def test_new_img_like_side_effect():
img1 = Nifti1Image(np.ones((2, 2, 2, 2)), affine=np.eye(4))
hash1 = joblib.hash(img1)
new_img_like(img1, np.ones((2, 2, 2, 2)), img1.affine.copy(),
copy_header=True)
hash2 = joblib.hash(img1)
assert_equal(hash1, hash2)
def test_new_img_like_mgz():
"""Check that new images can be generated with bool MGZ type
This is usually when computing masks using MGZ inputs, e.g.
when using plot_stap_map
"""
ref_img = nibabel.load(os.path.join(datadir, 'test.mgz'))
data = np.ones(ref_img.get_data().shape, dtype=np.bool)
affine = ref_img.affine
new_img_like(ref_img, data, affine, copy_header=False)
def test_new_img_like():
# Give a list to new_img_like
data = np.zeros((5, 6, 7))
data[2:4, 1:5, 3:6] = 1
affine = np.diag((4, 3, 2, 1))
img = nibabel.Nifti1Image(data, affine=affine)
img2 = new_img_like([img, ], data)
np.testing.assert_array_equal(img.get_data(), img2.get_data())
# test_new_img_like_with_nifti2image_copy_header
img_nifti2 = nibabel.Nifti2Image(data, affine=affine)
img2_nifti2 = new_img_like([img_nifti2, ], data, copy_header=True)
np.testing.assert_array_equal(img_nifti2.get_data(), img2_nifti2.get_data())
def test_new_img_like_mgz():
"""Check that new images can be generated with bool MGZ type
This is usually when computing masks using MGZ inputs, e.g.
when using plot_stap_map
"""
if not LooseVersion(nibabel.__version__) >= LooseVersion('1.2.0'):
# Old nibabel do not support MGZ files
raise SkipTest
ref_img = nibabel.load(os.path.join(datadir, 'test.mgz'))
data = np.ones(ref_img.get_data().shape, dtype=np.bool)
affine = ref_img.get_affine()
new_img_like(ref_img, data, affine, copy_header=False)
def test_encode_nii():
mni = datasets.load_mni152_template()
encoded = html_stat_map._encode_nii(mni)
decoded = html_stat_map._decode_nii(encoded)
assert np.allclose(mni.get_data(), decoded.get_data())
mni = image.new_img_like(mni, np.asarray(mni.get_data(), dtype='>f8'))
encoded = html_stat_map._encode_nii(mni)
decoded = html_stat_map._decode_nii(encoded)
assert np.allclose(mni.get_data(), decoded.get_data())
mni = image.new_img_like(mni, np.asarray(mni.get_data(), dtype='<i4'))
encoded = html_stat_map._encode_nii(mni)
decoded = html_stat_map._decode_nii(encoded)
assert np.allclose(mni.get_data(), decoded.get_data())
def clean_img(img):
""" Remove nan/inf entries."""
img = check_niimg(img)
img_data = img.get_data()
img_data[np.isnan(img_data)] = 0
img_data[np.isinf(img_data)] = 0
return new_img_like(img, img_data, copy_header=True)
def flip_img_lr(img):
""" Convenience function to flip image on X axis"""
# This won't work for all image formats! But
# does work for those that we're working with...
assert isinstance(img, nib.nifti1.Nifti1Image)
img = new_img_like(img, data=img.get_data()[::-1], copy_header=True)
return img
def new_nii_like(ref_img, data, affine=None, copy_header=True):
"""
Coerces `data` into NiftiImage format like `ref_img`
Parameters
----------
ref_img : str or img_like
Reference image
data : (S [x T]) array_like
Data to be saved
affine : (4 x 4) array_like, optional
Transformation matrix to be used. Default: `ref_img.affine`
copy_header : bool, optional
Whether to copy header from `ref_img` to new image. Default: True
Returns
-------
nii : :obj:`nibabel.nifti1.Nifti1Image`
NiftiImage
"""
ref_img = check_niimg(ref_img)
nii = new_img_like(ref_img,
data.reshape(ref_img.shape[:3] + data.shape[1:]),
affine=affine,
copy_header=copy_header)
nii.set_data_dtype(data.dtype)
return nii
def test_view_img():
mni = datasets.load_mni152_template()
with warnings.catch_warnings(record=True) as w:
# Create a fake functional image by resample the template
img = image.resample_img(mni, target_affine=3 * np.eye(3))
html_view = html_stat_map.view_img(img)
_check_html(html_view)
html_view = html_stat_map.view_img(img, threshold='95%')
_check_html(html_view)
html_view = html_stat_map.view_img(img, bg_img=mni)
_check_html(html_view)
html_view = html_stat_map.view_img(img, bg_img=None)
_check_html(html_view)
html_view = html_stat_map.view_img(img, threshold=2., vmax=4.)
_check_html(html_view)
html_view = html_stat_map.view_img(img, symmetric_cmap=False)
img_4d = image.new_img_like(img, img.get_data()[:, :, :, np.newaxis])
assert len(img_4d.shape) == 4
html_view = html_stat_map.view_img(img_4d, threshold=2., vmax=4.)
