def make_bundle_dict(bundle_names=BUNDLES):
"""
Create a bundle dictionary, needed for the segmentation
Parameters
----------
bundle_names : list, optional
A list of the bundles to be used in this case. Default: all of them
"""
templates = afd.read_templates()
# For the arcuate, we need to rename a few of these and duplicate the SLF
# ROI:
templates['ARC_roi1_L'] = templates['SLF_roi1_L']
templates['ARC_roi1_R'] = templates['SLF_roi1_R']
templates['ARC_roi2_L'] = templates['SLFt_roi2_L']
templates['ARC_roi2_R'] = templates['SLFt_roi2_R']
afq_bundles = {}
for name in bundle_names:
# Considder hard coding since we might have different rulse for
# some tracts
for hemi in ['_R', '_L']:
afq_bundles[name + hemi] = {'ROIs': [templates[name + '_roi1' +
hemi],
templates[name + '_roi2' +
hemi]],
'rules': [True, True]}
return afq_bundles
def test_segment():
dpd.fetch_stanford_hardi()
hardi_dir = op.join(fetcher.dipy_home, "stanford_hardi")
hardi_fdata = op.join(hardi_dir, "HARDI150.nii.gz")
hardi_fbval = op.join(hardi_dir, "HARDI150.bval")
hardi_fbvec = op.join(hardi_dir, "HARDI150.bvec")
file_dict = afd.read_stanford_hardi_tractography()
mapping = file_dict['mapping.nii.gz']
streamlines = file_dict['tractography_subsampled.trk']
templates = afd.read_templates()
bundles = {'CST_L': {'ROIs': [templates['CST_roi1_L'],
templates['CST_roi2_L']],
'rules': [True, True]},
'CST_R': {'ROIs': [templates['CST_roi1_R'],
templates['CST_roi1_R']],
'rules': [True, True]}}
fiber_groups = seg.segment(hardi_fdata,
hardi_fbval,
hardi_fbvec,
streamlines,
bundles,
mapping=mapping,
as_generator=True)
# We asked for 2 fiber groups:
npt.assert_equal(len(fiber_groups), 2)
# There happen to be 8 fibers in the right CST:
CST_R_sl = list(fiber_groups['CST_R'])
npt.assert_equal(len(CST_R_sl), 8)
# Calculate the tract profile for a volume of all-ones:
tract_profile = seg.calculate_tract_profile(
np.ones(nib.load(hardi_fdata).shape[:3]),
CST_R_sl)
npt.assert_equal(tract_profile, np.ones(100))
def make_bundle_dict(bundle_names=BUNDLES):
"""
Create a bundle dictionary, needed for the segmentation
Parameters
----------
bundle_names : list, optional
A list of the bundles to be used in this case. Default: all of them
"""
templates = afd.read_templates()
# For the arcuate, we need to rename a few of these and duplicate the SLF
# ROI:
templates['ARC_roi1_L'] = templates['SLF_roi1_L']
templates['ARC_roi1_R'] = templates['SLF_roi1_R']
templates['ARC_roi2_L'] = templates['SLFt_roi2_L']
templates['ARC_roi2_R'] = templates['SLFt_roi2_R']
afq_bundles = {}
# Each bundles gets a digit identifier (to be stored in the tractogram)
uid = 1
for name in bundle_names:
# Considder hard coding since we might have different rulse for
# some tracts
for hemi in ['_R', '_L']:
afq_bundles[name + hemi] = {'ROIs': [templates[name + '_roi1' +
hemi],
templates[name + '_roi2' +
hemi]],
'rules': [True, True],
'uid': uid}
uid += 1
return afq_bundles
def test_BundleDict():
"""
Tests bundle dict
"""
# test defaults
afq_bundles = api.BundleDict()
# bundles restricted within hemisphere
# NOTE: FA and FP cross midline so are removed
# NOTE: all others generate two bundles
num_hemi_bundles = (len(api.BUNDLES) - 2) * 2
# bundles that cross the midline
num_whole_bundles = 2
assert len(afq_bundles) == num_hemi_bundles + num_whole_bundles
# Arcuate Fasciculus
afq_bundles = api.BundleDict(["ARC"])
assert len(afq_bundles) == 2
# Forceps Minor
afq_bundles = api.BundleDict(["FA"])
assert len(afq_bundles) == 1
# Cingulum Hippocampus
# not included but exists in templates
afq_bundles = api.BundleDict(["HCC"])
assert len(afq_bundles) == 2
# Test "custom" bundle
afq_templates = afd.read_templates()
afq_bundles = api.BundleDict({
"custom_bundle": {
"ROIs": [afq_templates["FA_L"], afq_templates["FP_R"]],
"rules": [True, True],
"cross_midline": False,
"uid": 1
}
})
afq_bundles.get("custom_bundle")
assert len(afq_bundles) == 1
# Vertical Occipital Fasciculus
# not included and does not exist in afq templates
with pytest.raises(ValueError, match="VOF_R is not in AFQ templates"):
afq_bundles = api.BundleDict(["VOF"])
afq_bundles["VOF_R"]
afq_bundles = api.BundleDict(["VOF"], seg_algo="reco80")
assert len(afq_bundles) == 2
afq_bundles = api.BundleDict(["whole_brain"], seg_algo="reco80")
assert len(afq_bundles) == 1
def main():
with open('config.json') as config_json:
config = json.load(config_json)
data_file = str(config['data_file'])
data_bval = str(config['data_bval'])
data_bvec = str(config['data_bvec'])
img = nib.load(data_file)
print("Calculating DTI...")
