def generate_ss(modDir, ssDir, cases, ncpu, cut_coords):
# reorder both skeleton/* and warped/* according to caseId
warpedImgs = glob(pjoin(modDir, 'warped', '*_to_target.nii.gz'))
warpedImgs.sort()
skelImgs = glob(pjoin(modDir, 'skeleton', '*_to_target_skel.nii.gz'))
skelImgs.sort()
makeDirectory(ssDir)
pool = Pool(ncpu)
for fg, bg, c in zip(image.iter_img(skelImgs), image.iter_img(warpedImgs),
cases):
print('Taking screen shot of ', c)
output_file = pjoin(ssDir, f'{c}.png')
pool.apply_async(func=plotting.plot_stat_map,
args=(fg, ),
kwds={
'bg_img': bg,
'dim': False,
'annotate': False,
'draw_cross': False,
'cut_coords': cut_coords,
'resampling_interpolation': 'nearest',
'output_file': output_file
},
error_callback=RAISE)
pool.close()
pool.join()
'''
def plot_ica_components(components_img, **kwargs):
""" Plot the components IC spatial maps in a grid."""
import math
from nilearn.image import iter_img
from nilearn.plotting import plot_stat_map
from matplotlib import pyplot as plt
from matplotlib import gridspec
n_ics = len(list(iter_img(components_img)))
n_rows = math.ceil(n_ics / 2)
fig = plt.figure(figsize=(6, 3 * n_rows), facecolor='black')
gs = gridspec.GridSpec(n_rows, 2)
plots = []
for i, ic_img in enumerate(iter_img(components_img)):
ax = plt.subplot(gs[i])
p = plot_stat_map(ic_img,
display_mode="z",
title="IC {}".format(i + 1),
cut_coords=1,
colorbar=False,
figure=fig,
axes=ax,
**kwargs)
plots.append(p)
for p in plots:
p.close()
return fig
def test_plot_img_comparison():
fig, axes = plt.subplots(2, 1)
axes = axes.ravel()
kwargs = {"shape": (3, 2, 4), "length": 5}
query_images, mask_img = data_gen.generate_fake_fmri(
rand_gen=np.random.RandomState(0), **kwargs)
# plot_img_comparison doesn't handle 4d images ATM
query_images = list(image.iter_img(query_images))
target_images, _ = data_gen.generate_fake_fmri(
rand_gen=np.random.RandomState(1), **kwargs)
target_images = list(image.iter_img(target_images))
target_images[0] = query_images[0]
masker = NiftiMasker(mask_img).fit()
correlations = plotting.plot_img_comparison(
target_images, query_images, masker, axes=axes, src_label="query")
assert len(correlations) == len(query_images)
assert correlations[0] == pytest.approx(1.)
ax_0, ax_1 = axes
# 5 scatterplots
assert len(ax_0.collections) == 5
assert len(ax_0.collections[0].get_edgecolors() == masker.transform(
target_images[0]).ravel().shape[0])
assert ax_0.get_ylabel() == "query"
assert ax_0.get_xlabel() == "image set 1"
# 5 regression lines
assert len(ax_0.lines) == 5
assert ax_0.lines[0].get_linestyle() == "--"
assert ax_1.get_title() == "Histogram of imgs values"
assert len(ax_1.patches) == 5 * 2 * 128
correlations_1 = plotting.plot_img_comparison(
target_images, query_images, masker, plot_hist=False)
assert np.allclose(correlations, correlations_1)
def cluster_binary_img(binary_img, mask_img, min_region_size='exhaustive'):
# get voxel resolution in binary_img
# NOTE: function currently assumes equal width in x,y,z direction
voxel_sizes = binary_img.header.get_zooms()
# if not specfied by user, cluster exhaustive, i.e. assign each and every
# voxel to one and only one cluster
if min_region_size == 'exhaustive':
min_region_size_ = _get_voxel_volume(voxel_sizes) - 1
else:
min_region_size_ = min_region_size
# count overall number of 1s in the binary image
total_n_voxels = np.count_nonzero(binary_img.get_fdata())
# extract clusters in binary image
cluster_imgs, indices = connected_regions(
maps_img=binary_img,
min_region_size=min_region_size_,
extract_type='connected_components',
smoothing_fwhm=None,
mask_img=mask_img)
# Get sizes of clusters (number of voxels that have been assigned to each region)
# As a sanity check + for user information get size of every region and
# count overall number of voxels that have been assigned to that region
cluster_sizes = []
total_n_voxels_assigned = 0
for idx, cluster_img in enumerate(iter_img(cluster_imgs)):
cluster_img_data = cluster_img.get_fdata()
cluster_img_size = np.count_nonzero(cluster_img_data)
cluster_sizes.append(cluster_img_size)
total_n_voxels_assigned += cluster_img_size
if total_n_voxels_assigned != total_n_voxels:
raise ValueError(
'Number of voxels in output clustered image is different from total number of voxels in input binary image '
)
# Collapse the extracted cluster images to one cluster atlas image
cluster_imgs_labeled = []
for idx, cluster_img in enumerate(iter_img(cluster_imgs), start=1):
cluster_img_labeled = math_img(
f"np.where(cluster_img == 1,{idx},cluster_img)",
cluster_img=cluster_img)
cluster_imgs_labeled.append(cluster_img_labeled)
cluster_img_atlas = math_img("np.sum(imgs,axis=3)",
imgs=cluster_imgs_labeled)
# plot the cluster atlas image
plotting.plot_roi(cluster_img_atlas,
title='Clustered Binary Image',
draw_cross=False)
return cluster_sizes, cluster_img_atlas
def generate_ss(modDir, ssDir, cases, ncpu, cut_coords):
# reorder both skeleton/* and warped/* according to caseId
warpedImgs= glob(pjoin(modDir, 'warped', '*_to_target.nii.gz'))
warpedImgs.sort()
skelImgs= glob(pjoin(modDir, 'skeleton', '*_to_target_skel.nii.gz'))
skelImgs.sort()
makeDirectory(ssDir)
pool= Pool(ncpu)
for fg,bg,c in zip(image.iter_img(skelImgs), image.iter_img(warpedImgs), cases):
print('Taking screen shot of ', c)
output_file = pjoin(ssDir, f'{c}.png')
def load_vols(niimgs):
"""Loads a nifti image (or a bail of) into a list qof 3D volumes.
Parameters
----------
niimgs: 3 or 4D Niimg-like object
If niimgs is an iterable, checks if data is really 4D. Then,
considering that it is a list of niimg and load them one by one.
If niimg is a string, consider it as a path to Nifti image and
call nibabel.load on it. If it is an object, check if get_data
and get_affine methods are present, raise an Exception otherwise.
Returns
-------
niimgs_: list of nifti image objects
The loaded volumes.
"""
# try loading 4d
try:
niimgs = list(check_niimg_4d(niimgs, return_iterator=True))
except TypeError:
# probably not 4d
niimgs = [check_niimg(niimgs)]
except ValueError:
# probably inconsisten affines
pass
try:
# try loading volumes one-by-one
if isinstance(niimgs, _basestring):
niimgs = [niimgs]
return [check_niimg(niimg, ensure_ndim=3) for niimg in niimgs]
except TypeError:
pass
# collect the loaded volumes into a list
if is_niimg(niimgs):
# should be 3d, squash 4th dimension otherwise
if niimgs.shape[-1] == 1:
return [
nibabel.Nifti1Image(niimgs.get_data()[:, :, :, 0],
niimgs.get_affine())
]
else:
return list(iter_img(niimgs))
else:
niimgs = list(niimgs)
if len(niimgs) == 1:
niimgs = niimgs[0]
return list(iter_img(niimgs))
def test_component_sign():
# We should have a heuristic that flips the sign of components in
# CanICA to have more positive values than negative values, for
# instance by making sure that the largest value is positive.
# make data (SVD)
rng = np.random.RandomState(0)
shape = (20, 10, 1)
affine = np.eye(4)
components = _make_canica_components(shape)
# make +ve
for mp in components:
mp[rng.randn(*mp.shape) > .8] *= -5.
assert_less_equal(mp.max(), -mp.min()) # goal met ?
