def read_aal_atlas(resample_to=None):
"""
Reads the AAL atlas [1]_.
Parameters
----------
template : nib.Nifti1Image class instance, optional
If provided, this is the template used and AAL atlas should be
registered and aligned to this template
.. [1] Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O,
Delcroix N, Mazoyer B, Joliot M. (2002). Automated anatomical
labeling of activations in SPM using a macroscopic anatomical
parcellation of the MNI MRI single-subject brain. Neuroimage. 2002;
15(1):273-89.
"""
file_dict, folder = fetch_aal_atlas()
out_dict = {}
for f in file_dict:
if f.endswith('.txt'):
out_dict['labels'] = pd.read_csv(op.join(folder, f))
else:
out_dict['atlas'] = nib.load(op.join(folder, f))
if resample_to is not None:
data = out_dict['atlas'].get_fdata()
oo = []
for ii in range(data.shape[-1]):
oo.append(
reg.resample(data[..., ii], resample_to,
out_dict['atlas'].affine, resample_to.affine))
out_dict['atlas'] = nib.Nifti1Image(np.stack(oo, -1),
resample_to.affine)
return out_dict
def visualize_roi(roi,
affine_or_mapping=None,
static_img=None,
roi_affine=None,
static_affine=None,
reg_template=None,
scene=None,
color=np.array([1, 0, 0]),
opacity=1.0,
inline=False,
interact=False):
"""
Render a region of interest into a VTK viz as a volume
"""
if not isinstance(roi, np.ndarray):
if isinstance(roi, str):
roi = nib.load(roi).get_fdata()
else:
roi = roi.get_fdata()
if affine_or_mapping is not None:
if isinstance(affine_or_mapping, np.ndarray):
# This is an affine:
if (static_img is None or roi_affine is None
or static_affine is None):
raise ValueError(
"If using an affine to transform an ROI, "
"need to also specify all of the following",
"inputs: `static_img`, `roi_affine`, ", "`static_affine`")
roi = reg.resample(roi, static_img, roi_affine, static_affine)
else:
# Assume it is a mapping:
if (isinstance(affine_or_mapping, str)
or isinstance(affine_or_mapping, nib.Nifti1Image)):
if reg_template is None or static_img is None:
raise ValueError(
"If using a mapping to transform an ROI, need to ",
"also specify all of the following inputs: ",
"`reg_template`, `static_img`")
affine_or_mapping = reg.read_mapping(affine_or_mapping,
static_img, reg_template)
roi = auv.patch_up_roi(
affine_or_mapping.transform_inverse(
roi, interpolation='nearest')).astype(bool)
if scene is None:
scene = window.Scene()
roi_actor = actor.contour_from_roi(roi, color=color, opacity=opacity)
scene.add(roi_actor)
if inline:
tdir = tempfile.gettempdir()
fname = op.join(tdir, "fig.png")
window.snapshot(scene, fname=fname)
display.display_png(display.Image(fname))
return _inline_interact(scene, inline, interact)
def _streamlines(row,
wm_labels,
odf_model="DTI",
directions="det",
n_seeds=2,
random_seeds=False,
force_recompute=False,
wm_fa_thresh=0.2):
"""
wm_labels : list
The values within the segmentation that are considered white matter. We
will use this part of the image both to seed tracking (seeding
throughout), and for stopping.