if not op.exists('./dti_FA.nii.gz'):
dti_params = dti.fit_dti(data_file, data_bval, data_bvec, out_dir='.')
else:
dti_params = {'FA': './dti_FA.nii.gz', 'params': './dti_params.nii.gz'}
tg = nib.streamlines.load('csa_prob.trk').tractogram
streamlines = tg.apply_affine(np.linalg.inv(img.affine)).streamlines
# Use only a small portion of the streamlines, for expedience:
streamlines = streamlines[::100]
templates = afd.read_templates()
bundle_names = ["CST", "ILF"]
bundles = {}
for name in bundle_names:
for hemi in ['_R', '_L']:
bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi1' + hemi]
],
'rules': [True, True]
}
print("Registering to template...")
MNI_T2_img = dpd.read_mni_template()
bvals, bvecs = read_bvals_bvecs(data_bval, data_bvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=100)
mapping = reg.syn_register_dwi(data_file, gtab)
reg.write_mapping(mapping, './mapping.nii.gz')
print("Segmenting fiber groups...")
fiber_groups = seg.segment(data_file,
data_bval,
data_bvec,
streamlines,
bundles,
reg_template=MNI_T2_img,
mapping=mapping,
as_generator=False,
affine=img.affine)
"""
def make_bundle_dict(bundle_names=BUNDLES, seg_algo="afq", resample_to=False):
"""
Create a bundle dictionary, needed for the segmentation
Parameters
----------
bundle_names : list, optional
A list of the bundles to be used in this case. Default: all of them
resample_to : Nifti1Image, optional
If set, templates will be resampled to the affine and shape of this
image.
"""
if seg_algo == "afq":
templates = afd.read_templates(resample_to=resample_to)
callosal_templates = afd.read_callosum_templates(
resample_to=resample_to)
# For the arcuate, we need to rename a few of these and duplicate the
# SLF ROI:
templates['ARC_roi1_L'] = templates['SLF_roi1_L']
templates['ARC_roi1_R'] = templates['SLF_roi1_R']
templates['ARC_roi2_L'] = templates['SLFt_roi2_L']
templates['ARC_roi2_R'] = templates['SLFt_roi2_R']
afq_bundles = {}
# Each bundles gets a digit identifier (to be stored in the tractogram)
uid = 1
for name in bundle_names:
# Consider hard coding since we might have different rules for
# some tracts
if name in ["FA", "FP"]:
afq_bundles[name] = {
'ROIs': [
templates[name + "_L"], templates[name + "_R"],
callosal_templates["Callosum_midsag"]
],
'rules': [True, True, True],
'prob_map':
templates[name + "_prob_map"],
'cross_midline':
True,
'uid':
uid
}
uid += 1
# SLF is a special case, because it has an exclusion ROI:
elif name == "SLF":
for hemi in ['_R', '_L']:
afq_bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi2' + hemi],
templates["SLFt_roi2" + hemi]
],
'rules': [True, True, False],
'prob_map':
templates[name + hemi + '_prob_map'],
'cross_midline':
False,
'uid':
uid
}
uid += 1
else:
for hemi in ['_R', '_L']:
afq_bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi2' + hemi]
],
'rules': [True, True],
'prob_map':
templates[name + hemi + '_prob_map'],
'cross_midline':
False,
'uid':
uid
}
uid += 1
elif seg_algo == "reco":
afq_bundles = {}
uid = 1
bundle_dict = afd.read_hcp_atlas_16_bundles()
afq_bundles["whole_brain"] = bundle_dict["whole_brain"]
for name in bundle_names:
if name in ['CCMid', 'CC_ForcepsMajor', 'CC_ForcepsMinor', 'MCP']:
afq_bundles[name] = bundle_dict[name]
afq_bundles[name]['uid'] = uid