# synthesize data with given components
data = _make_data_from_components(components, affine, shape, rng=rng,
n_subjects=2)
mask_img = nibabel.Nifti1Image(np.ones(shape, dtype=np.int8), affine)
# run CanICA many times (this is known to produce different results)
canica = CanICA(n_components=4, random_state=rng, mask=mask_img)
for _ in range(3):
canica.fit(data)
for mp in iter_img(canica.masker_.inverse_transform(
canica.components_)):
mp = mp.get_data()
assert_less_equal(-mp.min(), mp.max())
def test_iterator_generator():
# Create a list of random images
rng = np.random.RandomState(42)
list_images = [
Nifti1Image(
rng.random_sample((10, 10, 10)), np.eye(4)
)
for i in range(10)
]
cc = _utils.concat_niimgs(list_images)
assert cc.shape[-1] == 10
assert_array_almost_equal(get_data(cc)[..., 0], get_data(list_images[0]))
# Same with iteration
i = image.iter_img(list_images)
cc = _utils.concat_niimgs(i)
assert cc.shape[-1] == 10
assert_array_almost_equal(get_data(cc)[..., 0], get_data(list_images[0]))
# Now, a generator
b = []
g = nifti_generator(b)
cc = _utils.concat_niimgs(g)
assert cc.shape[-1] == 10
assert len(b) == 10
def create_provenance_dataframe(bids_sources, harmonized_niis, b0_means,
harmonization_corrections):
series_confounds = []
nvols_per_image = [get_nvols(img) for img in harmonized_niis]
total_vols = np.sum(nvols_per_image)
# Check whether the bids sources are per file or per volume
if not len(bids_sources) == total_vols:
images_per_volume = []
for source_image, img_nvols in zip(bids_sources, nvols_per_image):
images_per_volume.extend([source_image] * img_nvols)
if not len(images_per_volume) == total_vols:
raise Exception("Mismatch in number of images and BIDS sources")
bids_sources = images_per_volume
for correction, harmonized_nii, b0_mean, nvols in zip(harmonization_corrections,
harmonized_niis,
b0_means,
nvols_per_image):
series_confounds.append(
pd.DataFrame({
"image_mean": [img.get_fdata().mean() for img in iter_img(harmonized_nii)],
"series_b0_mean": [b0_mean] * nvols,
"series_b0_correction": [correction] * nvols}))
image_df = pd.concat(series_confounds, axis=0, ignore_index=True)
image_df['original_file'] = bids_sources
return image_df
def plotrsn10(nii_ff, workdir, resultjpg_ff, threshold):
'''
plotrsn10('PNAS_Smith09_rsn10.nii.gz',r'c:\temp',r'c:\temp\test.jpg')
'''
z = [8, -4, -10, 30, -34, 50, 14, 22, 46, 48]
ii = 0
images = []
fig = plt.figure(figsize=(4, 6), dpi=300)
for img in image.iter_img(nii_ff):
# img is now an in-memory 3D img
tempimage = join(workdir, 'RSN%02d.jpg' % (ii + 1))
display = plotting.plot_stat_map(img,
figure=fig,
threshold=threshold,
display_mode="z",
cut_coords=[(z[ii])],
colorbar=False)
display.annotate(size=30)
display.savefig(tempimage)
images.append(tempimage)
plt.clf()
ii += 1
plt.close()
row1 = concat_n_images(images[0:5])
row2 = concat_n_images(images[5:10])
output = np.vstack((row1, 255 * np.ones(
(10, row1.shape[1], 3), dtype=np.uint8), row2))
fig = plt.figure(figsize=(output.shape[0] // 30, output.shape[1] // 30),
dpi=100)
plt.axis('off')
plt.imshow(output)
fig.savefig(resultjpg_ff, bbox_inches='tight')
def get_prob_atlas_label(prob_map, prob_labels, coord, thresh=None):
label_prob = list()
for slices in iter_img(prob_map):
label_prob.append(slices.get_data()[coord[0], coord[1], coord[2]])
# Get probability above a certain threshold or max:
if thresh is None:
thresh = np.max(label_prob)
if thresh == 0:
thresh = 1
label_idx = np.where(np.asarray(label_prob) >= thresh)[0]
labels_out = list()
proba_out = list()
for idx in label_idx:
proba_out.append(label_prob[idx])
labels_out.append(prob_labels[idx])
return labels_out, proba_out
def filter_ics(comps_img, mask, zscore=2., mode='+-'):
"""
Generator for masking and thresholding each IC spatial map.
Parameters
----------
comps_img: img-like
The 'raw' ICC maps image.
mask: img-like
If not None. Will apply this masks in the end of the process.
thr: float
The threshold value.
zscore: bool
If True will calculate the z-score of the ICC before thresholding.
mode: str
Choices: '+' for positive threshold,
'+-' for positive and negative threshold and
'-' for negative threshold.
Returns
-------
icc_filts: list of nibabel.NiftiImage
Thresholded and masked ICCs.
"""
# store the average value of the blob in a list
mask = niimg.load_img(mask)
for i, icimg in enumerate(iter_img(comps_img)):
yield filter_icc(icimg, mask=mask, thr=zscore, zscore=True, mode=mode)
def filter_ics(comps_img, mask, zscore=2., mode='+-'):
"""
Generator for masking and thresholding each IC spatial map.
Parameters
----------
comps_img: img-like
The 'raw' ICC maps image.
mask: img-like
If not None. Will apply this masks in the end of the process.
thr: float
The threshold value.
zscore: bool
If True will calculate the z-score of the ICC before thresholding.
mode: str
Choices: '+' for positive threshold,
'+-' for positive and negative threshold and
'-' for negative threshold.
Returns
-------
icc_filts: list of nibabel.NiftiImage
Thresholded and masked ICCs.