"""
streamlines_file = _get_fname(
row, '%s_%s_streamlines.trk' % (odf_model, directions))
if not op.exists(streamlines_file) or force_recompute:
if odf_model == "DTI":
params_file = _dti(row)
elif odf_model == "CSD":
params_file = _csd(row)
dwi_img = nib.load(row['dwi_file'])
dwi_data = dwi_img.get_data()
if 'seg_file' in row.index:
# If we found a white matter segmentation in the
# expected location:
seg_img = nib.load(row['seg_file'])
seg_data_orig = seg_img.get_data()
# For different sets of labels, extract all the voxels that
# have any of these values:
wm_mask = np.sum(
np.concatenate([(seg_data_orig == l)[..., None]
for l in wm_labels], -1), -1)
# Resample to DWI data:
wm_mask = np.round(
reg.resample(wm_mask, dwi_data[..., 0], seg_img.affine,
dwi_img.affine)).astype(int)
else:
# Otherwise, we'll identify the white matter based on FA:
dti_fa = nib.load(_dti_fa(row)).get_data()
wm_mask = dti_fa > wm_fa_thresh
streamlines = aft.track(params_file,
directions=directions,
n_seeds=n_seeds,
random_seeds=random_seeds,
seed_mask=wm_mask,
stop_mask=wm_mask)
aus.write_trk(streamlines_file,
dtu.move_streamlines(streamlines,
np.linalg.inv(dwi_img.affine)),
affine=dwi_img.affine)
return streamlines_file
def save_wm_mask(subject):
s3 = boto3.resource('s3')
boto3.setup_default_session(profile_name='cirrus')
bucket = s3.Bucket('hcp-dki')
path = '%s/%s_white_matter_mask.nii.gz' % (subject, subject)
if not exists(path, bucket.name):
bucket = setup_boto()
with tempfile.TemporaryDirectory() as tempdir:
try:
dwi_file = op.join(tempdir, 'data.nii.gz')
seg_file = op.join(tempdir, 'aparc+aseg.nii.gz')
data_files = {}
data_files[dwi_file] = \
'HCP_900/%s/T1w/Diffusion/data.nii.gz' % subject
data_files[seg_file] = \
'HCP_900/%s/T1w/aparc+aseg.nii.gz' % subject
for k in data_files.keys():
if not op.exists(k):
bucket.download_file(data_files[k], k)
seg_img = nib.load(seg_file)
dwi_img = nib.load(dwi_file)
seg_data_orig = seg_img.get_data()
# Corpus callosum labels:
cc_mask = ((seg_data_orig == 251) |
(seg_data_orig == 252) |
(seg_data_orig == 253) |
(seg_data_orig == 254) |
(seg_data_orig == 255))
# Cerebral white matter in both hemispheres + corpus callosum
wm_mask = ((seg_data_orig == 41) | (seg_data_orig == 2) |
(cc_mask))
dwi_data = dwi_img.get_data()
resamp_wm = np.round(reg.resample(wm_mask, dwi_data[..., 0],
seg_img.affine,
dwi_img.affine)).astype(int)
wm_file = op.join(tempdir, 'wm.nii.gz')
nib.save(nib.Nifti1Image(resamp_wm.astype(int),
dwi_img.affine),
wm_file)
boto3.setup_default_session(profile_name='cirrus')
s3 = boto3.resource('s3')
s3.meta.client.upload_file(
wm_file,
'hcp-dki',
path)
return subject, True
except Exception as err:
return subject, err.args
else:
return subject, True
def _resample_mask(mask_data, dwi_data, mask_affine, dwi_affine):
'''
Helper function
Resamples mask to dwi if necessary
'''
mask_type = mask_data.dtype
if ((dwi_data is not None) and (dwi_affine is not None)
and (dwi_data[..., 0].shape != mask_data.shape)):
return np.round(
reg.resample(mask_data.astype(float), dwi_data[..., 0],
mask_affine, dwi_affine)).astype(mask_type)
else:
return mask_data
def save_wm_mask(subject):
s3 = boto3.resource('s3')
boto3.setup_default_session(profile_name='cirrus')
bucket = s3.Bucket('hcp-dki')
path = '%s/%s_white_matter_mask.nii.gz' % (subject, subject)