uid += 1
else:
for hemi in ["_R", "_L"]:
afq_bundles[name + hemi] = bundle_dict[name + hemi]
afq_bundles[name + hemi]['uid'] = uid
uid += 1
else:
raise ValueError("Input: %s is not a valid input`seg_algo`" % seg_algo)
return afq_bundles
def test_segment():
templates = afd.read_templates()
bundles = {
'CST_L': {
'ROIs': [templates['CST_roi1_L'], templates['CST_roi2_L']],
'rules': [True, True],
'prob_map': templates['CST_L_prob_map'],
'cross_midline': None
},
'CST_R': {
'ROIs': [templates['CST_roi1_R'], templates['CST_roi1_R']],
'rules': [True, True],
'prob_map': templates['CST_R_prob_map'],
'cross_midline': None
}
}
segmentation = seg.Segmentation()
segmentation.segment(bundles,
tg,
hardi_fdata,
hardi_fbval,
hardi_fbvec,
mapping=mapping)
fiber_groups = segmentation.fiber_groups
# We asked for 2 fiber groups:
npt.assert_equal(len(fiber_groups), 2)
# Here's one of them:
CST_R_sl = fiber_groups['CST_R']
# Let's make sure there are streamlines in there:
npt.assert_(len(CST_R_sl) > 0)
# Calculate the tract profile for a volume of all-ones:
tract_profile = afq_profile(np.ones(nib.load(hardi_fdata).shape[:3]),
CST_R_sl.streamlines, np.eye(4))
npt.assert_almost_equal(tract_profile, np.ones(100))
clean_sl = seg.clean_bundle(CST_R_sl)
npt.assert_equal(len(clean_sl), len(CST_R_sl))
# What if you don't have probability maps?
bundles = {
'CST_L': {
'ROIs': [templates['CST_roi1_L'], templates['CST_roi2_L']],
'rules': [True, True],
'cross_midline': False
},
'CST_R': {
'ROIs': [templates['CST_roi1_R'], templates['CST_roi1_R']],
'rules': [True, True],
'cross_midline': False
}
}
segmentation.segment(bundles,
tg,
hardi_fdata,
hardi_fbval,
hardi_fbvec,
mapping=mapping)
fiber_groups = segmentation.fiber_groups
# This condition should still hold
npt.assert_equal(len(fiber_groups), 2)
npt.assert_(len(fiber_groups['CST_R']) > 0)
# Test with the return_idx kwarg set to True:
segmentation = seg.Segmentation(return_idx=True)
segmentation.segment(bundles,
tg,
hardi_fdata,
hardi_fbval,
hardi_fbvec,
mapping=mapping)
fiber_groups = segmentation.fiber_groups
npt.assert_equal(len(fiber_groups), 2)
npt.assert_(len(fiber_groups['CST_R']['sl']) > 0)
npt.assert_(len(fiber_groups['CST_R']['idx']) > 0)
# get bundles for reco method
bundles = afd.read_hcp_atlas_16_bundles()
bundle_names = ['whole_brain', 'CST_R', 'CST_L']
for key in list(bundles):
if key not in bundle_names:
bundles.pop(key, None)
# Try recobundles method
segmentation = seg.Segmentation(seg_algo='Reco',
progressive=False,
greater_than=10,
rm_small_clusters=1,
rng=np.random.RandomState(seed=8))
fiber_groups = segmentation.segment(bundles, tg, hardi_fdata, hardi_fbval,
hardi_fbvec)
# This condition should still hold
npt.assert_equal(len(fiber_groups), 2)
npt.assert_(len(fiber_groups['CST_R']) > 0)
# Test with the return_idx kwarg set to True:
segmentation = seg.Segmentation(seg_algo='Reco',
progressive=False,
greater_than=10,
rm_small_clusters=1,
rng=np.random.RandomState(seed=8),
return_idx=True)
fiber_groups = segmentation.segment(bundles, tg, hardi_fdata, hardi_fbval,
hardi_fbvec)
fiber_groups = segmentation.fiber_groups
npt.assert_equal(len(fiber_groups), 2)
npt.assert_(len(fiber_groups['CST_R']['sl']) > 0)
npt.assert_(len(fiber_groups['CST_R']['idx']) > 0)
out_dir='.')