"""
# store the average value of the blob in a list
mask = niimg.load_img(mask)
for i, icimg in enumerate(iter_img(comps_img)):
yield filter_icc(icimg, mask=mask, thr=zscore, zscore=True, mode=mode)
def plot_pro(self, ita, save=False, item_file='group', name='vmf', choose=None, cut_coords=None):
ita[ita > 0.1] = 0
for component in ita:
if component.max() < -component.min():
component *= -1
if hasattr(self, "masker_"):
self.components_img_ = self.masker_.inverse_transform(ita)
components_img = self.components_img_
warnings.filterwarnings("ignore")
for i, cur_img in enumerate(iter_img(components_img)):
if cut_coords is not None and i in cut_coords.keys():
display = plot_stat_map(cur_img, cut_coords=cut_coords[i], dim=-.5, threshold=4e-3,
cmap=plt.get_cmap('autumn'))
else:
display = plot_stat_map(cur_img, dim=-.5, threshold=4e-3,
cmap=plt.get_cmap('autumn'))
if save:
if choose is not None:
display.savefig('{}/brain/{}/{}/SVAE-item{}-c.png'.format(RESULT_DIR, name, item_file, choose[i] + 1), dpi=200)
else:
display.savefig('{}/brain/{}/{}/SVAE-item{}-c.png'.format(RESULT_DIR, name, item_file, i + 1), dpi=200)
if save is False:
show()
def get_peak_coords(clust_img):
"""
Gets MNI coordinates of peak voxels within each cluster of `clust_img`
Parameters
----------
clust_img : 4D-niimg_like
4D image of brain regions, where each volume is a separated cluster
Returns
------
coords : (N, 3) numpy.ndarray
Coordinates of peak voxels in `clust_img`
"""
# check cluster image and make it 4D, if not already
clust_img = check_niimg(clust_img, atleast_4d=True)
# create empty arrays to hold cluster size + peak coordinates
clust_size = np.zeros(clust_img.shape[-1])
maxcoords = np.zeros((clust_img.shape[-1], 3))
# iterate through clusters and get info
for n, cluster in enumerate(image.iter_img(clust_img)):
cluster = np.abs(cluster.get_data())
clust_size[n] = np.sum(cluster != 0)
maxcoords[n] = center_of_mass(cluster == cluster.max())
# sort peak coordinates by cluster size
maxcoords = np.floor(maxcoords)[np.argsort(clust_size)[::-1]]
# convert coordinates to MNI space
coords = coord_ijk_to_xyz(clust_img.affine, maxcoords)
return coords
def plot(self, downsample=1, out_base="."):
out_path = os.path.join(out_base, self.subject, self.name, self.task)
os.makedirs(out_path, exist_ok=True)
raw = nib.load(self.path)
M = np.max(raw.get_data())
n = raw.shape[3]
mean = nimage.mean_img(raw)
xyzcuts = nilplot.find_xyz_cut_coords(mean)
xcuts = nilplot.find_cut_slices(mean, "x")
ycuts = nilplot.find_cut_slices(mean, "y")
zcuts = nilplot.find_cut_slices(mean, "z")
del raw
nrange = range(0, n, downsample)
for i, img in enumerate(nimage.iter_img(self.path)):
if i in nrange:
nilplot.plot_epi(nimage.math_img("img / %f" % (M), img=img),
colorbar=False,
output_file="%s/orth_epi%0d.png" %
(out_path, i),
annotate=True,
cut_coords=xyzcuts,
cmap="gist_heat")
nilplot.plot_epi(nimage.math_img("img / %f" % (M), img=img),
colorbar=False,
output_file="%s/x_epi%0d.png" % (out_path, i),
annotate=True,
display_mode="x",
cut_coords=xcuts,
cmap="gist_heat")
nilplot.plot_epi(nimage.math_img("img / %f" % (M), img=img),
colorbar=False,
output_file="%s/y_epi%0d.png" % (out_path, i),
annotate=True,
display_mode="y",
cut_coords=ycuts,
cmap="gist_heat")
nilplot.plot_epi(nimage.math_img("img / %f" % (M), img=img),
colorbar=False,
output_file="%s/z_epi%0d.png" % (out_path, i),
annotate=True,
display_mode="z",
cut_coords=zcuts,
cmap="gist_heat")
slice_names = ["orth_epi", "x_epi", "y_epi", "z_epi"]
for slic in slice_names:
filenames = ["%s/%s%0d.png" % (out_path, slic, i) for i in nrange]
with imageio.get_writer('%s/%s.gif' % (out_path, slic),
mode='I') as writer:
for i, filename in zip(nrange, filenames):
image = Image.open(filename)
draw = ImageDraw.Draw(image)
fnt = ImageFont.truetype('Pillow/Tests/fonts/FreeMono.ttf',
16)
draw.text((2, 2), str(i), font=fnt, fill=(255, 0, 0, 255))
image.save(filename, "PNG")
image = imageio.imread(filename)
writer.append_data(image)
def load_vols(niimgs):
"""Loads a nifti image (or a bail of) into a list qof 3D volumes.
Parameters
----------
niimgs: 3 or 4D Niimg-like object
If niimgs is an iterable, checks if data is really 4D. Then,
considering that it is a list of niimg and load them one by one.
If niimg is a string, consider it as a path to Nifti image and
call nibabel.load on it. If it is an object, check if get_data
and get_affine methods are present, raise an Exception otherwise.
Returns
-------
niimgs_: list of nifti image objects
The loaded volumes.
"""
# try loading 4d
try:
niimgs = list(check_niimg_4d(niimgs, return_iterator=True))
except TypeError:
# probably not 4d
niimgs = [check_niimg(niimgs)]
except ValueError:
# probably inconsisten affines
pass
try:
# try loading volumes one-by-one
if isinstance(niimgs, _basestring): niimgs = [niimgs]
return [check_niimg(niimg, ensure_ndim=3) for niimg in niimgs]
except TypeError:
pass
# collect the loaded volumes into a list
if is_niimg(niimgs):
# should be 3d, squash 4th dimension otherwise
if niimgs.shape[-1] == 1:
return [nibabel.Nifti1Image(niimgs.get_data()[:, :, :, 0],
niimgs.get_affine())]
else:
return list(iter_img(niimgs))
else:
niimgs = list(niimgs)
if len(niimgs) == 1: niimgs = niimgs[0]
return list(iter_img(niimgs))
def _process_inputs(self):
""" validate and process inputs into useful form.
Returns a list of nilearn maskers and the list of corresponding label
names."""
import nilearn.input_data as nl
import nilearn.image as nli
label_data = nli.concat_imgs(self.inputs.label_files)
maskers = []
# determine form of label files, choose appropriate nilearn masker
if np.amax(label_data.dataobj) > 1: # 3d label file
n_labels = np.amax(label_data.dataobj)
maskers.append(nl.NiftiLabelsMasker(label_data))
else: # 4d labels
n_labels = label_data.shape[3]
if self.inputs.incl_shared_variance: # independent computation
for img in nli.iter_img(label_data):
maskers.append(
nl.NiftiMapsMasker(self._4d(img.dataobj, img.affine))
)
else: # one computation fitting all
maskers.append(nl.NiftiMapsMasker(label_data))
# check label list size
if not np.isclose(int(n_labels), n_labels):
raise ValueError(
"The label files {} contain invalid value {}. Check input.".format(
self.inputs.label_files, n_labels
)
)
if len(self.inputs.class_labels) != n_labels:
raise ValueError(
"The length of class_labels {} does not "
"match the number of regions {} found in "
"label_files {}".format(
self.inputs.class_labels, n_labels, self.inputs.label_files
)
)
if self.inputs.include_global:
global_label_data = label_data.dataobj.sum(axis=3) # sum across all regions
global_label_data = (
np.rint(global_label_data).astype(int).clip(0, 1)
) # binarize
global_label_data = self._4d(global_label_data, label_data.affine)
global_masker = nl.NiftiLabelsMasker(
global_label_data, detrend=self.inputs.detrend
)
maskers.insert(0, global_masker)
self.inputs.class_labels.insert(0, "GlobalSignal")
for masker in maskers:
masker.set_params(detrend=self.inputs.detrend)
return maskers
def _filter_ic_imgs(self, ic_file):
if self.zscore > 0:
do_zscore = True
else:
do_zscore = False
mask = niimg.load_img(self.mask_file)
return [filter_icc(icimg, mask=mask, thr=self.zscore, zscore=do_zscore, mode=self.mode)
for icimg in iter_img(ic_file)]
def _filter_ic_imgs(self, ic_file):
if self.zscore > 0:
do_zscore = True
else:
do_zscore = False
mask = niimg.load_img(self.mask_file)
return [filter_icc(icimg, mask=mask, thr=self.zscore, zscore=do_zscore, mode=self.mode)
for icimg in iter_img(ic_file)]
def plot_icmaps(self, outtype='png', **kwargs):
""" Plot the thresholded IC spatial maps and store the outputs in the ICA results folder.
Parameters
----------
outtype: str
Extension (without the '.') of the output files, will specify which plot image file you want.