if not exists(path, bucket.name):
bucket = setup_boto()
with tempfile.TemporaryDirectory() as tempdir:
try:
dwi_file = op.join(tempdir, 'data.nii.gz')
seg_file = op.join(tempdir, 'aparc+aseg.nii.gz')
data_files = {}
data_files[dwi_file] = \
'HCP_900/%s/T1w/Diffusion/data.nii.gz' % subject
data_files[seg_file] = \
'HCP_900/%s/T1w/aparc+aseg.nii.gz' % subject
for k in data_files.keys():
if not op.exists(k):
bucket.download_file(data_files[k], k)
seg_img = nib.load(seg_file)
dwi_img = nib.load(dwi_file)
seg_data_orig = seg_img.get_data()
# Corpus callosum labels:
cc_mask = ((seg_data_orig == 251) | (seg_data_orig == 252) |
(seg_data_orig == 253) | (seg_data_orig == 254) |
(seg_data_orig == 255))
# Cerebral white matter in both hemispheres + corpus callosum
wm_mask = ((seg_data_orig == 41) | (seg_data_orig == 2) |
(cc_mask))
dwi_data = dwi_img.get_data()
resamp_wm = np.round(
reg.resample(wm_mask, dwi_data[..., 0], seg_img.affine,
dwi_img.affine)).astype(int)
wm_file = op.join(tempdir, 'wm.nii.gz')
nib.save(
nib.Nifti1Image(resamp_wm.astype(int), dwi_img.affine),
wm_file)
boto3.setup_default_session(profile_name='cirrus')
s3 = boto3.resource('s3')
s3.meta.client.upload_file(wm_file, 'hcp-dki', path)
return subject, True
except Exception as err:
return subject, err.args
else:
return subject, True
def _streamlines(row,
wm_labels,
odf_model="DTI",
directions="det",
force_recompute=False):
"""
wm_labels : list
The values within the segmentation that are considered white matter. We
will use this part of the image both to seed tracking (seeding
throughout), and for stopping.
"""
streamlines_file = _get_fname(
row, '%s_%s_streamlines.trk' % (odf_model, directions))
if not op.exists(streamlines_file) or force_recompute:
if odf_model == "DTI":
params_file = _dti(row)
else:
raise (NotImplementedError)
seg_img = nib.load(row['seg_file'])
dwi_img = nib.load(row['dwi_file'])
seg_data_orig = seg_img.get_data()
# For different sets of labels, extract all the voxels that have any
# of these values:
wm_mask = np.sum(
np.concatenate([(seg_data_orig == l)[..., None]
for l in wm_labels], -1), -1)
dwi_data = dwi_img.get_data()
resamp_wm = np.round(
reg.resample(wm_mask, dwi_data[..., 0], seg_img.affine,
dwi_img.affine)).astype(int)
streamlines = aft.track(params_file,
directions='det',
seeds=2,
seed_mask=resamp_wm,
stop_mask=resamp_wm)
aus.write_trk(streamlines_file, streamlines, affine=row['dwi_affine'])
return streamlines_file
def read_callosum_templates(resample_to=False):
"""Load AFQ callosum templates from file
Returns
-------
dict with: keys: names of template ROIs and values: nibabel Nifti1Image
objects from each of the ROI nifti files.
"""
files, folder = fetch_callosum_templates()
template_dict = {}
for f in files:
img = nib.load(op.join(folder, f))
if resample_to:
if isinstance(resample_to, str):
resample_to = nib.load(resample_to)
img = nib.Nifti1Image(
reg.resample(img.get_fdata(), resample_to, img.affine,
resample_to.affine), resample_to.affine)
template_dict[f.split('.')[0]] = img
return template_dict
def _streamlines(row, wm_labels, odf_model="DTI", directions="det",
force_recompute=False):
"""
wm_labels : list
The values within the segmentation that are considered white matter. We
will use this part of the image both to seed tracking (seeding
throughout), and for stopping.