else:
dti_params = {'FA': './dti_FA.nii.gz', 'params': './dti_params.nii.gz'}
print("Tracking...")
if not op.exists('dti_streamlines.trk'):
streamlines = list(aft.track(dti_params['params']))
aus.write_trk('./dti_streamlines.trk', streamlines, affine=img.affine)
else:
tg = nib.streamlines.load('./dti_streamlines.trk').tractogram
streamlines = tg.apply_affine(np.linalg.inv(img.affine)).streamlines
# Use only a small portion of the streamlines, for expedience:
streamlines = streamlines[::100]
templates = afd.read_templates()
bundle_names = ["CST", "ILF"]
bundles = {}
for name in bundle_names:
for hemi in ['_R', '_L']:
bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi1' + hemi]
],
'rules': [True, True]
}
print("Registering to template...")
MNI_T2_img = dpd.read_mni_template()
aft.track(dti_params['params'],
directions="det",
seed_mask=wm_mask,
seeds=2,
stop_mask=FA,
stop_threshold=0.2,
step_size=step_size,
min_length=min_length_mm / step_size))
aus.write_trk('./dti_streamlines.trk', streamlines, affine=img.affine)
else:
tg = nib.streamlines.load('./dti_streamlines.trk').tractogram
streamlines = tg.apply_affine(np.linalg.inv(img.affine)).streamlines
print("We're looking at: %s streamlines" % len(streamlines))
templates = afd.read_templates()
templates['ARC_roi1_L'] = templates['SLF_roi1_L']
templates['ARC_roi1_R'] = templates['SLF_roi1_R']
templates['ARC_roi2_L'] = templates['SLFt_roi2_L']
templates['ARC_roi2_R'] = templates['SLFt_roi2_R']
bundle_names = ["ATR", "CGC", "CST", "HCC", "IFO", "ILF", "SLF", "ARC", "UNC"]
bundles = {}
for name in bundle_names:
for hemi in ['_R', '_L']:
bundles[name + hemi] = {
'ROIs': [templates[name + '_roi1' + hemi],
templates[name + '_roi2' + hemi]],
'rules': [True, True],
def test_segment():
dpd.fetch_stanford_hardi()
hardi_dir = op.join(fetcher.dipy_home, "stanford_hardi")
hardi_fdata = op.join(hardi_dir, "HARDI150.nii.gz")
hardi_img = nib.load(hardi_fdata)
hardi_fbval = op.join(hardi_dir, "HARDI150.bval")
hardi_fbvec = op.join(hardi_dir, "HARDI150.bvec")
file_dict = afd.read_stanford_hardi_tractography()
mapping = file_dict['mapping.nii.gz']
streamlines = file_dict['tractography_subsampled.trk']
streamlines = dts.Streamlines(
dtu.move_streamlines(streamlines[streamlines._lengths > 10],
np.linalg.inv(hardi_img.affine)))
templates = afd.read_templates()
bundles = {
'CST_L': {
'ROIs': [templates['CST_roi1_L'], templates['CST_roi2_L']],
'rules': [True, True],
'prob_map': templates['CST_L_prob_map'],
'cross_midline': None
},
'CST_R': {
'ROIs': [templates['CST_roi1_R'], templates['CST_roi1_R']],
'rules': [True, True],
'prob_map': templates['CST_R_prob_map'],
'cross_midline': None
}
}
fiber_groups = seg.segment(hardi_fdata, hardi_fbval, hardi_fbvec,
streamlines, bundles, mapping)
# We asked for 2 fiber groups:
npt.assert_equal(len(fiber_groups), 2)
# Here's one of them:
CST_R_sl = fiber_groups['CST_R']
# Let's make sure there are streamlines in there:
npt.assert_(len(CST_R_sl) > 0)
# Calculate the tract profile for a volume of all-ones:
tract_profile = seg.calculate_tract_profile(
np.ones(nib.load(hardi_fdata).shape[:3]), CST_R_sl)
npt.assert_almost_equal(tract_profile, np.ones(100))
# Test providing an array input to calculate_tract_profile:
tract_profile = seg.calculate_tract_profile(
np.ones(nib.load(hardi_fdata).shape[:3]),
seg._resample_bundle(CST_R_sl, 100))
npt.assert_almost_equal(tract_profile, np.ones(100))
clean_sl = seg.clean_fiber_group(CST_R_sl)
# Since there are only 8 streamlines here, nothing should happen:
npt.assert_equal(clean_sl, CST_R_sl)
# Setting minimum number of streamlines to a smaller number and
# threshold to a relatively small number will exclude some streamlines:
clean_sl = seg.clean_fiber_group(CST_R_sl, min_sl=2, clean_threshold=2)
npt.assert_equal(len(clean_sl), 3)