Returns
-------
all_icc_plot_f: str
iccs_plot_f: str
sliced_ic_plots: list of str
"""
# specify the file paths
all_icc_plot_f = op.join(
self.ica_dir,
'all_components_zscore_{}.{}'.format(self.zscore, outtype))
iccs_plot_f = op.join(
self.ica_dir,
'ic_components_zscore_{}.{}'.format(self.zscore, outtype))
icc_multi_slice = op.join(self.ica_dir, 'ic_map_{}_zscore_{}.{}')
# make the plots
fig1 = plot_ica_components(self._icc_imgs, **kwargs)
fig1.savefig(iccs_plot_f,
facecolor=fig1.get_facecolor(),
edgecolor='none')
fig2 = plot_all_components(self._icc_imgs, **kwargs)
fig2.savefig(all_icc_plot_f,
facecolor=fig2.get_facecolor(),
edgecolor='none')
# make the multi sliced IC plots
sliced_ic_plots = []
for i, img in enumerate(iter_img(self._icc_imgs)):
fig3 = plot_multi_slices(img,
cut_dir="z",
n_cuts=24,
n_cols=4,
title="IC {}\n(z-score {})".format(
i + 1, self.zscore),
title_fontsize=32,
plot_func=None,
**kwargs)
# prepare the output file name/path
out_f = icc_multi_slice.format(i + 1, self.zscore, outtype)
fig3.savefig(out_f,
facecolor=fig3.get_facecolor(),
edgecolor='none')
sliced_ic_plots.append(out_f)
return all_icc_plot_f, iccs_plot_f, sliced_ic_plots
def _save_results(annotated_names, maps_img, dimension):
maps_img = nibabel.load(maps_img)
for i, img in enumerate(image.iter_img(maps_img)):
cut_coords = plotting.find_xyz_cut_coords(img)
if annotated_names is not None:
annotated_name = annotated_names.iloc[i].Difumo_names
else:
annotated_name = None
_plot_dl_maps(img, cut_coords, annotated_name, i, dimension)
return
def generate_ss(modDir, ssDir, cases, ncpu):
# reorder both skeleton/* and warped/* according to caseId
warpedImgs= glob(pjoin(modDir, 'warped', '*_to_target.nii.gz'))
skelImgs= glob(pjoin(modDir, 'skeleton', '*_to_target_skel.nii.gz'))
warpedImgs= orderCases(warpedImgs, cases)
skelImgs= orderCases(skelImgs, cases)
makeDirectory(ssDir)
pool= Pool(ncpu)
for fg,bg,c in zip(image.iter_img(skelImgs), image.iter_img(warpedImgs), cases):
print('Taking screen shot of ', c)
output_file = pjoin(ssDir, f'{c}.png')
pool.apply_async(func= plotting.plot_stat_map, args= (fg, ),
kwds= {'bg_img':bg, 'dim':False, 'annotate':False, 'draw_cross':False, 'output_file':output_file, })
pool.close()
pool.join()
def get_image(self):
image_path = self.update_image_path() # update image path to make sure get correct image
if self.image_info is not None:
img = nib.load(image_path)
if len(img.shape) == 3:
print("3D")
return [img]
else:
print("4D")
return list(image.iter_img(img))
def _run_interface(self, runtime):
ext = '.nii.gz' if self.inputs.compress else '.nii'
self._results['out_files'] = []
out_pattern = fname_presuffix(self.inputs.in_file, suffix='_%05d' + ext,
newpath=runtime.cwd, use_ext=False)
for i, im in enumerate(iter_img(nb.load(self.inputs.in_file))):
out_file = out_pattern % i
im.to_filename(out_file)
self._results['out_files'].append(out_file)
return runtime
def run_mini_pipeline():
atlas = datasets.fetch_atlas_msdl()
atlas_img = atlas['maps']
labels = pd.read_csv(atlas['labels'])['name']
masker = NiftiMapsMasker(maps_img=atlas_img, standardize=True,
memory='/tmp/nilearn', verbose=0)
data = datasets.fetch_adhd(number_subjects)
figures_folder = '../figures/'
count=0
for func_file, confound_file in zip(data.func, data.confounds):
# fit the data to the atlas mask, regress out confounds
time_series = masker.fit_transform(func_file, confounds=confound_file)
correlation = np.corrcoef(time_series.T)
#plotting starts here
plt.figure(figsize=(10, 10))
plt.imshow(correlation, interpolation="nearest")
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
corr_file = figures_folder+'subject_number_' + str(count) + '_correlation.pdf'
plt.savefig(corr_file)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in image.iter_img(atlas_img)]
threshold = 0.6
plotting.plot_connectome(correlation, atlas_region_coords, edge_threshold=threshold)
connectome_file = figures_folder+'subject_number_' + str(count) + '_connectome.pdf'
plt.savefig(connectome_file)
#graph setup
#binarize correlation matrix
correlation[correlation<threshold] = 0
correlation[correlation != 0] = 1
graph = nx.from_numpy_matrix(correlation)
partition=louvain.best_partition(graph)
values = [partition.get(node) for node in graph.nodes()]
plt.figure()
nx.draw_spring(graph, cmap = plt.get_cmap('jet'), node_color = values, node_size=30, with_labels=True)
graph_file = figures_folder+'subject_number_' + str(count) + '_community.pdf'
plt.savefig(graph_file)
count += 1
plt.close('all')
def _process_inputs(self):
''' validate and process inputs into useful form.
Returns a list of nilearn maskers and the list of corresponding label
names.'''
import nilearn.input_data as nl
import nilearn.image as nli
label_data = nli.concat_imgs(self.inputs.label_files)
maskers = []
# determine form of label files, choose appropriate nilearn masker
if np.amax(label_data.get_data()) > 1: # 3d label file
n_labels = np.amax(label_data.get_data())
maskers.append(nl.NiftiLabelsMasker(label_data))
else: # 4d labels
n_labels = label_data.get_data().shape[3]
if self.inputs.incl_shared_variance: # independent computation
for img in nli.iter_img(label_data):
maskers.append(
nl.NiftiMapsMasker(
self._4d(img.get_data(), img.affine)))
else: # one computation fitting all
maskers.append(nl.NiftiMapsMasker(label_data))
# check label list size
if not np.isclose(int(n_labels), n_labels):
raise ValueError(
'The label files {} contain invalid value {}. Check input.'
.format(self.inputs.label_files, n_labels))
if len(self.inputs.class_labels) != n_labels:
raise ValueError('The length of class_labels {} does not '
'match the number of regions {} found in '
'label_files {}'.format(self.inputs.class_labels,
n_labels,
self.inputs.label_files))
if self.inputs.include_global:
global_label_data = label_data.get_data().sum(
axis=3) # sum across all regions
global_label_data = np.rint(global_label_data).astype(int).clip(
0, 1) # binarize
global_label_data = self._4d(global_label_data, label_data.affine)
global_masker = nl.NiftiLabelsMasker(
global_label_data, detrend=self.inputs.detrend)
maskers.insert(0, global_masker)
self.inputs.class_labels.insert(0, 'GlobalSignal')
for masker in maskers:
masker.set_params(detrend=self.inputs.detrend)
return maskers
def _calculate_nmse(self, original_nii, corrected_nii):
"""Calculate NMSE from the applied preprocessing operation."""
outputs = self._list_outputs()
output_file = outputs.get('nmse_text')
pres = []
posts = []
differences = []
for orig_img, corrected_img in zip(iter_img(original_nii),
iter_img(corrected_nii)):
orig_data = orig_img.get_fdata()
corrected_data = corrected_img.get_fdata()
baseline = orig_data.mean()
pres.append(baseline)
posts.append(corrected_data.mean())
scaled_diff = np.abs(corrected_data - orig_data).mean() / baseline
differences.append(scaled_diff)
title = str(self.__class__)[:-2].split('.')[-1]
pd.DataFrame({
title + "_pre": pres,
title + "_post": posts,
title + "_change": differences
}).to_csv(output_file, index=False)
def save_info(info, dimension):
"""Save found records
Parameters
----------
info : dict
Contains meta-data assigned to each atlas name such as
overlap proportion, etc
Each atlas dict contains following attributes:
'intersection' : sparse matrix
dot product between DiFuMo regions and regions in target
atlas (existing pre-defined)
'target_size' : np.ndarray
Size of each region estimated in target atlas
'overlap_proportion' : list of pd.Series
Each list contains the proportion of overlap estimated
between this region and all region in target sizes.
Sorted according to most strong hit in the overlap.