"""
streamlines_file = _get_fname(row,
'%s_%s_streamlines.trk' % (odf_model,
directions))
if not op.exists(streamlines_file) or force_recompute:
if odf_model == "DTI":
params_file = _dti(row)
else:
raise(NotImplementedError)
seg_img = nib.load(row['seg_file'])
dwi_img = nib.load(row['dwi_file'])
seg_data_orig = seg_img.get_data()
# For different sets of labels, extract all the voxels that have any
# of these values:
wm_mask = np.sum(np.concatenate([(seg_data_orig == l)[..., None]
for l in wm_labels], -1), -1)
dwi_data = dwi_img.get_data()
resamp_wm = np.round(reg.resample(wm_mask, dwi_data[..., 0],
seg_img.affine,
dwi_img.affine)).astype(int)
streamlines = aft.track(params_file,
directions='det',
seeds=2,
seed_mask=resamp_wm,
stop_mask=resamp_wm)
aus.write_trk(streamlines_file, streamlines,
affine=row['dwi_affine'])
return streamlines_file
def _wm_mask(self, row, wm_fa_thresh=0.2):
wm_mask_file = self._get_fname(row, '_wm_mask.nii.gz')
if self.force_recompute or not op.exists(wm_mask_file):
dwi_img = nib.load(row['dwi_file'])
dwi_data = dwi_img.get_fdata()
if 'seg_file' in row.index:
# If we found a white matter segmentation in the
# expected location:
seg_img = nib.load(row['seg_file'])
seg_data_orig = seg_img.get_fdata()
# For different sets of labels, extract all the voxels that
# have any of these values:
wm_mask = np.sum(
np.concatenate([(seg_data_orig == l)[..., None]
for l in self.wm_labels], -1), -1)
# Resample to DWI data:
wm_mask = np.round(
reg.resample(wm_mask, dwi_data[..., 0], seg_img.affine,
dwi_img.affine)).astype(int)
meta = dict(source=row['seg_file'], wm_labels=self.wm_labels)
else:
# Otherwise, we'll identify the white matter based on FA:
fa_fname = self._dti_fa(row)
dti_fa = nib.load(fa_fname).get_fdata()
wm_mask = dti_fa > wm_fa_thresh
meta = dict(source=fa_fname, fa_threshold=wm_fa_thresh)
# Dilate to be sure to reach the gray matter:
wm_mask = binary_dilation(wm_mask) > 0
nib.save(nib.Nifti1Image(wm_mask.astype(int), row['dwi_affine']),
wm_mask_file)
meta_fname = self._get_fname(row, '_wm_mask.json')
afd.write_json(meta_fname, meta)
return wm_mask_file
def segment_afq(self, tg=None):
"""
Assign streamlines to bundles using the waypoint ROI approach
Parameters
----------
tg : StatefulTractogram class instance
"""
if tg is None:
tg = self.tg
else:
self.tg = tg
self.tg.to_vox()
# For expedience, we approximate each streamline as a 100 point curve:
fgarray = np.array(_resample_tg(tg, 100))
