def main():
start = time.time()
with open('config.json') as config_json:
config = json.load(config_json)
# Load the data
dmri_image = nib.load(config['data_file'])
dmri = dmri_image.get_data()
print('Dmri' + str(dmri.shape))
#aparc_im = nib.load(config['freesurfer'])
aparc_im = nib.load("volume.nii.gz")
aparc = aparc_im.get_data()
print('Aparc' + str(aparc.shape))
end = time.time()
print('Loaded Files: ' + str((end - start)))
# Create the white matter mask
start = time.time()
wm_regions = [
2, 41, 16, 17, 28, 60, 51, 53, 12, 52, 12, 52, 13, 18, 54, 50, 11, 251,
252, 253, 254, 255, 10, 49, 46, 7
]
wm_mask = np.zeros(aparc.shape)
for l in wm_regions:
wm_mask[aparc == l] = 1
print('Created white matter mask: ' + str(time.time() - start))
# Create the gradient table from the bvals and bvecs
start = time.time()
bvals, bvecs = read_bvals_bvecs(config['data_bval'], config['data_bvec'])
gtab = gradient_table(bvals, bvecs, b0_threshold=100)
end = time.time()
print('Created Gradient Table: ' + str((end - start)))
# Create the csa model and calculate peaks
start = time.time()
csa_model = CsaOdfModel(gtab, sh_order=6)
print('Created CSA Model: ' + str(time.time() - start))
csa_peaks = peaks_from_model(csa_model,
dmri,
default_sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=wm_mask)
print('Generated peaks: ' + str(time.time() - start))
save_peaks('peaks.pam5', csa_peaks)
def test_io_peaks():
with InTemporaryDirectory():
fname = 'test.pam5'
pam = PeaksAndMetrics()
pam.affine = np.eye(4)
pam.peak_dirs = np.random.rand(10, 10, 10, 5, 3)
pam.peak_values = np.zeros((10, 10, 10, 5))
pam.peak_indices = np.zeros((10, 10, 10, 5))
pam.shm_coeff = np.zeros((10, 10, 10, 45))
pam.sphere = default_sphere
pam.B = np.zeros((45, default_sphere.vertices.shape[0]))
pam.total_weight = 0.5
pam.ang_thr = 60
pam.gfa = np.zeros((10, 10, 10))
pam.qa = np.zeros((10, 10, 10, 5))
pam.odf = np.zeros((10, 10, 10, default_sphere.vertices.shape[0]))
save_peaks(fname, pam)
pam2 = load_peaks(fname, verbose=True)
npt.assert_array_equal(pam.peak_dirs, pam2.peak_dirs)
pam2.affine = None
fname2 = 'test2.pam5'
save_peaks(fname2, pam2, np.eye(4))
pam2_res = load_peaks(fname2, verbose=True)
npt.assert_array_equal(pam.peak_dirs, pam2_res.peak_dirs)
pam3 = load_peaks(fname2, verbose=False)
for attr in [
'peak_dirs', 'peak_values', 'peak_indices', 'gfa', 'qa',
'shm_coeff', 'B', 'odf'
]:
npt.assert_array_equal(getattr(pam3, attr), getattr(pam, attr))
npt.assert_equal(pam3.total_weight, pam.total_weight)
npt.assert_equal(pam3.ang_thr, pam.ang_thr)
npt.assert_array_almost_equal(pam3.sphere.vertices,
pam.sphere.vertices)
fname3 = 'test3.pam5'
pam4 = PeaksAndMetrics()
npt.assert_raises(ValueError, save_peaks, fname3, pam4)
fname4 = 'test4.pam5'
del pam.affine
save_peaks(fname4, pam, affine=None)
fname5 = 'test5.pkm'
npt.assert_raises(IOError, save_peaks, fname5, pam)
pam.affine = np.eye(4)
fname6 = 'test6.pam5'
save_peaks(fname6, pam, verbose=True)
del pam.shm_coeff
save_peaks(fname6, pam, verbose=False)
pam.shm_coeff = np.zeros((10, 10, 10, 45))
del pam.odf
save_peaks(fname6, pam)
pam_tmp = load_peaks(fname6, True)
npt.assert_equal(pam_tmp.odf, None)
fname7 = 'test7.paw'
npt.assert_raises(IOError, load_peaks, fname7)
del pam.shm_coeff
save_peaks(fname6, pam, verbose=True)
fname_shm = 'shm.nii.gz'
fname_dirs = 'dirs.nii.gz'
fname_values = 'values.nii.gz'
fname_indices = 'indices.nii.gz'
fname_gfa = 'gfa.nii.gz'
pam.shm_coeff = np.ones((10, 10, 10, 45))
peaks_to_niftis(pam,
fname_shm,
fname_dirs,
fname_values,
fname_indices,
fname_gfa,
reshape_dirs=False)
os.path.isfile(fname_shm)
os.path.isfile(fname_dirs)
os.path.isfile(fname_values)
os.path.isfile(fname_indices)
os.path.isfile(fname_gfa)
def run(self,
input_files,
bvalues_files,
bvectors_files,
mask_files,
sh_order=6,
odf_to_sh_order=8,
b0_threshold=50.0,
bvecs_tol=0.01,
extract_pam_values=False,
parallel=False,
nbr_processes=None,
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 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.