_check_html(html_view)
# Check that all warnings were expected
warnings_set = set(warning_.category for warning_ in w)
expected_set = set([FutureWarning, UserWarning,
DeprecationWarning])
assert warnings_set.issubset(expected_set), (
"the following warnings were not expected: {}").format(
warnings_set.difference(expected_set))
def plot_tbss(img, mean_FA_skeleton, start, end, row_l=6, step=1, title='',
axis='z', pngfile=None):
''' Inspired from plot_two_maps. Plots a TBSS contrast map over the
skeleton of a mean FA map'''
# Dilate tbss map
import numpy as np
from skimage.morphology import cube, dilation
from nilearn import image
d = np.array(image.load_img(img).dataobj)
dil_tbss = dilation(d, cube(2))
dil_tbss_img = image.new_img_like(img, dil_tbss)
slice_nb = int(abs(((end - start) / float(step))))
images = []
for line in range(int(slice_nb/float(row_l) + 1)):
opt = {'title':{True:title,
False:None}[line==0],
'colorbar':False,
'black_bg':True,
'display_mode':axis,
'threshold':0.2,
'cmap': cm.Greens,
'cut_coords':range(start + line * row_l * step,
start + (line+1) * row_l * step,
step)}
method = 'plot_stat_map'
opt.update({'stat_map_img': mean_FA_skeleton})
t = getattr(plotting, method).__call__(**opt)
try:
# Add overlay
t.add_overlay(dil_tbss_img, cmap=cm.hot, threshold=0.95, colorbar=True)
except TypeError:
print img, 'probably empty tbss map'
pass
# Converting to PIL and appending it to the list
buf = io.BytesIO()
t.savefig(buf)
buf.seek(0)
im = Image.open(buf)
images.append(im)
# Joining the images
imsize = images[0].size
out = Image.new('RGBA', size=(imsize[0], len(images)*imsize[1]))
for i, im in enumerate(images):
box = (0, i * imsize[1], imsize[0], (i+1) * imsize[1])
out.paste(im, box)
if pngfile is None:
import tempfile
pngfile = tempfile.mkstemp(suffix='.png')[1]
print 'Saving to...', pngfile, '(%s)'%title
out.save(pngfile)
def test_resample_stat_map():
# Start with simple simulated data
bg_img, data = _simulate_img()
# Now double the voxel size and mess with the affine
affine = 2 * np.eye(4)
affine[3, 3] = 1
affine[0, 1] = 0.1
stat_map_img = Nifti1Image(data, affine)
# Make a mask for the stat image
mask_img = new_img_like(stat_map_img, data > 0, stat_map_img.affine)
# Now run the resampling
stat_map_img, mask_img = html_stat_map._resample_stat_map(
stat_map_img, bg_img, mask_img, resampling_interpolation='nearest')
# Check positive isotropic, near-diagonal affine
_check_affine(stat_map_img.affine)
_check_affine(mask_img.affine)
# Check voxel size matches bg_img
assert stat_map_img.affine[0, 0] == bg_img.affine[0, 0], (
"stat_map_img was not resampled at the resolution of background")
assert mask_img.affine[0, 0] == bg_img.affine[0, 0], (
"mask_img was not resampled at the resolution of background")
def test_new_img_like():
# Give a list to new_img_like
data = np.zeros((5, 6, 7))
data[2:4, 1:5, 3:6] = 1
affine = np.diag((4, 3, 2, 1))
img = nibabel.Nifti1Image(data, affine=affine)
img2 = new_img_like([img, ], data)
np.testing.assert_array_equal(img.get_data(), img2.get_data())
def join_networks(self, network_indices):
"""Return a NiftiImage containing a binarised version of the sum of
the RSN images of each of the `network_indices`."""
oimg = self._get_img(network_indices[0]).get_data()
for idx in network_indices[1:]:
oimg += self._get_img(idx).get_data()
return niimg.new_img_like(self._get_img(network_indices[0]),
oimg.astype(bool))
def _run_interface(self, runtime):
t1_img = nli.load_img(self.inputs.in_file)
t1_data = t1_img.get_data()
epi_data = nli.load_img(self.inputs.ref_file).get_data()
# We assume the image is already masked
mask = t1_data > 0
t1_min, t1_max = np.unique(t1_data)[[1, -1]]
epi_min, epi_max = np.unique(epi_data)[[1, -1]]
scale_factor = (epi_max - epi_min) / (t1_max - t1_min)
inv_data = mask * ((t1_max - t1_data) * scale_factor + epi_min)
out_file = fname_presuffix(self.inputs.in_file, suffix='_inv', newpath=runtime.cwd)
nli.new_img_like(t1_img, inv_data, copy_header=True).to_filename(out_file)
self._results['out_file'] = out_file
return runtime
def inject_skullstripped(subjects_dir, subject_id, skullstripped):
mridir = op.join(subjects_dir, subject_id, 'mri')
t1 = op.join(mridir, 'T1.mgz')
bm_auto = op.join(mridir, 'brainmask.auto.mgz')
bm = op.join(mridir, 'brainmask.mgz')
if not op.exists(bm_auto):
img = nb.load(t1)
mask = nb.load(skullstripped)
bmask = new_img_like(mask, mask.get_data() > 0)
resampled_mask = resample_to_img(bmask, img, 'nearest')
masked_image = new_img_like(img, img.get_data() * resampled_mask.get_data())
masked_image.to_filename(bm_auto)
if not op.exists(bm):
copyfile(bm_auto, bm, copy=True, use_hardlink=True)
return subjects_dir, subject_id
def rescale(source, target):
import nibabel as nib
import numpy as np
from nilearn import image
n = nib.load(source)
d = np.array(n.dataobj)
s = n.dataobj.slope
i = image.new_img_like(n, d/s)
i.to_filename(target)
log.info('Rescaling done: %s rescaled to %s'%(source, target))
def compute_confounds(imgs, mask_img, n_confounds=5, get_randomized_svd=False,
compute_not_mask=False):
"""
"""
confounds = []
if not isinstance(imgs, collections.Iterable) or \
isinstance(imgs, _basestring):
imgs = [imgs, ]
img = _utils.check_niimg_4d(imgs[0])
shape = img.shape[:3]
affine = get_affine(img)
if isinstance(mask_img, _basestring):
mask_img = _utils.check_niimg_3d(mask_img)
if not _check_same_fov(img, mask_img):
mask_img = resample_img(
mask_img, target_shape=shape, target_affine=affine,
interpolation='nearest')
if compute_not_mask:
print("Non mask based confounds extraction")
not_mask_data = np.logical_not(mask_img.get_data().astype(np.int))
whole_brain_mask = masking.compute_multi_epi_mask(imgs)
not_mask = np.logical_and(not_mask_data, whole_brain_mask.get_data())
mask_img = new_img_like(img, not_mask.astype(np.int), affine)
for img in imgs:
print("[Confounds Extraction] {0}".format(img))
img = _utils.check_niimg_4d(img)
print("[Confounds Extraction] high ariance confounds computation]")
high_variance = high_variance_confounds(img, mask_img=mask_img,
n_confounds=n_confounds)
if compute_not_mask and get_randomized_svd:
signals = masking.apply_mask(img, mask_img)
non_constant = np.any(np.diff(signals, axis=0) != 0, axis=0)
signals = signals[:, non_constant]
signals = signal.clean(signals, detrend=True)
print("[Confounds Extraction] Randomized SVD computation")
U, s, V = randomized_svd(signals, n_components=n_confounds,
random_state=0)
if high_variance is not None:
confound_ = np.hstack((U, high_variance))
else:
confound_ = U
else:
confound_ = high_variance
confounds.append(confound_)
return confounds
def get_largest_blobs(ic_maps):
""" Generator for the largest blobs in each IC spatial map.
These should be masked and thresholded.