# comment _aNNe
# in general, this might cause errors:
# if rois were traversed by streamlines in just a few voxels
# and if streamlines were so long or resolution so high
# that one hundredth of a streamline length was more than a voxel,
# then the contact check below (closest distance streamline to ROI < voxel width) can fail when resampling to 100 points
# To be cartain that the resampling does not cause problems,
# the number of resamplign points has to be larger than the length of the streamline in voxels in native space!
# end comment
n_streamlines = fgarray.shape[0]
streamlines_in_bundles = np.zeros(
(n_streamlines, len(self.bundle_dict)))
min_dist_coords = np.zeros((n_streamlines, len(self.bundle_dict), 2),
dtype=int)
self.fiber_groups = {}
if self.return_idx:
out_idx = np.arange(n_streamlines, dtype=int)
if self.filter_by_endpoints:
aal_atlas = afd.read_aal_atlas()['atlas'].get_fdata()
# This atlas is not yet aligned to template space
resample_to = self.reg_template
if isinstance(resample_to, str):
resample_to = nib.load(resample_to)
allVolumes = []
# aal atlas and more has mutiple volumes to represent overlapping areas separately
# move through all volumes, register them to the template
# put them together
# safe with affine of the template
# this puts aal atlas in the sam espace as template before it is warped to native space _aNNe
for ii in range(aal_atlas.get_fdata().shape[-1]):
vol = aal_atlas.get_fdata()
vol = vol[..., ii]
trafo = reg.resample(
vol, # moving (according to reg.resample)
resample_to, # static
aal_atlas.affine, # moving affine
resample_to.affine) # static affine
allVolumes.append(np.asarray(trafo))
aal_atlas = np.stack(allVolumes, axis=3)
aal_atlas = nib.Nifti1Image(aal_atlas, resample_to.affine)
################for debugging: save AAL Atlas after registering to template ############
# path_for_debugging = '/debugpath/'
# nib.save(atlas_inFSL_space,debugpath+'AAL_registered_to_template.nii.gz')
#########################################################################################
# We need to calculate the size of a voxel, so we can transform
# from mm to voxel units:
R = self.img_affine[0:3, 0:3]
vox_dim = np.mean(np.diag(np.linalg.cholesky(R.T.dot(R))))
dist_to_aal = self.dist_to_aal / vox_dim
self.logger.info("Assigning Streamlines to Bundles")
# Tolerance is set to the square of the distance to the corner
# because we are using the squared Euclidean distance in calls to
# `cdist` to make those calls faster.
tol = dts.dist_to_corner(self.img_affine)**2
for bundle_idx, bundle in enumerate(self.bundle_dict):
self.logger.info(f"Finding Streamlines for {bundle}")
warped_prob_map, include_roi, exclude_roi = \
self._get_bundle_info(bundle_idx, bundle)
########for debugging: save the warped probability map that is actually used in segment_afq() ##########
# path_for_debugging = '/debugpath/'
# nib.save(nib.Nifti1Image(warped_prob_map.astype(np.float32),
# self.img_affine),
# debugpath+'warpedprobmap_'+bundle+'as_used.nii.gz')
############################################################################################
fiber_probabilities = dts.values_from_volume(
warped_prob_map, fgarray, np.eye(4))
fiber_probabilities = np.mean(fiber_probabilities, -1)
idx_above_prob = np.where(
fiber_probabilities > self.prob_threshold)
self.logger.info((f"{len(idx_above_prob[0])} streamlines exceed"
" the probability threshold."))
crosses_midline = self.bundle_dict[bundle]['cross_midline']
for sl_idx in tqdm(idx_above_prob[0]):
sl = tg.streamlines[sl_idx]
if fiber_probabilities[sl_idx] > self.prob_threshold:
if crosses_midline is not None:
if self.crosses[sl_idx]:
# This means that the streamline does
# cross the midline:
if crosses_midline:
# This is what we want, keep going
pass
else:
# This is not what we want,
# skip to next streamline
continue
is_close, dist = \
self._check_sl_with_inclusion(sl,
include_roi,
tol)
if is_close:
is_far = \
self._check_sl_with_exclusion(sl,
exclude_roi,
tol)
if is_far:
min_dist_coords[sl_idx, bundle_idx, 0] =\
np.argmin(dist[0], 0)[0]
min_dist_coords[sl_idx, bundle_idx, 1] =\
np.argmin(dist[1], 0)[0]
streamlines_in_bundles[sl_idx, bundle_idx] =\
fiber_probabilities[sl_idx]
self.logger.info(
(f"{np.sum(streamlines_in_bundles[:, bundle_idx] > 0)} "
"streamlines selected with waypoint ROIs"))
# Eliminate any fibers not selected using the plane ROIs:
possible_fibers = np.sum(streamlines_in_bundles, -1) > 0
tg = StatefulTractogram(tg.streamlines[possible_fibers], self.img,
Space.VOX)
if self.return_idx:
out_idx = out_idx[possible_fibers]
streamlines_in_bundles = streamlines_in_bundles[possible_fibers]
min_dist_coords = min_dist_coords[possible_fibers]
bundle_choice = np.argmax(streamlines_in_bundles, -1)