'overlap_size' : list
Each list contain overlap in estimated sizes for all
regions in target atlas.
dimension : int
DiFuMo atlas dimension
Returns
-------
data : pd.DataFrame
"""
html = "https://parietal-inria.github.io/DiFuMo/{0}/html/{1}.html"
table = set_difumo_storage()
maps_img = nibabel.load(fetch_difumo(dimension=dimension).maps)
for i, img in enumerate(image.iter_img(maps_img)):
cut_coords = plotting.find_xyz_cut_coords(img)
for n in [64, 128, 256, 512, 1024]:
labels = fetch_difumo(dimension=n).labels['Difumo_names'].to_list()
# Proportion of overlap with each index of difumo component
this_img_info = info[n]['overlap_proportion'][i]
identified_components = this_img_info.index[1:6]
if len(identified_components) != 0:
# grabbing the top five from the overlapped list
for identified_component in identified_components:
table['dimension'].append(dimension)
table['component'].append(i + 1)
table['overlap_against'].append(n)
table['identified'].append(identified_component + 1)
table['label'].append(labels[identified_component])
return pd.DataFrame(table)
def test_threshold_img():
# to check whether passes with valid threshold inputs
shape = (10, 20, 30)
maps, _ = testing.generate_maps(shape, n_regions=4)
affine = np.eye(4)
mask_img = nibabel.Nifti1Image(np.ones((shape), dtype=np.int8), affine)
for img in iter_img(maps):
# when threshold is a float value
thr_maps_img = threshold_img(img, threshold=0.8)
# when we provide mask image
thr_maps_percent = threshold_img(img, threshold=1, mask_img=mask_img)
# when threshold is a percentile
thr_maps_percent2 = threshold_img(img, threshold='2%')
def test_threshold_img():
# to check whether passes with valid threshold inputs
shape = (10, 20, 30)
maps, _ = data_gen.generate_maps(shape, n_regions=4)
affine = np.eye(4)
mask_img = nibabel.Nifti1Image(np.ones((shape), dtype=np.int8), affine)
for img in iter_img(maps):
# when threshold is a float value
thr_maps_img = threshold_img(img, threshold=0.8)
# when we provide mask image
thr_maps_percent = threshold_img(img, threshold=1, mask_img=mask_img)
# when threshold is a percentile
thr_maps_percent2 = threshold_img(img, threshold='2%')
def split_4d(in_file, out_dir):
"""
Split 4D file into 3D files in out_dir
"""
img_4d = nib.load(in_file)
if not op.isdir(out_dir):
mkdir(out_dir)
out_files = []
for i, img_3d in enumerate(image.iter_img(img_4d)):
out_file = op.join(out_dir, 'f{0:05d}.nii.gz'.format(i))
img_3d.to_filename(out_file)
out_files.append(out_file)
return out_files
def plot_ica_components(components_img, **kwargs):
""" Plot the components IC spatial maps in a grid."""
import math
from nilearn.image import iter_img
from nilearn.plotting import plot_stat_map
from matplotlib import pyplot as plt
from matplotlib import gridspec
n_ics = len(list(iter_img(components_img)))
n_rows = math.ceil(n_ics/2)
fig = plt.figure(figsize=(6, 3*n_rows), facecolor='black')
gs = gridspec.GridSpec(n_rows, 2)
plots = []
for i, ic_img in enumerate(iter_img(components_img)):
ax = plt.subplot(gs[i])
p = plot_stat_map(ic_img, display_mode="z", title="IC {}".format(i+1),
cut_coords=1, colorbar=False, figure=fig, axes=ax, **kwargs)
plots.append(p)
for p in plots:
p.close()
return fig
def test_component_sign():
# Regression test
# We should have a heuristic that flips the sign of components in
# DictLearning to have more positive values than negative values, for
# instance by making sure that the largest value is positive.
data, mask_img, components, rng = _make_canica_test_data(n_subjects=2, noisy=True)
for mp in components:
assert_less_equal(-mp.min(), mp.max())
dict_learning = DictLearning(n_components=4, random_state=rng, mask=mask_img, smoothing_fwhm=0.0, alpha=1)
dict_learning.fit(data)
for mp in iter_img(dict_learning.masker_.inverse_transform(dict_learning.components_)):
mp = mp.get_data()
assert_less_equal(np.sum(mp[mp <= 0]), np.sum(mp[mp > 0]))
def test_component_sign():
# We should have a heuristic that flips the sign of components in
# CanICA to have more positive values than negative values, for
# instance by making sure that the largest value is positive.
data, mask_img, components, rng = _make_canica_test_data(n_subjects=2,
noisy=True)
# run CanICA many times (this is known to produce different results)
canica = CanICA(n_components=4, random_state=rng, mask=mask_img)
for _ in range(3):
canica.fit(data)
for mp in iter_img(canica.components_img_):
mp = get_data(mp)
assert_less_equal(-mp.min(), mp.max())
def test_component_sign():
# We should have a heuristic that flips the sign of components in
# CanICA to have more positive values than negative values, for
# instance by making sure that the largest value is positive.
data, mask_img, components, rng = _make_canica_test_data(n_subjects=2,
noisy=True)
# run CanICA many times (this is known to produce different results)
canica = CanICA(n_components=4, random_state=rng, mask=mask_img)
for _ in range(3):
canica.fit(data)
for mp in iter_img(canica.components_img_):
mp = mp.get_data()
assert_less_equal(-mp.min(), mp.max())
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 test_component_sign():
# Regression test
# We should have a heuristic that flips the sign of pipelining in
# DictLearning to have more positive values than negative values, for
# instance by making sure that the largest value is positive.
data, mask_img, components, init = _make_test_data(n_subjects=2,
noisy=True)
dict_fact = fMRIDictFact(n_components=4, random_state=0,
mask=mask_img,
smoothing_fwhm=0.)
dict_fact.fit(data)
for mp in iter_img(dict_fact.components_img_):
mp = mp.get_data()
assert(np.sum(mp[mp <= 0]) <= np.sum(mp[mp > 0]))
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 plot_pro(self,
ita,
save=False,
item_file='group',
name='vmf',
choose=None,
cut_coords=None):
for component in ita:
if component.max() < -component.min():
component *= -1
if hasattr(self, "masker_"):
self.components_img_ = self.masker_.inverse_transform(ita)
components_img = self.components_img_
warnings.filterwarnings("ignore")
display = plot_prob_atlas(components_img,
title='All components',
view_type='filled_contours')
if save:
display.savefig('{}/brain/{}/{}/pro.png'.format(
RESULT_DIR, name, item_file),
dpi=200)
for i, cur_img in enumerate(iter_img(components_img)):
if cut_coords is not None:
display = plot_stat_map(cur_img,
cut_coords=cut_coords[i],
dim=-.5,
threshold=1e-3,
cmap=plt.get_cmap('autumn'))
else:
display = plot_stat_map(cur_img,
dim=-.5,
threshold=1e-3,
cmap=plt.get_cmap('autumn'))
if save:
if choose is not None:
display.savefig('{}/brain/{}/{}/item{}.png'.format(
RESULT_DIR, name, item_file, choose[i] + 1),
dpi=200)
else:
display.savefig('{}/brain/{}/{}/item{}.png'.format(
RESULT_DIR, name, item_file, i + 1),
dpi=200)
if save is False:
show()
def plot_icmaps(self, outtype='png', **kwargs):
""" Plot the thresholded IC spatial maps and store the outputs in the ICA results folder.
Parameters
----------
outtype: str
Extension (without the '.') of the output files, will specify which plot image file you want.