Parameters
----------
ic_maps: sequence of niimg-like
Returns
-------
blobs: generator of niimg-like
"""
# store the average value of the blob in a list
for i, icimg in enumerate(iter_img(ic_maps)):
yield niimg.new_img_like(icimg, largest_connected_component(icimg.get_data()))
def dicom2nii(filename):
dicomObject = dicom.read_file(filename)
niftiObject = dicomreaders.mosaic_to_nii(dicomObject)
temp_data = niftiObject.get_data()
output_image_correct = nib.orientations.apply_orientation(
temp_data, ornt_transform)
correct_object = new_img_like(templateFunctionalVolume,
output_image_correct,
copy_header=True)
# print(nib.aff2axcodes(niftiObject.affine))
splitList = filename.split('/')
# fullNiftiFilename='/'+os.path.join(*splitList[0:-1] , splitList[-1].split('.')[0]+'.nii.gz')
fullNiftiFilename = os.path.join(tmp_folder,
splitList[-1].split('.')[0] + '.nii.gz')
print('fullNiftiFilename=', fullNiftiFilename)
correct_object.to_filename(fullNiftiFilename)
return fullNiftiFilename
def signal_fluctuation_sensitivity(img: niimg_like) -> nib.nifti1.Nifti1Image:
"""Compute voxelwise SFS given an img in MNI space and an array containing
a CSF confounding regressor"""
# first_term is the "first term" of the SFS, as referred to in the paper.
meanimg = voxelwise_mean(img)
first_term = meanimg.get_data() / global_mean_within_mni(img)
# Similary, the second term is the "second term" in the paper.
stdimg = voxelwise_std(img)
second_term = stdimg.get_data() / confound_std(img)
# SFS is the product of both terms. Here we return it as an image.
sfs = first_term * second_term
return image.new_img_like(img,
data=sfs,
affine=meanimg.affine,
copy_header=True)
def _get_data_and_json_view(black_bg, cbar):
# simple simulated data for stat_img and background
bg_img, data = _simulate_img()
stat_map_img, data = _simulate_img()
# make a mask
mask_img = new_img_like(stat_map_img, data > 0, stat_map_img.affine)
# Get color bar and data ranges
colors = colorscale('cold_hot', data.ravel(), threshold=0,
symmetric_cmap=True, vmax=1)
# Build a sprite
json_view = html_stat_map._json_view_data(
bg_img, stat_map_img, mask_img, bg_min=0, bg_max=1, black_bg=black_bg,
colors=colors, cmap='cold_hot', colorbar=cbar)
return data, json_view
def test_get_data():
img, *_ = data_gen.generate_fake_fmri(shape=(10, 11, 12))
data = get_data(img)
assert data.shape == img.shape
assert data is img._data_cache
mask_img = new_img_like(img, data > 0)
data = get_data(mask_img)
assert data.dtype == np.dtype('int8')
img_3d = index_img(img, 0)
with tempfile.TemporaryDirectory() as tempdir:
filename = os.path.join(tempdir, 'img_{}.nii.gz')
img_3d.to_filename(filename.format('a'))
img_3d.to_filename(filename.format('b'))
data = get_data(filename.format('a'))
assert len(data.shape) == 3
data = get_data(filename.format('*'))
assert len(data.shape) == 4
def copy_header(in_file, data_file, out_file=None):
""" Use nilearn.image.new_img_like to copy the header
from `in_file` to `data_file` and return the result.
Returns
-------
out_file: str
The absolute path to the output file.
"""
import nilearn.image as niimg
img = niimg.load_img(data_file)
return niimg.new_img_like(
in_file,
img.get_data(),
affine=img.affine, copy_header=True
)
def single_volume_zstat_denoising(model_filename, model_name, n_features, filenames, window, prediction_dir,
n_gpus=1, batch_size=1, model_kwargs=None, n_outputs=None,
sequence_kwargs=None, spacing=None, sequence=None,
strict_model_loading=True, metric_names=None,
verbose=True, resample_predictions=False, **unused_kwargs):
import torch
model, dataset, basename = load_volumetric_model_and_dataset(model_name, model_filename, model_kwargs, n_outputs,
n_features, strict_model_loading, n_gpus, sequence,
sequence_kwargs, filenames, window, spacing,
metric_names)
dataset.extract_sub_volumes = False
print("Dataset: ", len(dataset))
with torch.no_grad():
completed = set()
batch = list()
for idx in range(len(dataset)):
x_filename, subject_id = get_feature_filename_and_subject_id(dataset, idx, verbose=False)
while type(x_filename) == list:
x_filename = x_filename[0]
if x_filename in completed:
continue
if verbose:
print("Reading:", x_filename)
x_image, ref_image = load_images_from_dataset(dataset, idx, resample_predictions)
if len(x_image.shape) == 4:
volumes_per_image = x_image.shape[3]
prediction_data = np.zeros(x_image.shape)
else:
volumes_per_image = 1
prediction_data = np.zeros(x_image.shape + (volumes_per_image,))
data = get_nibabel_data(x_image)
for image_idx in range(volumes_per_image):
batch.append(data[..., image_idx][..., None])
if len(batch) >= batch_size or image_idx == volumes_per_image - 1:
prediction = pytorch_predict_batch_array(model, batch, n_gpus)
prediction = np.moveaxis(prediction, 0, -1).squeeze()
prediction_data[..., (image_idx - prediction.shape[-1] + 1):(image_idx + 1)] = prediction
batch = list()
pred_image = new_img_like(ref_niimg=x_image, data=prediction_data)
output_filename = os.path.join(prediction_dir, "_".join((subject_id,
basename,
os.path.basename(x_filename))))
if verbose:
print("Writing:", output_filename)
pred_image.to_filename(output_filename)
completed.add(x_filename)
def resize(image, new_shape, interpolation="linear"):
if image.shape == new_shape:
return image
else:
image = reorder_img(image, resample=interpolation)
zoom_level = np.divide([float(i) for i in new_shape],
[float(i) for i in image.shape])
new_spacing = np.divide(image.header.get_zooms(), zoom_level)
new_data = resample_to_spacing(image.get_data(),
image.header.get_zooms(),
new_spacing,
interpolation=interpolation)
new_affine = np.copy(image.affine)
np.fill_diagonal(new_affine, new_spacing.tolist() + [1])
new_affine[:3, 3] += calculate_origin_offset(new_spacing,
image.header.get_zooms())
return new_img_like(image, new_data, affine=new_affine)
def gen_img_list(uatlas):
"""
Return list of boolean nifti masks where each masks corresponds to a unique atlas label for the provided atlas
parcellation. Path string to Nifti1Image is input.
Parameters
----------
uatlas : str
File path to atlas parcellation Nifti1Image in MNI template space.
Returns
-------
img_list : list
List of binarized Nifti1Images corresponding to ROI masks for each unique atlas label.
