
parallel=True,
nbr_processes=None)
time_parallel = time.time() - start_time
print("peaks_from_model using " + str(multiprocessing.cpu_count()) +
" process ran in :" + str(time_parallel) + " seconds")
"""
``peaks_from_model`` using 8 processes ran in :114.425682068 seconds
"""
start_time = time.time()
csd_peaks = peaks_from_model(model=csd_model,
Distribution Function) and return for
example the peaks and their indices, or GFA which is similar to FA but for ODF
based models. This function mainly needs a reconstruction model, the data and a
sphere as input. The sphere is an object that represents the spherical discrete
grid where the ODF values will be evaluated.
"""
sphere = get_sphere('symmetric724')
start_time = time.time()
csapeaks_parallel = peaks_from_model(model=csamodel,
data=data,
sphere=sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=None,
return_odf=False,
normalize_peaks=True,
npeaks=5,
parallel=True,
nbr_processes=2) # default multiprocessing.cpu_count()
time_parallel = time.time() - start_time
print("peaks_from_model using 2 processes ran in : " +
str(time_parallel) + " seconds")
"""
peaks_from_model using 2 process ran in : 114.333221912 seconds, using 2 process
"""
start_time = time.time()
csapeaks = peaks_from_model(model=csamodel,
def run(self,
input_files,
bvalues,
bvectors,
mask_files,
b0_threshold=0.0,
extract_pam_values=False,
out_dir='',
out_pam='peaks.pam5',
out_shm='shm.nii.gz',
out_peaks_dir='peaks_dirs.nii.gz',
out_peaks_values='peaks_values.nii.gz',
out_peaks_indices='peaks_indices.nii.gz',
out_gfa='gfa.nii.gz'):
""" Workflow for peaks computation. Peaks computation is done by 'globing'
``input_files`` and saves the peaks in a directory specified by
``out_dir``.
Parameters
----------
input_files : string
Path to the input volumes. This path may contain wildcards to
process multiple inputs at once.
bvalues : string
Path to the bvalues files. This path may contain wildcards to use
multiple bvalues files at once.
bvectors : string
Path to the bvalues files. This path may contain wildcards to use
multiple bvalues files at once.
mask_files : string
Path to the input masks. This path may contain wildcards to use
multiple masks at once. (default: No mask used)
b0_threshold : float, optional
Threshold used to find b=0 directions
extract_pam_values : bool, optional
Wheter or not to save pam volumes as single nifti files.
out_dir : string, optional
Output directory (default input file directory)
out_pam : string, optional
Name of the peaks volume to be saved (default 'peaks.pam5')
out_shm : string, optional
Name of the shperical harmonics volume to be saved
(default 'shm.nii.gz')
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved
(default 'peaks_dirs.nii.gz')
out_peaks_values : string, optional
Name of the peaks values volume to be saved
(default 'peaks_values.nii.gz')
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved
(default 'peaks_indices.nii.gz')
out_gfa : string, optional
Name of the generalise fa volume to be saved (default 'gfa.nii.gz')
"""
io_it = self.get_io_iterator()
for dwi, bval, bvec, maskfile, opam, oshm, opeaks_dir, \
opeaks_values, opeaks_indices, ogfa in io_it:
logging.info('Computing fiber odfs for {0}'.format(dwi))
vol = nib.load(dwi)
data = vol.get_data()
affine = vol.get_affine()
bvals, bvecs = read_bvals_bvecs(bval, bvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold)
mask_vol = nib.load(maskfile).get_data().astype(np.bool)
sh_order = 8
if data.shape[-1] < 15:
raise ValueError('You need at least 15 unique DWI volumes to '
'compute fiber odfs. You currently have: {0}'
' DWI volumes.'.format(data.shape[-1]))
elif data.shape[-1] < 30:
sh_order = 6
response, ratio = auto_response(gtab, data)
response = list(response)
logging.info(
'Eigenvalues for the frf of the input data are :{0}'.format(
response[0]))
logging.info(
'Ratio for smallest to largest eigen value is {0}'.format(
ratio))
peaks_sphere = get_sphere('symmetric362')
csa_model = CsaOdfModel(gtab, sh_order)
peaks_csa = peaks_from_model(model=csa_model,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask_vol,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csa.affine = affine
save_peaks(opam, peaks_csa)
if extract_pam_values:
peaks_to_niftis(peaks_csa,
oshm,
opeaks_dir,
opeaks_values,
opeaks_indices,
ogfa,
reshape_dirs=True)
logging.info('Peaks saved in {0}'.format(os.path.dirname(opam)))
return io_it