b0_threshold : float, optional
Threshold used to find b0 volumes.
bvecs_tol : float, optional
Threshold used so that norm(bvec)=1.
extract_pam_values : bool, optional
Whether or not to save pam volumes as single nifti files.
parallel : bool, optional
Whether to use parallelization in peak-finding during the
calibration procedure.
nbr_processes : int, optional
If `parallel` is True, the number of subprocesses to use
(default multiprocessing.cpu_count()).
out_dir : string, optional
Output directory. (default current directory)
out_pam : string, optional
Name of the peaks volume to be saved.
out_shm : string, optional
Name of the spherical harmonics volume to be saved.
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved.
out_peaks_values : string, optional
Name of the peaks values volume to be saved.
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved.
out_gfa : string, optional
Name of the generalized FA volume to be saved.
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))
data, affine = load_nifti(dwi)
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 be 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 = load_nifti_data(maskfile).astype(bool)
peaks_sphere = default_sphere
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=parallel,
nbr_processes=nbr_processes)
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 run(self,
input_files,
bvalues_files,
bvectors_files,
mask_files,
b0_threshold=50.0,
bvecs_tol=0.01,
roi_center=None,
roi_radii=10,
fa_thr=0.7,
frf=None,
extract_pam_values=False,
sh_order=8,
odf_to_sh_order=8,
parallel=False,
nbr_processes=None,
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 b0 volumes.
bvecs_tol : float, optional
Bvecs should be unit vectors.
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]`.
roi_radii : int or array-like, optional
radii of cuboid ROI in voxels.
fa_thr : float, optional
FA threshold for calculating the response function.
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 multiplied by 10**-4 . If None
the fiber response function will be computed automatically.
extract_pam_values : bool, optional
Save or not to save pam volumes as single nifti files.
sh_order : int, optional
Spherical harmonics order 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.
parallel : bool, optional
Whether to use parallelization in peak-finding during the
calibration procedure.
nbr_processes : int, optional
If `parallel` is True, the number of subprocesses to use
(default multiprocessing.cpu_count()).
out_dir : string, optional
Output directory. (default current directory)
out_pam : string, optional
Name of the peaks volume to be saved.
out_shm : string, optional
Name of the spherical harmonics volume to be saved.
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved.
out_peaks_values : string, optional
Name of the peaks values volume to be saved.
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved.
out_gfa : string, optional
Name of the generalized FA volume to be saved.