"""
import gc
import os.path as op
from nilearn.image import new_img_like
if not op.isfile(uatlas):
raise ValueError('\nERROR: User-specified atlas input not found! Check that the file(s) specified with the -ua '
'flag exist(s)')
bna_img = nib.load(uatlas)
bna_data = np.around(np.asarray(bna_img.dataobj)).astype('uint16')
# Get an array of unique parcels
bna_data_for_coords_uniq = np.unique(bna_data)
# Number of parcels:
par_max = len(bna_data_for_coords_uniq) - 1
img_stack = []
for idx in range(1, par_max + 1):
roi_img = bna_data == bna_data_for_coords_uniq[idx].astype('uint16')
img_stack.append(roi_img.astype('uint16'))
img_stack = np.array(img_stack)
img_list = []
for idy in range(par_max):
img_list.append(new_img_like(bna_img, img_stack[idy]))
del img_stack
bna_img.uncache()
gc.collect()
return img_list
def get_foreground_from_set_of_files(set_of_files,
background_value=0,
tolerance=0.00001,
return_image=False):
for i, image_file in enumerate(set_of_files):
image = read_image(image_file)
is_foreground = np.logical_or(
image.get_data() < (background_value - tolerance),
image.get_data() > (background_value + tolerance))
if i == 0:
foreground = np.zeros(is_foreground.shape, dtype=np.uint8)
foreground[is_foreground] = 1
if return_image:
return new_img_like(image, foreground)
else:
return foreground
def resize(image, new_shape, interpolation='linear'):
image = reorder_img(image, resample=interpolation)
# print('reorder_img', image)
# print(image.shape)
## 两次相除
zoom_level = np.divide(new_shape, image.shape)
new_spacing = np.divide(image.header.get_zooms(), zoom_level)
# print('new_spacing', new_spacing)
new_data = resample_to_spacing(image.get_data(),
image.header.get_zooms(),
new_spacing,
interpolation=interpolation)
new_affine = np.copy(image.affine)
np.fill_diagonal(new_affine, new_spacing.tolist() + [1])
new_affine[:3, 3] += calculate_origin_offset(new_spacing,
image.header.get_zooms())
return new_img_like(image, new_data, affine=new_affine)
def test_nifti_spheres_masker_inverse_overlap():
rng = np.random.RandomState(42)
# Test overlapping data in inverse_transform
affine = np.eye(4)
shape = (5, 5, 5)
data = rng.random_sample(shape + (5, ))
fmri_img = nibabel.Nifti1Image(data, affine)
# Apply mask image - to allow inversion
mask_img = new_img_like(fmri_img, np.ones(shape))
seeds = [(0, 0, 0), (2, 2, 2)]
# Inverse data
inv_data = rng.random_sample(len(seeds))
overlapping_masker = NiftiSpheresMasker(seeds,
radius=1,
allow_overlap=True,
mask_img=mask_img).fit()
overlapping_masker.inverse_transform(inv_data)
overlapping_masker = NiftiSpheresMasker(seeds,
radius=2,
allow_overlap=True,
mask_img=mask_img).fit()
overlap = overlapping_masker.inverse_transform(inv_data)
# Test whether overlapping data is averaged
assert_array_almost_equal(get_data(overlap)[1, 1, 1], np.mean(inv_data))
noverlapping_masker = NiftiSpheresMasker(seeds,
radius=1,
allow_overlap=False,
mask_img=mask_img).fit()
noverlapping_masker.inverse_transform(inv_data)
noverlapping_masker = NiftiSpheresMasker(seeds,
radius=2,
allow_overlap=False,
mask_img=mask_img).fit()
with pytest.raises(ValueError, match='Overlap detected'):
noverlapping_masker.inverse_transform(inv_data)
def test_img_to_signals_labels_non_float_type(target_dtype):
fake_fmri_data = np.random.RandomState(0).rand(10, 10, 10, 10) > 0.5
fake_affine = np.eye(4, 4).astype(np.float64)
fake_fmri_img_orig = nibabel.Nifti1Image(
fake_fmri_data.astype(np.float64),
fake_affine,
)
fake_fmri_img_target_dtype = new_img_like(
fake_fmri_img_orig, fake_fmri_data.astype(target_dtype))
fake_mask_data = np.ones((10, 10, 10), dtype=np.uint8)
fake_mask = nibabel.Nifti1Image(fake_mask_data, fake_affine)
masker = NiftiLabelsMasker(fake_mask)
masker.fit()
timeseries_int = masker.transform(fake_fmri_img_target_dtype)
timeseries_float = masker.transform(fake_fmri_img_orig)
assert np.sum(timeseries_int) != 0
assert np.allclose(timeseries_int, timeseries_float)
def _merge_mask(in_files):
in_imgs = [nib.load(in_file) for in_file in in_files]
outshape = first(in_imgs).shape
assert all(in_img.shape == outshape
for in_img in in_imgs), "Mask shape mismatch"
in_data = [
np.asanyarray(in_img.dataobj).astype(np.bool) for in_img in in_imgs
]
outarr = np.logical_and.reduce(in_data)
outimg = new_img_like(first(in_imgs), outarr, copy_header=True)
merged_file = _merge_fname(in_files)
nib.save(outimg, merged_file)
return merged_file
def save2volbord_bci(data, outfile, bfp_path, smooth_std=0):
'''Save output to brainordinates'''
a = loadmat(join(bfp_path, 'supp_data', 'bord_ind.mat'))
v = load_img(
join(bfp_path, 'supp_data', 'BCI-DNI_brain.pvc.frac.3mm.nii.gz'))
img_dat = np.zeros(v.shape)
img_dat[np.unravel_index(a['ind'], img_dat.shape, order='F')] = data[:,
None]
if smooth_std > 0:
img_dat = gaussian_filter(img_dat,
sigma=(smooth_std, smooth_std, smooth_std),
order=0)
v2 = new_img_like(v, img_dat)
v2.to_filename(outfile)
def extract_clusters(folder):
from nilearn.image import get_data, new_img_like
os.chdir(folder)
effects = [i.split('_where')[0] for i in os.listdir() if 'where' in i]
for eff in effects:
out_dir = f'{eff}_cluster_masks';mkdir(out_dir)
cmap = f'{eff}_cluster_map.nii.gz'
cluster_data = get_data(cmap)
for clust in np.unique(cluster_data):
if clust > 0:
mask_data = np.zeros(cluster_data.shape)
mask_data[np.where(cluster_data == clust)] = 1
out_mask = new_img_like(nib.load(cmap),mask_data.astype(int),copy_header=True)
nib.save(out_mask,f'{out_dir}/cluster_{clust}_mask.nii.gz')
def saveAsNiftiImage(dicomDataObject, fullNiftiFilename, cfg, reference):
"""
This function takes in a dicom data object written in bytes, what you expect
the dicom file to be called (we will use the same name format for the nifti
file), and the config file while will have (1) the axes transformation for the
dicom file and (2) the header information from a reference scan.
Used externally.