# What if you don't have probability maps?
bundles = {
'CST_L': {
'ROIs': [templates['CST_roi1_L'], templates['CST_roi2_L']],
'rules': [True, True],
'cross_midline': False
},
'CST_R': {
'ROIs': [templates['CST_roi1_R'], templates['CST_roi1_R']],
'rules': [True, True],
'cross_midline': False
}
}
fiber_groups = seg.segment(hardi_fdata, hardi_fbval, hardi_fbvec,
streamlines, bundles, mapping)
# This condition should still hold
npt.assert_equal(len(fiber_groups), 2)
npt.assert_(len(fiber_groups['CST_R']) > 0)
def main():
with open('config.json') as config_json:
config = json.load(config_json)
#Paths to data
data_file = str(config['data_file'])
data_bval = str(config['data_bval'])
data_bvec = str(config['data_bvec'])
img = nib.load(data_file)
"""
print("Calculating DTI...")
if not op.exists('./dti_FA.nii.gz'):
dti_params = dti.fit_dti(data_file, data_bval, data_bvec, out_dir='.')
else:
dti_params = {'FA': './dti_FA.nii.gz',
'params': './dti_params.nii.gz'}
"""
#tg = nib.streamlines.load('track.trk').tractogram
tg = nib.streamlines.load(config['tck_data']).tractogram
streamlines = tg.apply_affine(np.linalg.inv(img.affine)).streamlines
# Use only a small portion of the streamlines, for expedience:
#streamlines = streamlines[::100]
templates = afd.read_templates()
bundle_names = ["CST", "ILF"]
bundles = {}
for name in bundle_names:
for hemi in ['_R', '_L']:
bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi1' + hemi]
],
'rules': [True, True]
}
print("Registering to template...")
if not op.exists('mapping.nii.gz'):
gtab = gradient_table(data_bval, data_bvec)
mapping = reg.syn_register_dwi(data_file, gtab)
reg.write_mapping(mapping, './mapping.nii.gz')
else:
mapping = reg.read_mapping('./mapping.nii.gz', img, MNI_T2_img)
"""
MNI_T2_img = dpd.read_mni_template()
bvals, bvecs = read_bvals_bvecs(data_bval, data_bvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=100)
mapping = reg.syn_register_dwi(data_file, gtab)
reg.write_mapping(mapping, './mapping.nii.gz')
"""
print("Segmenting fiber groups...")