# We do another round through, so that we can orient all the
# streamlines within a bundle in the same orientation with respect to
# the ROIs. This order is ARBITRARY but CONSISTENT (going from ROI0
# to ROI1).
self.logger.info("Re-orienting streamlines to consistent directions")
for bundle_idx, bundle in enumerate(self.bundle_dict):
self.logger.info(f"Processing {bundle}")
select_idx = np.where(bundle_choice == bundle_idx)
if len(select_idx[0]) == 0:
# There's nothing here, set and move to the next bundle:
self._return_empty(bundle)
continue
# Use a list here, because ArraySequence doesn't support item
# assignment:
select_sl = list(tg.streamlines[select_idx])
# Sub-sample min_dist_coords:
min_dist_coords_bundle = min_dist_coords[select_idx]
for idx in range(len(select_sl)):
min0 = min_dist_coords_bundle[idx, bundle_idx, 0]
min1 = min_dist_coords_bundle[idx, bundle_idx, 1]
if min0 > min1:
select_sl[idx] = select_sl[idx][::-1]
# Set this to StatefulTractogram object for filtering/output:
select_sl = StatefulTractogram(select_sl, self.img, Space.VOX)
if self.filter_by_endpoints:
self.logger.info("Filtering by endpoints")
# Create binary masks and warp these into subject's DWI space:
aal_targets = afd.bundles_to_aal([bundle], atlas=aal_atlas)[0]
aal_idx = []
for targ in aal_targets:
if targ is not None:
aal_roi = np.zeros(aal_atlas.shape[:3])
aal_roi[targ[:, 0], targ[:, 1], targ[:, 2]] = 1
warped_roi = self.mapping.transform_inverse(
aal_roi, interpolation='nearest')
aal_idx.append(np.array(np.where(warped_roi > 0)).T)
else:
aal_idx.append(None)
self.logger.info("Before filtering "
f"{len(select_sl)} streamlines")
new_select_sl = clean_by_endpoints(select_sl.streamlines,
aal_idx[0],
aal_idx[1],
tol=dist_to_aal,
return_idx=self.return_idx)
# Generate immediately:
new_select_sl = list(new_select_sl)
# We need to check this again:
if len(new_select_sl) == 0:
# There's nothing here, set and move to the next bundle:
self._return_empty(bundle)
continue
if self.return_idx:
temp_select_sl = []
temp_select_idx = np.empty(len(new_select_sl), int)
for ii, ss in enumerate(new_select_sl):
temp_select_sl.append(ss[0])
temp_select_idx[ii] = ss[1]
select_idx = select_idx[0][temp_select_idx]
new_select_sl = temp_select_sl
select_sl = StatefulTractogram(new_select_sl, self.img,
Space.RASMM)
self.logger.info("After filtering "
f"{len(select_sl)} streamlines")
if self.return_idx:
self.fiber_groups[bundle] = {}
self.fiber_groups[bundle]['sl'] = select_sl
self.fiber_groups[bundle]['idx'] = out_idx[select_idx]
else:
self.fiber_groups[bundle] = select_sl
return self.fiber_groups
def track(params_file,
directions="det",
max_angle=30.,
sphere=None,
seed_mask=None,
seed_threshold=0,
n_seeds=1,
random_seeds=False,
rng_seed=None,
stop_mask=None,
stop_threshold=0,
step_size=0.5,
min_length=10,
max_length=1000,
odf_model="DTI",
tracker="local"):
"""
Tractography
Parameters
----------
params_file : str, nibabel img.
Full path to a nifti file containing CSD spherical harmonic
coefficients, or nibabel img with model params.
directions : str
How tracking directions are determined.
One of: {"det" | "prob"}
max_angle : float, optional.
The maximum turning angle in each step. Default: 30
sphere : Sphere object, optional.