"""
niftiObject = dicomreaders.mosaic_to_nii(dicomDataObject)
temp_data = niftiObject.get_fdata()
output_image_correct = nib.orientations.apply_orientation(
temp_data, cfg.axesTransform)
correct_object = new_img_like(reference,
output_image_correct,
copy_header=True)
correct_object.to_filename(fullNiftiFilename)
return fullNiftiFilename
def fit(self, X=None, y=None): # noqa
super(HemisphereMasker, self).fit(X, y)
# x, y, z
hemi_mask_data = reorder_img(self.mask_img_).get_data().astype(np.bool)
xvals = hemi_mask_data.shape[0]
midpt = np.ceil(xvals / 2.0)
if self.hemi == "r":
other_hemi_slice = slice(midpt, xvals)
else:
other_hemi_slice = slice(0, midpt)
hemi_mask_data[other_hemi_slice] = False
mask_data = self.mask_img_.get_data() * hemi_mask_data
self.mask_img_ = new_img_like(self.mask_img_, data=mask_data)
return self
def test_vol_to_surf(kind, n_scans, use_mask):
img, mask_img = data_gen.generate_mni_space_img(n_scans)
if not use_mask:
mask_img = None
if n_scans == 1:
img = image.new_img_like(img, image.get_data(img).squeeze())
fsaverage = datasets.fetch_surf_fsaverage()
mesh = surface.load_surf_mesh(fsaverage["pial_left"])
inner_mesh = surface.load_surf_mesh(fsaverage["white_left"])
center_mesh = np.mean([mesh[0], inner_mesh[0]], axis=0), mesh[1]
proj = surface.vol_to_surf(
img, mesh, kind="depth", inner_mesh=inner_mesh, mask_img=mask_img)
other_proj = surface.vol_to_surf(
img, center_mesh, kind=kind, mask_img=mask_img)
correlation = pearsonr(proj.ravel(), other_proj.ravel())[0]
assert correlation > .99
with pytest.raises(ValueError, match=".*interpolation.*"):
surface.vol_to_surf(img, mesh, interpolation="bad")
def _run_interface(self, runtime):
self._merged_file = None
if not isdefined(self.inputs.in_files):
self._results["merged_file"] = False
return runtime
in_imgs = [nib.load(in_file) for in_file in self.inputs.in_files]
if len(in_imgs) == 0:
self._results["merged_file"] = False
return runtime
idim = dimensions.index(self.inputs.dimension)
sizes = [niftidim(in_img, idim) for in_img in in_imgs]
outshape = list(first(in_imgs).shape)
while len(outshape) < idim + 1:
outshape.append(1)
outshape[idim] = sum(sizes)
movd_shape = [outshape[idim], *outshape[:idim], *outshape[idim + 1:]]
movd_outarr = np.zeros(movd_shape, dtype=np.float64)
i = 0
for in_img, size in zip(in_imgs, sizes):
in_data = in_img.get_fdata()
while len(in_data.shape) < idim + 1:
in_data = np.expand_dims(in_data, len(in_data.shape))
movd_outarr[i:i + size] = np.moveaxis(in_data, idim, 0)
i += size
outarr = np.moveaxis(movd_outarr, 0, idim)
outimg = new_img_like(first(in_imgs), outarr, copy_header=True)
merged_file = op.abspath("merged.nii.gz")
nib.save(outimg, merged_file)
self._results["merged_file"] = merged_file
return runtime
def _crop_img_to(img, slices, copy=True):
"""Crops image to a smaller size
Crop img to size indicated by slices and adjust affine
accordingly
Parameters
----------
img: Niimg-like object
See http://nilearn.github.io/manipulating_images/input_output.html
Img to be cropped. If slices has less entries than img
has dimensions, the slices will be applied to the first len(slices)
dimensions
slices: list of slices
Defines the range of the crop.
E.g. [slice(20, 200), slice(40, 150), slice(0, 100)]
defines a 3D cube
copy: boolean
Specifies whether cropped data is to be copied or not.
Default: True
Returns
-------
cropped_img: Niimg-like object
See http://nilearn.github.io/manipulating_images/input_output.html
Cropped version of the input image
"""
img = check_niimg(img)
data = img.get_data()
affine = img.affine
cropped_data = data[slices]
if copy:
cropped_data = cropped_data.copy()
linear_part = affine[:3, :3]
old_origin = affine[:3, 3]
new_origin_voxel = np.array([s.start for s in slices])
new_origin = old_origin + linear_part.dot(new_origin_voxel)
new_affine = np.eye(4)
new_affine[:3, :3] = linear_part
new_affine[:3, 3] = new_origin
return new_img_like(img, cropped_data, new_affine)
def segment_t1w(t1w, basename, nclass=3, beta=0.1, max_iter=100):
"""
A function to use FSL's FAST to segment an anatomical
image into GM, WM, and CSF prob maps.
Parameters
----------
t1w : str
File path to an anatomical T1-weighted image.
basename : str
A basename to use for output files.
Returns
-------
out : str
File path to the probability map Nifti1Image consisting of GM, WM,
and CSF in the 4th dimension.
"""
from dipy.segment.tissue import TissueClassifierHMRF
from nilearn.image import new_img_like
print("Segmenting T1w...")
t1w_img = nib.load(t1w)
hmrf = TissueClassifierHMRF()
PVE = hmrf.classify(t1w_img.get_fdata(), nclass, beta,
max_iter=max_iter)[2]
new_img_like(t1w_img, PVE[..., 2]).to_filename(
f"{os.path.dirname(os.path.abspath(t1w))}/{basename}_{'pve_0.nii.gz'}")
new_img_like(t1w_img, PVE[..., 1]).to_filename(
f"{os.path.dirname(os.path.abspath(t1w))}/{basename}_{'pve_1.nii.gz'}")
new_img_like(t1w_img, PVE[..., 0]).to_filename(
f"{os.path.dirname(os.path.abspath(t1w))}/{basename}_{'pve_2.nii.gz'}")
out = {} # the outputs
out["wm_prob"] = f"{os.path.dirname(os.path.abspath(t1w))}/{basename}_" \
f"pve_0.nii.gz"
out["gm_prob"] = f"{os.path.dirname(os.path.abspath(t1w))}/{basename}_" \
f"pve_1.nii.gz"
out["csf_prob"] = f"{os.path.dirname(os.path.abspath(t1w))}/{basename}_" \