fiber_groups = seg.segment(data_file,
data_bval,
data_bvec,
streamlines,
bundles,
reg_template=MNI_T2_img,
mapping=mapping,
as_generator=False,
affine=img.affine)
path = os.getcwd() + '/tract1/'
if not os.path.exists(path):
os.makedirs(path)
for fg in fiber_groups:
streamlines = fiber_groups[fg]
fname = fg + ".tck"
trg = nib.streamlines.Tractogram(streamlines,
affine_to_rasmm=img.affine)
nib.streamlines.save(trg, path + fname)
def make_bundle_dict(bundle_names=BUNDLES):
"""
Create a bundle dictionary, needed for the segmentation
Parameters
----------
bundle_names : list, optional
A list of the bundles to be used in this case. Default: all of them
"""
templates = afd.read_templates()
callosal_templates = afd.read_callosum_templates()
# For the arcuate, we need to rename a few of these and duplicate the SLF
# ROI:
templates['ARC_roi1_L'] = templates['SLF_roi1_L']
templates['ARC_roi1_R'] = templates['SLF_roi1_R']
templates['ARC_roi2_L'] = templates['SLFt_roi2_L']
templates['ARC_roi2_R'] = templates['SLFt_roi2_R']
afq_bundles = {}
# Each bundles gets a digit identifier (to be stored in the tractogram)
uid = 1
for name in bundle_names:
# Consider hard coding since we might have different rules for
# some tracts
if name in ["FA", "FP"]:
afq_bundles[name] = {
'ROIs': [
templates[name + "_L"], templates[name + "_R"],
callosal_templates["Callosum_midsag"]
],
'rules': [True, True, True],
'prob_map':
templates[name + "_prob_map"],
'cross_midline':
True,
'uid':
uid
}
uid += 1
# SLF is a special case, because it has an exclusion ROI:
elif name == "SLF":
for hemi in ['_R', '_L']:
afq_bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi2' + hemi],
templates["SLFt_roi2" + hemi]
],
'rules': [True, True, False],
'prob_map':
templates[name + hemi + '_prob_map'],
'cross_midline':
False,
'uid':
uid
}
uid += 1
else:
for hemi in ['_R', '_L']:
afq_bundles[name + hemi] = {
'ROIs': [
templates[name + '_roi1' + hemi],
templates[name + '_roi2' + hemi]
],
'rules': [True, True],
'prob_map':
templates[name + hemi + '_prob_map'],
'cross_midline':
False,
'uid':
uid
}
uid += 1
return afq_bundles
def test_segment():
dpd.fetch_stanford_hardi()
hardi_dir = op.join(fetcher.dipy_home, "stanford_hardi")
hardi_fdata = op.join(hardi_dir, "HARDI150.nii.gz")
hardi_fbval = op.join(hardi_dir, "HARDI150.bval")
hardi_fbvec = op.join(hardi_dir, "HARDI150.bvec")
file_dict = afd.read_stanford_hardi_tractography()
mapping = file_dict['mapping.nii.gz']
streamlines = file_dict['tractography_subsampled.trk']
templates = afd.read_templates()
bundles = {'CST_L': {'ROIs': [templates['CST_roi1_L'],
templates['CST_roi2_L']],
'rules': [True, True],
'prob_map': templates['CST_L_prob_map'],
'cross_midline': False},
'CST_R': {'ROIs': [templates['CST_roi1_R'],
templates['CST_roi1_R']],
'rules': [True, True],
'prob_map': templates['CST_R_prob_map'],
'cross_midline': False}}
fiber_groups = seg.segment(hardi_fdata,
hardi_fbval,
hardi_fbvec,
streamlines,
bundles,
mapping=mapping,
as_generator=True)
# We asked for 2 fiber groups:
npt.assert_equal(len(fiber_groups), 2)
# There happen to be 5 fibers in the right CST:
CST_R_sl = fiber_groups['CST_R']
npt.assert_equal(len(CST_R_sl), 5)
# Calculate the tract profile for a volume of all-ones:
tract_profile = seg.calculate_tract_profile(
np.ones(nib.load(hardi_fdata).shape[:3]),
CST_R_sl)
npt.assert_almost_equal(tract_profile, np.ones(100))
# Test providing an array input to calculate_tract_profile:
tract_profile = seg.calculate_tract_profile(
np.ones(nib.load(hardi_fdata).shape[:3]),
seg._resample_bundle(CST_R_sl, 100))
npt.assert_almost_equal(tract_profile, np.ones(100))
clean_sl = seg.clean_fiber_group(CST_R_sl)
# Since there are only 5 streamlines here, nothing should happen:
npt.assert_equal(clean_sl, CST_R_sl)
# Setting minimum number of streamlines to a smaller number and
# threshold to a relatively small number will exclude some streamlines:
clean_sl = seg.clean_fiber_group(CST_R_sl, min_sl=2, clean_threshold=2)
npt.assert_equal(len(clean_sl), 3)
# What if you don't have probability maps?
bundles = {'CST_L': {'ROIs': [templates['CST_roi1_L'],
templates['CST_roi2_L']],
'rules': [True, True],
'cross_midline': False},
'CST_R': {'ROIs': [templates['CST_roi1_R'],
templates['CST_roi1_R']],
'rules': [True, True],
'cross_midline': False}}
fiber_groups = seg.segment(hardi_fdata,
hardi_fbval,
hardi_fbvec,
streamlines,
bundles,
mapping=mapping,
as_generator=True)
# This condition should still hold
npt.assert_equal(len(fiber_groups), 2)
# But one of the streamlines has switched identities without the
# probability map to guide selection
npt.assert_equal(len(fiber_groups['CST_R']), 6)