Returns
-------
all_icc_plot_f: str
iccs_plot_f: str
sliced_ic_plots: list of str
"""
# specify the file paths
all_icc_plot_f = op.join(self.ica_dir, 'all_components_zscore_{}.{}'.format(self.zscore, outtype))
iccs_plot_f = op.join(self.ica_dir, 'ic_components_zscore_{}.{}'.format(self.zscore, outtype))
icc_multi_slice = op.join(self.ica_dir, 'ic_map_{}_zscore_{}.{}')
# make the plots
fig1 = plot_ica_components(self._icc_imgs, **kwargs)
fig1.savefig(iccs_plot_f, facecolor=fig1.get_facecolor(), edgecolor='none')
fig2 = plot_all_components(self._icc_imgs, **kwargs)
fig2.savefig(all_icc_plot_f, facecolor=fig2.get_facecolor(), edgecolor='none')
# make the multi sliced IC plots
sliced_ic_plots = []
for i, img in enumerate(iter_img(self._icc_imgs)):
fig3 = plot_multi_slices(img,
cut_dir="z",
n_cuts=24,
n_cols=4,
title="IC {}\n(z-score {})".format(i+1, self.zscore),
title_fontsize=32,
plot_func=None,
**kwargs)
# prepare the output file name/path
out_f = icc_multi_slice.format(i+1, self.zscore, outtype)
fig3.savefig(out_f, facecolor=fig3.get_facecolor(), edgecolor='none')
sliced_ic_plots.append(out_f)
return all_icc_plot_f, iccs_plot_f, sliced_ic_plots
def test_iterator_generator():
# Create a list of random images
l = [Nifti1Image(np.random.random((10, 10, 10)), np.eye(4)) for i in range(10)]
cc = _utils.concat_niimgs(l)
assert_equal(cc.shape[-1], 10)
assert_array_almost_equal(cc.get_data()[..., 0], l[0].get_data())
# Same with iteration
i = image.iter_img(l)
cc = _utils.concat_niimgs(i)
assert_equal(cc.shape[-1], 10)
assert_array_almost_equal(cc.get_data()[..., 0], l[0].get_data())
# Now, a generator
b = []
g = nifti_generator(b)
cc = _utils.concat_niimgs(g)
assert_equal(cc.shape[-1], 10)
assert_equal(len(b), 10)
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 plot_components(ica_image, hemi='', out_dir=None,
bg_img=datasets.load_mni152_template()):
print("Plotting %s components..." % hemi)
# Determine threshoold and vmax for all the plots
# get nonzero part of the image for proper thresholding of
# r- or l- only component
nonzero_img = ica_image.get_data()[np.nonzero(ica_image.get_data())]
thr = stats.scoreatpercentile(np.abs(nonzero_img), 90)
vmax = stats.scoreatpercentile(np.abs(nonzero_img), 99.99)
for ci, ic_img in enumerate(iter_img(ica_image)):
title = _title_from_terms(terms=ica_image.terms, ic_idx=ci, label=hemi)
fh = plt.figure(figsize=(14, 6))
plot_stat_map(ic_img, axes=fh.gca(), threshold=thr, vmax=vmax,
colorbar=True, title=title, black_bg=True, bg_img=bg_img)
# Save images instead of displaying
if out_dir is not None:
save_and_close(out_path=op.join(
out_dir, '%s_component_%i.png' % (hemi, ci)))
def plot_components_summary(ica_image, hemi='', out_dir=None,
bg_img=datasets.load_mni152_template()):
print("Plotting %s components summary..." % hemi)
n_components = ica_image.get_data().shape[3]
# Determine threshoold and vmax for all the plots
# get nonzero part of the image for proper thresholding of
# r- or l- only component
nonzero_img = ica_image.get_data()[np.nonzero(ica_image.get_data())]
thr = stats.scoreatpercentile(np.abs(nonzero_img), 90)
vmax = stats.scoreatpercentile(np.abs(nonzero_img), 99.99)
for ii, ic_img in enumerate(iter_img(ica_image)):
ri = ii % 5 # row i
ci = (ii / 5) % 5 # column i
pi = ii % 25 + 1 # plot i
fi = ii / 25 # figure i
if ri == 0 and ci == 0:
fh = plt.figure(figsize=(30, 20))
print('Plot %03d of %d' % (fi + 1, np.ceil(n_components / 25.)))
ax = fh.add_subplot(5, 5, pi)
title = _title_from_terms(terms=ica_image.terms, ic_idx=ii, label=hemi)
colorbar = ci == 4
plot_stat_map(
ic_img, axes=ax, threshold=thr, vmax=vmax, colorbar=colorbar,
title=title, black_bg=True, bg_img=bg_img)
if (ri == 4 and ci == 4) or ii == n_components - 1:
out_path = op.join(
out_dir, '%s_components_summary%02d.png' % (hemi, fi + 1))
save_and_close(out_path)
# first_rsn is a 3D image.
#
# We can then plot it
plotting.plot_stat_map(first_rsn)
###############################################################################
# Looping on all volumes in a 4D file
# -----------------------------------
#
# If we want to plot all the volumes in this 4D file, we can use iter_img
# to loop on them.
#
# Then we give a few arguments to plot_stat_map in order to have a more
# compact display.
for img in image.iter_img(rsn):
# img is now an in-memory 3D img
plotting.plot_stat_map(img, threshold=3, display_mode="z", cut_coords=1,
colorbar=False)
###############################################################################
# plotting.show is useful to force the display of figures when running
# outside IPython
plotting.show()
#########################################################################
# |
#
# ______
#
def _apply_mask_to_4dimg(self, imgs, **kwargs):
masker = NiftiMasker(mask_img=self.load_mask(), **kwargs)
return (masker.fit_transform(img) for img in iter_img(imgs))
correlation = connectome_measure.fit_transform([timeseries_each_subject])
# saving each subject correlation to correlations
correlations.append(correlation)
# Mean of all correlations
import numpy as np
mean_correlations = np.mean(correlations, axis=0).reshape(n_regions_extracted,
n_regions_extracted)
###############################################################################
# Plot resulting connectomes
# ----------------------------
import matplotlib.pyplot as plt
from nilearn import image
regions_imgs = image.iter_img(regions_extracted_img)
coords_connectome = [plotting.find_xyz_cut_coords(img) for img in regions_imgs]
title = 'Correlation interactions between %d regions' % n_regions_extracted
plt.figure()
plt.imshow(mean_correlations, interpolation="nearest",
vmax=1, vmin=-1, cmap=plt.cm.bwr)
plt.colorbar()
plt.title(title)
plotting.plot_connectome(mean_correlations, coords_connectome,
edge_threshold='90%', title=title)
################################################################################
# Plot regions extracted for only one specific network
# ----------------------------------------------------
# First, we plot a network of index=4 without region extraction (left plot)
####################################################################
# To visualize we plot the outline of all components on one figure
from nilearn.plotting import plot_prob_atlas
# Plot all ICA components together
plot_prob_atlas(canica_components_img, title='All ICA components')
####################################################################
# Finally, we plot the map for each ICA component separately
from nilearn.image import iter_img
from nilearn.plotting import plot_stat_map, show
for i, cur_img in enumerate(iter_img(canica_components_img)):
plot_stat_map(cur_img, display_mode="z", title="IC %d" % i,
cut_coords=1, colorbar=False)