f"pve_2.nii.gz"
del PVE
t1w_img.uncache()
gc.collect()
return out
def save2volgord_bci(data, out_dir, vol_name, bfp_path, fsl_path,
default_value):
vol = load_img(
join(bfp_path, 'supp_data', 'Vol_BCI_grayord32k.mask.nii.gz'))
a = loadmat(join(bfp_path, 'supp_data', 'bci_grayordinates_vol_ind.mat'))
ind = a['bci_vol_ind'] - 1
gordvol = np.zeros(vol.shape) + default_value
val_gind = ~np.isnan(ind)
ind2 = np.int32(ind[val_gind])
ind2 = np.unravel_index(np.int32(ind2), vol.shape, order='F')
gordvol[ind2] = data[val_gind.squeeze()]
grod = new_img_like(vol, gordvol)
grod.set_data_dtype(np.float64)
outfile = join(out_dir, vol_name + '.nii.gz')
grod.to_filename(outfile)
def _interpolate_frames(data: Union[Nifti1Image, npt.ArrayLike],
mask: npt.ArrayLike, censor: npt.ArrayLike,
t_r: float) -> Union[Nifti1Image, npt.ArrayLike]:
'''
Interpolates `censor` using `img` data in `mask`
using lombscargle non-uniform spectral interpolation
Arguments:
data: Input data to censor where last index denotes time-points
[N1 x ,..., x T]
mask: Non-censored array indices from uncensored data
censor: Censored array indices that were removed from `img`
t_r: Repetition time
'''
if not censor.any():
return data
is_nifti = False
if isinstance(data, Nifti1Image):
sgls = _image_to_signals(data)
is_nifti = True
else:
sgls = data
t_num_samples = len(censor) + len(mask)
# Lombscargle interpolate expects already censored data
if sgls.shape[1] == t_num_samples:
sgls = sgls[:, mask]
t = np.arange(0, t_num_samples) * t_r
interp_vals = lombscargle_interpolate(t=t[mask], x=sgls, s=t)
res = np.empty((sgls.shape[0], t_num_samples), dtype=sgls.dtype)
res[:, mask] = sgls
res[:, censor] = interp_vals[:, censor]
res = res.reshape((*data.shape[:-1], t_num_samples))
if is_nifti:
return nimg.new_img_like(data, res, copy_header=True)
return res
def split_bilateral_rois(maps_img):
"""Convenience function for splitting bilateral ROIs
into two unilateral ROIs"""
new_rois = []
for map_img in iter_img(maps_img):
for hemi in ["L", "R"]:
hemi_mask = HemisphereMasker(hemisphere=hemi)
hemi_mask.fit(map_img)
if hemi_mask.mask_img_.get_data().sum() > 0:
hemi_vectors = hemi_mask.transform(map_img)
hemi_img = hemi_mask.inverse_transform(hemi_vectors)
new_rois.append(hemi_img.get_data())
new_maps_data = np.concatenate(new_rois, axis=3)
new_maps_img = new_img_like(maps_img, data=new_maps_data, copy_header=True)
print("Changed from %d ROIs to %d ROIs" % (maps_img.shape[-1], new_maps_img.shape[-1]))
return new_maps_img
def get_foreground_from_set_of_files(set_of_files,
background_value=0,
tolerance=0.00001,
return_image=False):
for i, image_file in enumerate(set_of_files):
# "read_image" luc nay chi doc nguyen hinh, ko thuc hien xu ly gi ca !
image = read_image(image_file)
# La foreground khi gia tri khac 0.
is_foreground = np.logical_or(
image.get_data() < (background_value - tolerance),
image.get_data() > (background_value + tolerance))
if i == 0:
foreground = np.zeros(is_foreground.shape, dtype=np.uint8)
foreground[is_foreground] = 1
if return_image:
return new_img_like(image, foreground)
else:
return foreground
def __init__(
self,
sessions=None,
smoothing_fwhm=None,
standardize=False,
detrend=False,
low_pass=None,
high_pass=None,
t_r=None,
target_affine=None,
target_shape=None,
mask_strategy="background",
mask_args=None,
sample_mask=None,
memory_level=1,
memory=Memory(cachedir=None),
verbose=0,
):
# Use grey matter mask computed for Neurovault analysis
# ('https://github.com/NeuroVault/neurovault_analysis/')
target_img = nib.load(fetch_grey_matter_mask())
grey_voxels = (target_img.get_data() > 0).astype(int)
mask_img = new_img_like(target_img, grey_voxels, copy_header=True)
super(GreyMatterNiftiMasker, self).__init__(
mask_img=mask_img,
target_affine=mask_img.affine,
target_shape=mask_img.shape,
sessions=sessions,
smoothing_fwhm=smoothing_fwhm,
standardize=standardize,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
mask_strategy=mask_strategy,
mask_args=mask_args,
sample_mask=sample_mask,
memory_level=memory_level,
memory=memory,
verbose=verbose,
)
def test_view_stat_map():
mni = datasets.load_mni152_template()
# Create a fake functional image by resample the template
img = image.resample_img(mni, target_affine=3 * np.eye(3))
html = html_stat_map.view_stat_map(img)
_check_html(html)
html = html_stat_map.view_stat_map(img, threshold='95%')
_check_html(html)
html = html_stat_map.view_stat_map(img, bg_img=mni)
_check_html(html)
html = html_stat_map.view_stat_map(img, bg_img=None)
_check_html(html)
html = html_stat_map.view_stat_map(img, threshold=2., vmax=4.)
_check_html(html)
html = html_stat_map.view_stat_map(img, symmetric_cmap=False)
img_4d = image.new_img_like(img, img.get_data()[:, :, :, np.newaxis])
assert len(img_4d.shape) == 4
html = html_stat_map.view_stat_map(img_4d, threshold=2., vmax=4.)
_check_html(html)
def get_ROI_from_parcel(parcel, ROI, threshold=0):
"""
Extracts ROI from parcel
If 4D probabilistic parcel, a threshould must be defined to determine the cutoff for the ROI.
If 3d parcel (atlas), threshold is ignored.
Args:
parcel: 3D or 4D parcel
ROI: index of ROI. Should be 0 indexed. For 4D, extract the ROI_i slice in the 4th dimension.