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))
data, affine = load_nifti(dwi)
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 be 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 = load_nifti_data(maskfile).astype(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 radii:\n{0}'.format(roi_radii))
response, ratio = auto_response_ssst(gtab,
data,
roi_center=roi_center,
roi_radii=roi_radii,
fa_thr=fa_thr)
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 = default_sphere
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=parallel,
nbr_processes=nbr_processes)
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 test_io_peaks():
with InTemporaryDirectory():
fname = 'test.pam5'
sphere = get_sphere('repulsion724')
pam = PeaksAndMetrics()
pam.affine = np.eye(4)
pam.peak_dirs = np.random.rand(10, 10, 10, 5, 3)
pam.peak_values = np.zeros((10, 10, 10, 5))
pam.peak_indices = np.zeros((10, 10, 10, 5))
pam.shm_coeff = np.zeros((10, 10, 10, 45))
pam.sphere = sphere
pam.B = np.zeros((45, sphere.vertices.shape[0]))
pam.total_weight = 0.5
pam.ang_thr = 60
pam.gfa = np.zeros((10, 10, 10))
pam.qa = np.zeros((10, 10, 10, 5))
pam.odf = np.zeros((10, 10, 10, sphere.vertices.shape[0]))
save_peaks(fname, pam)
pam2 = load_peaks(fname, verbose=True)
npt.assert_array_equal(pam.peak_dirs, pam2.peak_dirs)
pam2.affine = None
fname2 = 'test2.pam5'
save_peaks(fname2, pam2, np.eye(4))
pam2_res = load_peaks(fname2, verbose=True)
npt.assert_array_equal(pam.peak_dirs, pam2_res.peak_dirs)
pam3 = load_peaks(fname2, verbose=False)
for attr in ['peak_dirs', 'peak_values', 'peak_indices',
'gfa', 'qa', 'shm_coeff', 'B', 'odf']:
npt.assert_array_equal(getattr(pam3, attr),
getattr(pam, attr))
npt.assert_equal(pam3.total_weight, pam.total_weight)
npt.assert_equal(pam3.ang_thr, pam.ang_thr)
npt.assert_array_almost_equal(pam3.sphere.vertices,
pam.sphere.vertices)
fname3 = 'test3.pam5'
pam4 = PeaksAndMetrics()
npt.assert_raises(ValueError, save_peaks, fname3, pam4)
fname4 = 'test4.pam5'
del pam.affine
save_peaks(fname4, pam, affine=None)
fname5 = 'test5.pkm'
npt.assert_raises(IOError, save_peaks, fname5, pam)
pam.affine = np.eye(4)
fname6 = 'test6.pam5'
save_peaks(fname6, pam, verbose=True)
del pam.shm_coeff
save_peaks(fname6, pam, verbose=False)
pam.shm_coeff = np.zeros((10, 10, 10, 45))
del pam.odf
save_peaks(fname6, pam)
pam_tmp = load_peaks(fname6, True)
npt.assert_equal(pam_tmp.odf, None)
fname7 = 'test7.paw'
npt.assert_raises(IOError, load_peaks, fname7)
del pam.shm_coeff
save_peaks(fname6, pam, verbose=True)
fname_shm = 'shm.nii.gz'
fname_dirs = 'dirs.nii.gz'
fname_values = 'values.nii.gz'
fname_indices = 'indices.nii.gz'
fname_gfa = 'gfa.nii.gz'
pam.shm_coeff = np.ones((10, 10, 10, 45))
peaks_to_niftis(pam, fname_shm, fname_dirs, fname_values,
fname_indices, fname_gfa, reshape_dirs=False)
os.path.isfile(fname_shm)
os.path.isfile(fname_dirs)
os.path.isfile(fname_values)
os.path.isfile(fname_indices)
os.path.isfile(fname_gfa)
def run(self, input_files, bvalues_files, bvectors_files, mask_files,
sh_order=6, odf_to_sh_order=8, b0_threshold=50.0, bvecs_tol=0.01,
extract_pam_values=False, parallel=False, nbr_processes=None,
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.
parallel : bool, optional
Whether to use parallelization in peak-finding during the
calibration procedure. Default: False
nbr_processes : int, optional
If `parallel` is True, the number of subprocesses to use
(default multiprocessing.cpu_count()).
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))
data, affine = load_nifti(dwi)
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=parallel,
nbr_processes=nbr_processes)
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 run(self, input_files, bvalues_files, bvectors_files, mask_files,
b0_threshold=50.0, 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, parallel=False, nbr_processes=None,
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)
parallel : bool, optional
Whether to use parallelization in peak-finding during the
calibration procedure. Default: False
nbr_processes : int, optional
If `parallel` is True, the number of subprocesses to use
(default multiprocessing.cpu_count()).