####################################################################
# Compare CanICA to dictionary learning
# -------------------------------------------------------------
# Dictionary learning is a sparsity based decomposition method for extracting
# spatial maps. It extracts maps that are naturally sparse and usually cleaner
# than ICA. Here, we will compare networks built with CanICA to networks built
# with Dictionary Learning.
#
# * Arthur Mensch et al. `Compressed online dictionary learning for fast resting-state fMRI decomposition
# <https://hal.archives-ouvertes.fr/hal-01271033/>`_,
# ISBI 2016, Lecture Notes in Computer Science
rois = labels['name'].T
n_r = len(rois)
l=360./n_r#roi label size in figures
visu = atlas_filename
all_ntwks = range(n_r)
networks = {'Auditory': [0,1],'striate' : [2],'DMN': [3,4,5,6],'Occ post' :[7],
'Motor': [8],'Attentional' : [9,10,11,12,14,15,16,17,18],
'Basal' : [13],'Visual secondary' : [19,20,21], 'Salience':[22,23,24],
'Temporal(STS)':[25,26],'Langage':[27,28,29,30,31],'Cereb':[32],
'Dors PCC': [33],'cing ins' :[34,35,36],'Ant IPS': [37,38],'All ROIs':all_ntwks}
coords = [] #chose regions representative coordinates, other wise it s computed with find_xyz_cut_coords
#coords = np.vstack((labels['x'], labels['y'], labels['z'])).T
if not coords:
coords =[plotting.find_xyz_cut_coords(roi) for roi in image.iter_img(atlas_filename)]
root='/neurospin/grip/protocols/MRI/AVCnn_Dhaif_2016/AVCnn/AVCnn_data/' #fichier reg et conca pret pour analyse
func_type_list = [ 'controlRSc','patientsRSc_LD', 'patientsRSc_LG']# #name of each group's directory for functional images
reg_dirs = [ root+'rgt']#name of each group's directory for regressors (regressor have to be .txt files)
reg_prefix = 'art_mv_fmv_wm_vent_ext_hv_' #art_mv_fmv_wm_vent_ext_hv_regressor prefix (regressors must have corresponding functional file name after prefix: swars_ab_123456.nii and reg1_reg2_swars_ab_123456.txt)
common = 4 #initial differing character between regressors and functional file names
#choose report directory and name (default location is in root, default name is atlas_naabsolute
main_title ='AVCnn_Cont_LG_LD_'+MC_correction #
save_dir = root + 'reports_test/'
try:
os.makedirs(save_dir)
except:
print('Warning could not make dir '+save_dir)
pass
def spatclust(img, min_cluster_size, threshold=None, index=None, mask=None):
"""
Spatially clusters `img`
Parameters
----------
img : str or img_like
Image file or object to be clustered
min_cluster_size : int
Minimum cluster size (in voxels)
threshold : float, optional
Whether to threshold `img` before clustering
index : array_like, optional
Whether to extract volumes from `img` for clustering
mask : (S,) array_like, optional
Boolean array for masking resultant data array
Returns
-------
clustered : :obj:`numpy.ndarray`
Boolean array of clustered (and thresholded) `img` data
"""
# we need a 4D image for `niimg.iter_img`, below
img = niimg.copy_img(check_niimg(img, atleast_4d=True))
# temporarily set voxel sizes to 1mm isotropic so that `min_cluster_size`
# represents the minimum number of voxels we want to be in a cluster,
# rather than the minimum size of the desired clusters in mm^3
if not np.all(np.abs(np.diag(img.affine)) == 1):
img.set_sform(np.sign(img.affine))
# grab desired volumes from provided image
if index is not None:
if not isinstance(index, list):
index = [index]
img = niimg.index_img(img, index)
# threshold image
if threshold is not None:
img = niimg.threshold_img(img, float(threshold))
clout = []
for subbrick in niimg.iter_img(img):
# `min_region_size` is not inclusive (as in AFNI's `3dmerge`)
# subtract one voxel to ensure we aren't hitting this thresholding issue
try:
clsts = connected_regions(subbrick,
min_region_size=int(min_cluster_size) - 1,
smoothing_fwhm=None,
extract_type='connected_components')[0]
# if no clusters are detected we get a TypeError; create a blank 4D
# image object as a placeholder instead
except TypeError:
clsts = niimg.new_img_like(subbrick,
np.zeros(subbrick.shape + (1,)))
# if multiple clusters detected, collapse into one volume
clout += [niimg.math_img('np.sum(a, axis=-1)', a=clsts)]
# convert back to data array and make boolean
clustered = utils.load_image(niimg.concat_imgs(clout).get_data()) != 0
# if mask provided, mask output
if mask is not None:
clustered = clustered[mask]
return clustered
def plot_all(self):
names = self.network_names
for idx, rsn in enumerate(niimg.iter_img(self._img)):
disp = niplot.plot_roi(rsn, title=names.get(idx, None))
def compare_components(images, labels, scoring="correlation", flip=True, memory=Memory(cachedir="nilearn_cache")):
assert len(images) == 2
assert len(labels) == 2
assert images[0].shape == images[1].shape
n_components = images[0].shape[3] # values @ 0 and 1 are the same
labels = [l.upper() for l in labels] # make input labels case insensitive
print("Loading images.")
for img in images:
img.get_data() # Just loaded to get them in memory..
print("Scoring closest components (by %s)" % str(scoring))
score_mat = np.zeros((n_components, n_components))
sign_mat = np.zeros((n_components, n_components), dtype=np.int)
c1_data = [None] * n_components
c2_data = [None] * n_components
c1_images = list(iter_img(images[0]))
c2_images = list(iter_img(images[1]))
lh_masker = HemisphereMasker(hemisphere="L", memory=memory).fit()
rh_masker = HemisphereMasker(hemisphere="R", memory=memory).fit()
for c1i, comp1 in enumerate(c1_images):
for c2i, comp2 in enumerate(c2_images):
# Make sure the two images align (i.e. not R and L opposite),
# and that only good voxels are compared (i.e. not full vs half)
if "R" in labels and "L" in labels:
if c1_data[c1i] is None or c2_data[c2i] is None:
R_img = comp1 if labels.index("R") == 0 else comp2 # noqa
L_img = comp1 if labels.index("L") == 0 else comp2 # noqa
masker = lh_masker # use same masker; ensures same size
if c1_data[c1i] is None:
c1_data[c1i] = masker.transform(flip_img_lr(R_img)).ravel()
if c2_data[c2i] is None:
c2_data[c2i] = masker.transform(L_img).ravel()
elif "R" in labels or "L" in labels:
masker = rh_masker if "R" in labels else lh_masker
if c1_data[c1i] is None:
c1_data[c1i] = masker.transform(comp1).ravel()
if c2_data[c2i] is None:
c2_data[c2i] = masker.transform(comp2).ravel()
else:
if c1_data[c1i] is None:
c1_data[c1i] = comp1.get_data().ravel()
if c2_data[c2i] is None:
c2_data[c2i] = comp2.get_data().ravel()
# Choose a scoring system.
# Score should indicate DISSIMILARITY
# Component sign is meaningless, so try both unless flip = False,
# and keep track of comparisons that had better score when flipping the sign
score = np.inf
if flip:
signs = [1, -1]
else:
signs = [1]
for sign in signs:
c1d, c2d = c1_data[c1i], sign * c2_data[c2i]
if not isinstance(scoring, string_types): # function
sc = scoring(c1d, c2d)
elif scoring == "l1norm":
sc = np.linalg.norm(c1d - c2d, ord=1)
elif scoring == "l2norm":
sc = np.linalg.norm(c1d - c2d, ord=2)
elif scoring == "correlation":
sc = 1 - stats.stats.pearsonr(c1d, c2d)[0]
else:
raise NotImplementedError(scoring)
if sc < score:
sign_mat[c1i, c2i] = sign
score = min(score, sc)
score_mat[c1i, c2i] = score
return score_mat, sign_mat
confound_filename = adhd_dataset.confounds[0]
# Computing some confounds
hv_confounds = mem.cache(nilearn.image.high_variance_confounds)(
fmri_filename)
time_series = masker.transform(fmri_filename,
confounds=[hv_confounds, confound_filename])
print("-- Computing graph-lasso inverse matrix ...")
from sklearn import covariance
gl = covariance.GraphLassoCV(verbose=2)
gl.fit(time_series)
# Displaying results ##########################################################
atlas_imgs = image.iter_img(msdl_atlas_dataset.maps)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in atlas_imgs]
title = "GraphLasso"
plotting.plot_connectome(-gl.precision_, atlas_region_coords,
edge_threshold='90%',
title="Sparse inverse covariance")
plotting.plot_connectome(gl.covariance_,
atlas_region_coords, edge_threshold='90%',
title="Covariance")
plot_matrices(gl.covariance_, gl.precision_, title)
plt.show()
def spatial_maps_goodness_of_fit(rsn_imgs, spatial_maps, mask_file, rsn_thr=4.0):
""" Goodness-of-fit values described as in Zhou et al., 2010, Brain.
Parameters
----------
rsn_imgs: list of niimg-like or 4D niimg-like
The RSN maps. They should be thresholded beforehand if `rsn_thr` is lower or equal than 0.
spatial_maps: list of niimg-like or 4D niimg-like
mask_file: niimg-like
An extra mask to apply to the thresholded RSN masks.
This is used to exclude values outside of the RSN blobs.
It is recommended to use a brain mask for this.
rsn_thr: float, optional
The threshold to apply to `rsn_imgs` to create the RSN masks.
If rsn_thr <= 0, no thresholding will be applied.
Returns
-------
gof_df: np.ndarray
A matrix of shape MxN, where M is len(rsn_imgs) and N is len(spatial_maps).
It contains the goodness-of-fit values.