If 3D, find values that are equal to ROI_i+1 (assumes 0 is used to reflect background)
"""
if len(parcel.shape) == 4:
# convert a probabilistic parcellation into an ROI mask
roi_mask = parcel.get_fdata()[:, :, :, ROI] > threshold
else:
roi_mask = parcel.get_fdata() == (ROI + 1)
assert np.sum(roi_mask) != 0, "ROI doesn't exist. Returned empty map"
roi_mask = image.new_img_like(parcel, roi_mask)
return roi_mask
def _run_interface(self, runtime):
mask_img = nib.load(self.inputs.mask_file)
mask = np.asanyarray(mask_img.dataobj).astype(bool)
mask = np.squeeze(mask)
min_coverage = self.inputs.min_coverage
if not isdefined(min_coverage) or not isinstance(min_coverage, float):
min_coverage = 1.0
self._min_coverage = min_coverage
self._out_files = []
self._coverage = []
for in_file in self.inputs.in_files:
in_img = nib.load(in_file)
in_bool = np.asanyarray(in_img.dataobj).astype(bool)
in_bool = np.squeeze(in_bool)
unmasked_n_voxels = np.count_nonzero(in_bool)
out_bool = np.logical_and(in_bool, mask)
masked_n_voxels = np.count_nonzero(out_bool)
coverage = float(masked_n_voxels) / float(unmasked_n_voxels)
self._coverage.append(coverage)
if coverage < min_coverage:
self._out_files.append(None)
continue
stem, _ = split_ext(in_file)
out_file = Path.cwd() / f"{stem}_masked.nii.gz"
out_img = new_img_like(in_img, out_bool, copy_header=True)
nib.save(out_img, out_file)
self._out_files.append(out_file)
return runtime
def write(self, out_prefix):
ties = np.sum(self.masks.to_list(), axis=0, dtype=np.uint16) > 1
if np.any(ties):
warn(
f"Atlases to be merged have {np.sum(ties):d} ties. "
"Resolving by closest center of mass"
)
centers_of_mass = np.vstack([*map(center_of_mass, self.masks)])
for coordinate in zip(*np.nonzero(ties)):
candidates = [*map(lambda m: m[coordinate], self.masks)]
distance = cdist(
np.asarray(coordinate, dtype=np.float64)[np.newaxis, :],
centers_of_mass[candidates, :]
)
indices = self.masks.index[candidates]
winner_index = indices[np.argmin(distance)]
warn(
f"Assigning coordinate {coordinate} to "
f"{self.labels.loc[winner_index]:s}"
)
for index in indices:
if index == winner_index:
continue
self.masks.loc[index][coordinate] = False
assert np.all(
np.sum(self.masks.to_list(), axis=0, dtype=np.uint16) <= 1
) # double check ties
atlas = np.sum(
[*map(lambda t: t[0] * t[1], self.masks.items())],
axis=0,
dtype=np.uint16
)
out_atlas_img = new_img_like(self.fixed_img, atlas, copy_header=True)
out_atlas_img.header["descrip"] = f"Generated by HALFpipe/Atlases version {__version__}"
nib.save(out_atlas_img, f"{out_prefix}.nii.gz")
self.labels.to_csv(f"{out_prefix}.txt", sep="\t", header=False)
def test_view_img_on_surf():
img = _get_img()
fsaverage = dict(fetch_surf_fsaverage())
html = html_surface.view_img_on_surf(img, threshold='92.3%')
check_html(html)
html = html_surface.view_img_on_surf(img, threshold=0, surf_mesh=fsaverage)
check_html(html)
html = html_surface.view_img_on_surf(img, threshold=.4)
check_html(html)
html = html_surface.view_img_on_surf(
img, threshold=.4, cmap='hot', black_bg=True)
check_html(html)
html = html_surface.view_img_on_surf(img, surf_mesh='fsaverage')
check_html(html)
assert_raises(DimensionError, html_surface.view_img_on_surf, [img, img])
img_4d = image.new_img_like(img, img.get_data()[:, :, :, np.newaxis])
assert len(img_4d.shape) == 4
html = html_surface.view_img_on_surf(img, threshold='92.3%')
check_html(html)
def __init__(
self,
sessions=None,
smoothing_fwhm=None,
standardize=False,
detrend=False,
low_pass=None,
high_pass=None,
t_r=None,
target_affine=None,
target_shape=None,
mask_strategy="background",
mask_args=None,
sample_mask=None,
memory_level=1,
memory=Memory(cachedir=None),
verbose=0,
):
# Create grey matter mask from mni template
target_img = datasets.load_mni152_template()
grey_voxels = (target_img.get_data() > 0).astype(int)
mask_img = new_img_like(target_img, grey_voxels, copy_header=True)
super(MniNiftiMasker, self).__init__(
mask_img=mask_img,
target_affine=mask_img.affine,
target_shape=mask_img.shape,
sessions=sessions,
smoothing_fwhm=smoothing_fwhm,
standardize=standardize,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
mask_strategy=mask_strategy,
mask_args=mask_args,
sample_mask=sample_mask,
memory_level=memory_level,
memory=memory,
verbose=verbose,
)
def create_parcel_atlas(parcel_list):
"""
Create a 3D Nifti1Image atlas parcellation of consecutive integer intensities from an input list of ROI's.
Parameters
----------
parcel_list : list
List of 3D boolean numpy arrays or binarized Nifti1Images corresponding to ROI masks.
Returns
-------
net_parcels_map_nifti : Nifti1Image
A nibabel-based nifti image consisting of a 3D array with integer voxel intensities corresponding to ROI
membership.
parcel_list_exp : list
List of 3D boolean numpy arrays or binarized Nifti1Images corresponding to ROI masks, prepended with a
background image of zeros.
"""
import gc
from nilearn.image import new_img_like, concat_imgs
parcel_list_exp = [
new_img_like(parcel_list[0], np.zeros(parcel_list[0].shape,
dtype=bool))
] + parcel_list
concatted_parcels = concat_imgs(parcel_list_exp, dtype=np.float32)
parcel_list_exp = np.array(range(len(parcel_list_exp))).astype("float32")
parcel_sum = np.sum(parcel_list_exp *
np.asarray(concatted_parcels.dataobj),
axis=3,
dtype=np.uint16)
par_max = np.max(parcel_list_exp)
outs = np.unique(parcel_sum[parcel_sum > par_max])
# Set overlapping cases to zero.
for out in outs:
parcel_sum[parcel_sum == out] = 0
net_parcels_map_nifti = nib.Nifti1Image(parcel_sum,
affine=parcel_list[0].affine)
del concatted_parcels, parcel_sum, parcel_list
gc.collect()
return net_parcels_map_nifti, parcel_list_exp
def map_plane(estimates,
atlas,
path,
suffix="",
plane="z",
cbar=False,
annotate=False,
vmin=None,
vmax=None,
cmaps=[],
print_fig=True,
verbose=False):
from nilearn import image, plotting
for f, feature in enumerate(estimates.columns):
stat_map = image.copy_img(atlas).get_data()
data = estimates[feature]
if verbose:
print("{:20s} Min: {:6.4f} Mean: {:6.4f} Max: {:6.4f}".format(
feature, min(data), np.mean(data), max(data)))
if not verbose and print_fig:
print("\n{}".format(feature))
for i, value in enumerate(data):
stat_map[stat_map == i + 1] = value
stat_map = image.new_img_like(atlas, stat_map)
display = plotting.plot_stat_map(stat_map,
display_mode=plane,
symmetric_cbar=False,
colorbar=cbar,
cmap=cmaps[f],
threshold=vmin,
vmax=vmax,
alpha=0.5,
annotate=annotate,
draw_cross=False)
file_name = "{}/{}{}.png".format(path, feature, suffix)
display.savefig(file_name, dpi=250)
transparent_background(file_name)
if print_fig:
plotting.show()
display.close()
def gen_img_list(uatlas_select):
from nilearn.image import new_img_like
bna_img = nib.load(uatlas_select)
bna_data = np.round(bna_img.get_data(), 1)
# Get an array of unique parcels
bna_data_for_coords_uniq = np.unique(bna_data)
# Number of parcels:
par_max = len(bna_data_for_coords_uniq) - 1
bna_data = bna_data.astype('int16')
img_stack = []
for idx in range(1, par_max + 1):
roi_img = bna_data == bna_data_for_coords_uniq[idx].astype('int16')
roi_img = roi_img.astype('int16')
img_stack.append(roi_img)
img_stack = np.array(img_stack).astype('int16')
img_list = []
for idy in range(par_max):
roi_img_nifti = new_img_like(bna_img, img_stack[idy])
img_list.append(roi_img_nifti)
return img_list
def _region_extractor_labels_image(atlas, extract_type='connected_components',
min_region_size=0):
""" Function takes atlas image denoted as labels for each region
and then imposes region extraction algorithm on the image to
split them into regions apart.