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))
data, affine = load_nifti(dwi)
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=parallel,
nbr_processes=nbr_processes)
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 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 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)
def tracking(folder):
print('Tracking in ' + folder)
output_folder = folder + 'dipy_out/'
# make a folder to save new data into
try:
Path(output_folder).mkdir(parents=True, exist_ok=True)
except OSError:
print('Could not create output dir. Aborting...')
return
# load data
print('Loading data...')
img = nib.load(folder + 'data.nii.gz')
dmri = np.asarray(img.dataobj)
affine = img.affine
mask, _ = load_nifti(folder + 'nodif_brain_mask.nii.gz')
bvals, bvecs = read_bvals_bvecs(folder + 'bvals', folder + 'bvecs')
gtab = gradient_table(bvals, bvecs)
# extract peaksoutput_folder + 'peak_vals.nii.gz'
if Path(output_folder + 'peaks.pam5').exists():
peaks = load_peaks(output_folder + 'peaks.pam5')
else:
print('Extracting peaks...')
response, ration = auto_response(gtab, dmri, roi_radius=10, fa_thr=.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
peaks = peaks_from_model(model=csd_model,
data=dmri,
sphere=default_sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=True)
save_peaks(output_folder + 'peaks.pam5', peaks, affine)
scaled = peaks.peak_dirs * np.repeat(
np.expand_dims(peaks.peak_values, -1), 3, -1)
cropped = scaled[:, :, :, :3, :].reshape(dmri.shape[:3] + (9, ))
save_nifti(output_folder + 'peaks.nii.gz', cropped, affine)
#save_nifti(output_folder + 'peak_dirs.nii.gz', peaks.peak_dirs, affine)
#save_nifti(output_folder + 'peak_vals.nii.gz', peaks.peak_values, affine)
# tracking
print('Tracking...')
maskdata, mask = median_otsu(dmri,
vol_idx=range(0, dmri.shape[3]),
median_radius=3,
numpass=1,
autocrop=True,
dilate=2)
tensor_model = TensorModel(gtab, fit_method='WLS')
tensor_fit = tensor_model.fit(maskdata)
fa = fractional_anisotropy(tensor_fit.evals)
fa[np.isnan(fa)] = 0
bla = np.average(fa)
tissue_classifier = ThresholdStoppingCriterion(fa, .1)
seeds = random_seeds_from_mask(fa > 1e-5, affine, seeds_count=1)
streamline_generator = LocalTracking(direction_getter=peaks,
stopping_criterion=tissue_classifier,
seeds=seeds,
affine=affine,
step_size=.5)
streamlines = Streamlines(streamline_generator)
save_trk(StatefulTractogram(streamlines, img, Space.RASMM),
output_folder + 'whole_brain.trk')
# Elef add CSD version and add MTMSCSD when is ready.
pass
pam = peaks_from_model(model,
data,
sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=mask,
parallel=parallel)
ten_model = TensorModel(gtab)
fa = ten_model.fit(data, mask).fa
save_nifti(ffa, fa, affine)
save_peaks(fpam5, pam, affine)
show_odfs_and_fa(fa, pam, mask, None, sphere, ftmp='odf.mmap', basis_type=None)
pve_csf, pve_gm, pve_wm = pve[..., 0], pve[..., 1], pve[..., 2]
cmc_classifier = CmcTissueClassifier.from_pve(
pve_wm,
pve_gm,
pve_csf,
step_size=step_size,
average_voxel_size=np.average(vox_size))
seed_mask = np.zeros(mask.shape)
seed_mask[mask > 0] = 1
seed_mask[pve_wm < 0.5] = 0
pass
pam = peaks_from_model(model, data, sphere,
relative_peak_threshold=.8,
min_separation_angle=45,
mask=mask, parallel=parallel)
ten_model = TensorModel(gtab)
fa = ten_model.fit(data, mask).fa
save_nifti(ffa, fa, affine)
save_peaks(fpam5, pam, affine)
show_odfs_and_fa(fa, pam, mask, None, sphere, ftmp='odf.mmap',
basis_type=None)
pve_csf, pve_gm, pve_wm = pve[..., 0], pve[..., 1], pve[..., 2]
cmc_classifier = CmcTissueClassifier.from_pve(
pve_wm,
pve_gm,
pve_csf,
step_size=step_size,
average_voxel_size=np.average(vox_size))
seed_mask = np.zeros(mask.shape)
seed_mask[mask > 0] = 1
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