The discretization of direction getting. default:
dipy.data.default_sphere.
seed_mask : array, optional.
Float or binary mask describing the ROI within which we seed for
tracking.
Default to the entire volume (all ones).
seed_threshold : float, optional.
A value of the seed_mask below which tracking is terminated.
Default to 0.
n_seeds : int or 2D array, optional.
The seeding density: if this is an int, it is is how many seeds in each
voxel on each dimension (for example, 2 => [2, 2, 2]). If this is a 2D
array, these are the coordinates of the seeds. Unless random_seeds is
set to True, in which case this is the total number of random seeds
to generate within the mask.
random_seeds : bool
Whether to generate a total of n_seeds random seeds in the mask.
Default: False.
rng_seed : int
random seed used to generate random seeds if random_seeds is
set to True. Default: None
stop_mask : array or str, optional.
If array: A float or binary mask that determines a stopping criterion
(e.g. FA).
If tuple: it contains a sequence that is interpreted as:
(pve_wm, pve_gm, pve_csf), each item of which is either a string
(full path) or a nibabel img to be used in particle filtering
tractography.
A tuple is required if tracker is set to "pft".
Defaults to no stopping (all ones).
stop_threshold : float or tuple, optional.
If float, this a value of the stop_mask below which tracking is
terminated (and stop_mask has to be an array).
If str, "CMC" for Continuous Map Criterion [Girard2014]_.
"ACT" for Anatomically-constrained tractography [Smith2012]_.
A string is required if the tracker is set to "pft".
Defaults to 0 (this means that if no stop_mask is passed,
we will stop only at the edge of the image).
step_size : float, optional.
The size (in mm) of a step of tractography. Default: 1.0
min_length: int, optional
The miminal length (mm) in a streamline. Default: 10
max_length: int, optional
The miminal length (mm) in a streamline. Default: 1000
odf_model : str, optional
One of {"DTI", "CSD", "DKI", "MSMT"}. Defaults to use "DTI"
tracker : str, optional
Which strategy to use in tracking. This can be the standard local
tracking ("local") or Particle Filtering Tracking ([Girard2014]_).
One of {"local", "pft"}. Default: "local"
Returns
-------
list of streamlines ()
References
----------
.. [Girard2014] Girard, G., Whittingstall, K., Deriche, R., &
Descoteaux, M. Towards quantitative connectivity analysis: reducing
tractography biases. NeuroImage, 98, 266-278, 2014.
"""
logger = logging.getLogger('AFQ.tractography')
logger.info("Loading Image...")
if isinstance(params_file, str):
params_img = nib.load(params_file)
else:
params_img = params_file
model_params = params_img.get_fdata()
affine = params_img.affine
odf_model = odf_model.upper()
directions = directions.lower()
logger.info("Generating Seeds...")
if isinstance(n_seeds, int):
if seed_mask is None:
seed_mask = np.ones(params_img.shape[:3])
elif seed_mask.dtype != 'bool':
seed_mask = seed_mask > seed_threshold
if random_seeds:
seeds = dtu.random_seeds_from_mask(seed_mask,
seeds_count=n_seeds,
seed_count_per_voxel=False,
affine=affine,
random_seed=rng_seed)
else:
seeds = dtu.seeds_from_mask(seed_mask,
density=n_seeds,
affine=affine)
else:
# If user provided an array, we'll use n_seeds as the seeds:
seeds = n_seeds
if sphere is None:
sphere = dpd.default_sphere
logger.info("Getting Directions...")