Parameters
----------
atlas : 3D Nifti-like image
An image contains labelled regions.
extract_type : 'connected_components', 'local_regions'
See nilearn.regions.connected_regions for full documentation
min_region_size : in mm^3
Minimum size of voxels in a region to be kept.
"""
atlas_img = check_niimg(atlas)
atlas_data = _safe_get_data(atlas_img)
affine = atlas_img.get_affine()
n_labels = np.unique(np.asarray(atlas_data))
reg_imgs = []
for label_id in n_labels:
if label_id == 0:
continue
print("[Region Extraction] Processing with label {0}".format(label_id))
region = (atlas_data == label_id) * atlas_data
reg_img = new_img_like(atlas_img, region)
regions, _ = connected_regions(reg_img, extract_type=extract_type,
min_region_size=min_region_size)
reg_imgs.append(regions)
regions_extracted = concat_niimgs(reg_imgs)
return regions_extracted, n_labels
def test_json_view_data():
# simple simulated data for stat_img and background
bg_img, data = _simulate_img()
stat_map_img, data = _simulate_img()
# make a mask
mask_img = new_img_like(stat_map_img, data > 0, stat_map_img.affine)
# Get color bar and data ranges
colors = colorscale('cold_hot', data.ravel(), threshold=0,
symmetric_cmap=True, vmax=1)
# Build a sprite
json_view = html_stat_map._json_view_data(
bg_img, stat_map_img, mask_img, bg_min=0, bg_max=1, colors=colors,
cmap='cold_hot', colorbar=True)
# Check the presence of critical fields
assert isinstance(json_view['bg_base64'], _basestring)
assert isinstance(json_view['stat_map_base64'], _basestring)
assert isinstance(json_view['cm_base64'], _basestring)
return json_view, data
def plot_wholebrain_test_stat(path, roi_img, name, type='contrast', l1=0, l2=1,
plot=True, save=None, burn=0.5, verbose=False,
invert=False, **kwargs):
''' Plot cluster-by-cluster z-scores across the whole brain for a
paired-samples contrast between the named effects n1 and n2.
Args:
path (str): path to all pickled PyMC3 trace results (one file per
region or cluster).
roi_img (str): path to map containing cluster/region labels.
name (str): name of factor whose levels we want to compare.
type (str): whether to search for the named factor as a 'contrast'
or as a 'term'.
l1 (int): index of first level to compare
l2 (int): index of second level to compare
plot (bool): Whether or not to plot the generated image.
save (str): Optional filename to write the resulting image to.
burn (float or int): burn-in (i.e., number of samples to drop
before comparison). If a float, interpreted as a proportion of
all available samples. If an int, interpreted as the number of
samples to drop.
invert (bool): whether to invert the sign of the test statistic
kwargs (dict): Any additional keywords to pass on to the nilearn
plot_stat_map function.
'''
roi_img = nb.load(roi_img) # Load label image
label_map = roi_img.get_data().round().astype(int)
result = np.zeros(roi_img.shape) # Empty volume for results
# Loop over region trace files
roi_traces = glob(path)
for rt in roi_traces:
label = int(re.search('(\d+)', basename(rt)).group(1))
obj = pickle.load(open(rt, 'rb'))
if hasattr(obj, 'trace'):
trace = obj.trace
if not hasattr(trace, name):
raise AttributeError("The MultiTrace object does not contain the "
"variable '%s'. Please make sure you have "
"the right name." % name)
if isinstance(burn, float):
_burn = round(len(trace[name]) * burn)
else:
_burn = burn
samp1 = trace[name][_burn:, l1]
if len(samp1.shape) > 1:
samp1 = samp1.mean(1)
if l2 is None:
mu = samp1
else:
samp2 = trace[name][_burn:, l2]
if len(samp2.shape) > 1:
samp2 = samp2.mean(1)
mu = samp1 - samp2
z = mu.mean() / mu.std()
else:
# if name not in obj['contrasts']:
if False:
raise AttributeError("The trace summary object does not contain the "
"variable '%s'. Please make sure you have "
"the right name." % name)
if type == 'contrast':
z = obj['contrasts'][name][2]
else:
z = obj['terms'][name]['z']
# Assign value to the correct voxels in the output image
if invert:
z *= -1
result[label_map == label] = z
# Write out image
output_img = new_img_like(roi_img, result, roi_img.affine)
if save is not None:
output_img.to_filename(save)
# Plot
if plot:
plotting.plot_stat_map(output_img, **kwargs)
return output_img
log_p_values = -np.log10(p_values)
# NAN values to zero
log_p_values[np.isnan(log_p_values)] = 0.
log_p_values[log_p_values > 10.] = 10.
# Visualize statistical p-values using plotting function `plot_stat_map`
from nilearn.plotting import plot_stat_map
# Before visualizing, we transform the computed p-values to Nifti-like image
# using function `new_img_like` from nilearn.
from nilearn.image import new_img_like
# First argument being a reference image and second argument should be p-values
# data to convert to a new image as output. This new image will have same header
# information as reference image.
log_p_values_img = new_img_like(fmri_img, log_p_values)
# Now, we visualize log p-values image on functional mean image as background
# with coordinates given manually and colorbar on the right side of plot (by
# default colorbar=True)
plot_stat_map(log_p_values_img, mean_img,
title="p-values", cut_coords=cut_coords)
#############################################################################
# **Selecting features using f_classif**: Feature selection method is also
# available in the scikit-learn Python package, where it has been extended to
# several classes, using the `sklearn.feature_selection.f_classif` function.
##############################################################################
# Build a mask from this statistical map (Improving the quality of the mask)
# --------------------------------------------------------------------------
l, n = find_region_names_using_cut_coords(dmn_coords, atlas_img,
labels=labels)
# where 'l' indicates new labels generated according to given atlas labels and
# coordinates
new_labels = l
# where 'n' indicates brain regions names labelled, generated according to given
# labels
region_names_involved = n
######################################################################
# Let's visualize
from nilearn.image import load_img
from nilearn import plotting
from nilearn.image import new_img_like
atlas_img = load_img(atlas_img)
affine = atlas_img.get_affine()
atlas_data = atlas_img.get_data()
for i, this_label in enumerate(new_labels):
this_data = (atlas_data == this_label)
this_data = this_data.astype(int)
this_img = new_img_like(atlas_img, this_data, affine)
plotting.plot_roi(this_img, cut_coords=dmn_coords[i],
title=region_names_involved[i])
plotting.show()
def cast_img(img, dtype=np.float32):
""" Cast image to the specified dtype"""
img = check_niimg(img)
img_data = img.get_data().astype(dtype)
return new_img_like(img, img_data, copy_header=True)