if directions == "det":
dg = DeterministicMaximumDirectionGetter
elif directions == "prob":
dg = ProbabilisticDirectionGetter
if odf_model == "DTI" or odf_model == "DKI":
evals = model_params[..., :3]
evecs = model_params[..., 3:12].reshape(params_img.shape[:3] + (3, 3))
odf = tensor_odf(evals, evecs, sphere)
dg = dg.from_pmf(odf, max_angle=max_angle, sphere=sphere)
elif odf_model == "CSD" or "MSMT":
dg = dg.from_shcoeff(model_params, max_angle=max_angle, sphere=sphere)
if tracker == "local":
if stop_mask is None:
stop_mask = np.ones(params_img.shape[:3])
if stop_mask.dtype == 'bool':
stopping_criterion = ThresholdStoppingCriterion(stop_mask, 0.5)
else:
stopping_criterion = ThresholdStoppingCriterion(
stop_mask, stop_threshold)
my_tracker = VerboseLocalTracking
elif tracker == "pft":
if not isinstance(stop_threshold, str):
raise RuntimeError(
"You are using PFT tracking, but did not provide a string ",
"'stop_threshold' input. ",
"Possible inputs are: 'CMC' or 'ACT'")
if not (isinstance(stop_mask, Iterable) and len(stop_mask) == 3):
raise RuntimeError(
"You are using PFT tracking, but did not provide a length "
"3 iterable for `stop_mask`. "
"Expected a (pve_wm, pve_gm, pve_csf) tuple.")
pves = []
pve_imgs = []
vox_sizes = []
for ii, pve in enumerate(stop_mask):
if isinstance(pve, str):
img = nib.load(pve)
else:
img = pve
pve_imgs.append(img)
pves.append(pve_imgs[-1].get_fdata())
average_voxel_size = np.mean(vox_sizes)
pve_wm_img, pve_gm_img, pve_csf_img = pve_imgs
pve_wm_data, pve_gm_data, pve_csf_data = pves
pve_wm_data = reg.resample(pve_wm_data, model_params[..., 0],
pve_wm_img.affine, params_img.affine)
pve_gm_data = reg.resample(pve_gm_data, model_params[..., 0],
pve_gm_img.affine, params_img.affine)
pve_csf_data = reg.resample(pve_csf_data, model_params[..., 0],
pve_csf_img.affine, params_img.affine)
vox_sizes.append(np.mean(params_img.header.get_zooms()[:3]))
my_tracker = VerboseParticleFilteringTracking
if stop_threshold == "CMC":
stopping_criterion = CmcStoppingCriterion.from_pve(
pve_wm_data,
pve_gm_data,
pve_csf_data,
step_size=step_size,
average_voxel_size=average_voxel_size)
elif stop_threshold == "ACT":
stopping_criterion = ActStoppingCriterion.from_pve(
pve_wm_data, pve_gm_data, pve_csf_data)
logger.info("Tracking...")
return _tracking(my_tracker,
seeds,
dg,
stopping_criterion,
params_img,
step_size=step_size,
min_length=min_length,
max_length=max_length,
random_seed=rng_seed)
for bundle in bundles:
for idx, roi in enumerate(bundles[bundle]['ROIs']):
warped_roi = transform_inverse_roi(roi,
mapping,
bundle_name=bundle)
print(roi)
nib.save(nib.Nifti1Image(warped_roi.astype(float), img.affine),
op.join(working_dir, f"{bundle}_{idx+1}.nii.gz"))
# Add voxels that aren't there yet:
if bundles[bundle]['rules'][idx]:
seed_roi = np.logical_or(seed_roi, warped_roi)
for ii, pp in enumerate(endpoint_spec[bundle].keys()):
roi = endpoint_spec[bundle][pp]
roi = reg.resample(roi.get_fdata(), MNI_T1w_img, roi.affine,
MNI_T1w_img.affine)
warped_roi = transform_inverse_roi(roi,
mapping,
bundle_name=bundle)
nib.save(nib.Nifti1Image(warped_roi.astype(float), img.affine),
op.join(working_dir, f"{bundle}_{pp}.nii.gz"))
nib.save(nib.Nifti1Image(seed_roi.astype(float), img.affine),
op.join(working_dir, 'seed_roi.nii.gz'))
sft = aft.track(sh_coeff,
seed_mask=seed_roi,
n_seeds=5,
tracker="pft",