Notes
-----
"These ICN templates were thresholded at a z-score 4.0 to be visually comparable to the
consistent ICNs published by Damoiseaux et al. (2006). A minor modification of previous
goodness-of-fit methods (Seeley et al., 2007b, 2009) was included here for template
matching, with goodness-of-fit scores calculated by multiplying
(i) the average z-score difference between voxels falling within the template and
voxels falling outside the template; and
(ii) the difference in the percentage of positive z-score voxels inside and outside the template.
This goodness-of-fit algorithm proves less vulnerable to inter-subject variability in shape,
size, location and strength of each ICN", than the one published in Seeley et al., 2007b.
This latter method only uses the value in (i).
Extracted from Zhou et al., 2010, Brain.
"""
rsn_img = niimg.load_img(rsn_imgs)
spm_img = niimg.load_img(spatial_maps)
n_rsns = rsn_img.shape[-1]
n_ics = spm_img.shape[-1]
gofs = np.zeros((n_rsns, n_ics), dtype=float)
# threshold the RSN templates
if rsn_thr > 0:
thr_rsns = (spatial_map(rsn, thr=rsn_thr, mode='+-')
for rsn in niimg.iter_img(rsn_img))
else:
thr_rsns = rsn_img
# for each RSN template and IC image
iter_rsn_ic = itertools.product(enumerate(niimg.iter_img(thr_rsns)),
enumerate(niimg.iter_img( spm_img)))
for (rsn_idx, rsn), (ic_idx, ic) in iter_rsn_ic:
ref_vol = rsn.get_data()
rsn_vol = np.zeros(rsn.shape, dtype=int)
#rsn_in = niimg.math_img('np.abs(img) > 0', img=rsn)
rsn_in = rsn_vol.copy()
rsn_in[np.abs(ref_vol) > 0] = 1
#rsn_out = niimg.math_img('img == 0', img=rsn)
rsn_out = rsn_vol.copy()
rsn_out[ref_vol == 0] = 1
if mask_file is not None:
# rsn_out = niimg.math_img('mask * img', mask=rsn_brain_mask, img=rsn_out)
rsn_brain_mask = niimg.resample_to_img(mask_file, rsn,
interpolation='nearest')
rsn_out = rsn_brain_mask.get_data() * rsn_out
# convert the mask arrays to image in order to resample
rsn_in = niimg.new_img_like(rsn, rsn_in)
rsn_out = niimg.new_img_like(rsn, rsn_out)
rsn_in = niimg.resample_to_img(rsn_in, ic, interpolation='nearest')
rsn_out = niimg.resample_to_img(rsn_out, ic, interpolation='nearest')
# apply the mask
#zscore_in = niimg.math_img('mask * img', mask=rsn_in, img=ic).get_data()
zscore_in = rsn_in.get_data() * ic.get_data()
#zscore_out = niimg.math_img('mask * img', mask=rsn_out, img=ic).get_data()
zscore_out = rsn_out.get_data() * ic.get_data()
#gof_term1
# calculate the the average z-score difference between voxels falling
# within the template and voxels falling outside the template
gof_term1 = zscore_in.mean() - zscore_out.mean()
#gof_term2
# the difference in the percentage of positive z-score voxels inside and outside the template.
n_pos_zscore_in = np.sum(zscore_in > 0)
n_pos_zscore_out = np.sum(zscore_out > 0)
n_pos_zscore_tot = n_pos_zscore_in + n_pos_zscore_out
if n_pos_zscore_tot != 0:
n_pos_zscore_pcnt = 100 / n_pos_zscore_tot
gof_term2 = (n_pos_zscore_in - n_pos_zscore_out) * n_pos_zscore_pcnt
else:
gof_term2 = 0
# global gof
gof = gof_term1 * gof_term2
# add the result
gofs[rsn_idx][ic_idx] = gof
return gofs
def spatial_maps_pairwise_similarity(imgs1, imgs2, mask_file, distance='correlation'):
""" Similarity values of each image in `imgs1` to each image in `imgs2`, both masked by `mask_file`.
These values are based on distance metrics, specified by `distance` argument.
The resulting similarity value is the complementary value of the distance,
i.e., '1 - <distance value>'.
The images in `imgs1` will be resampled to `imgs2` if their affine matrix don't match.
Parameters
----------
imgs1: list of niimg-like or 4D niimg-like
imgs2: list of niimg-like or 4D niimg-like
mask_file: niimg-like
distance: str
Valid values for `distance` are:
From scikit-learn: ['cityblock', 'cosine', 'euclidean', 'l1', 'l2', 'manhattan'].
From scipy.spatial.distance: ['braycurtis', 'canberra', 'chebyshev', 'correlation', 'dice', 'hamming',
'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'minkowski',
'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath',
'sqeuclidean', 'yule']
See the documentation for scipy.spatial.distance for details on these metrics.
Returns
-------
corrs: np.ndarray
A matrix of shape MxN, where M is len(imgs1) and N is len(imgs2).
It contains the similarity values.
"""
img1_ = niimg.load_img(imgs1)
img2_ = niimg.load_img(imgs2)
n_imgs1 = img1_.shape[-1]
n_imgs2 = img2_.shape[-1]
corrs = np.zeros((n_imgs1, n_imgs2), dtype=float)
mask_trnsf = niimg.resample_to_img(mask_file, niimg.index_img(img2_, 0),
interpolation='nearest',
copy=True)
for idx1, img1 in enumerate(niimg.iter_img(img1_)):
img1_resamp = niimg.resample_to_img(img1, niimg.index_img(img2_, 0), copy=True)
img1_masked = nimask.apply_mask(img1_resamp, mask_trnsf)
for idx2, img2 in enumerate(niimg.iter_img(img2_)):
img2_masked = nimask.apply_mask(img2, mask_trnsf)
dist = pairwise_distances(img1_masked.reshape(1, -1),
img2_masked.reshape(1, -1),
metric=distance)
# since this is a scalar value
dist = dist[0][0]
# since this is a distance, not a similarity value
corr = 1 - dist
# store it
corrs[idx1, idx2] = corr
return corrs
def plot_melodic_components(melodic_dir, in_file, tr=None,
out_file='melodic_reportlet.svg',
compress='auto', report_mask=None,
noise_components_file=None):
"""
Plots the spatiotemporal components extracted by FSL MELODIC
from functional MRI data.
Parameters
melodic_dir : str
Path pointing to the outputs of MELODIC
in_file : str
Path pointing to the reference fMRI dataset. This file
will be used to extract the TR value, if the ``tr`` argument
is not set. This file will be used to calculate a mask
if ``report_mask`` is not provided.
tr : float
Repetition time in seconds
out_file : str
Path where the resulting SVG file will be stored
compress : ``'auto'`` or bool
Whether SVG should be compressed. If ``'auto'``, compression
will be executed if dependencies are installed (SVGO)
report_mask : str
Path to a brain mask corresponding to ``in_file``
noise_components_file : str
A CSV file listing the indexes of components classified as noise
by some manual or automated (e.g. ICA-AROMA) procedure. If a
``noise_components_file`` is provided, then components will be
plotted with red/green colors (correspondingly to whether they
are in the file -noise components, red-, or not -signal, green-).
When all or none of the components are in the file, a warning
is printed at the top.
"""
from nilearn.image import index_img, iter_img
import nibabel as nb
import numpy as np
import pylab as plt
import seaborn as sns
from matplotlib.gridspec import GridSpec
import os
import re
from io import StringIO
sns.set_style("white")
current_palette = sns.color_palette()
in_nii = nb.load(in_file)
if not tr:
tr = in_nii.header.get_zooms()[3]
units = in_nii.header.get_xyzt_units()
if units:
if units[-1] == 'msec':
tr = tr / 1000.0
elif units[-1] == 'usec':
tr = tr / 1000000.0
elif units[-1] != 'sec':
NIWORKFLOWS_LOG.warning('Unknown repetition time units '
'specified - assuming seconds')
else:
NIWORKFLOWS_LOG.warning(
'Repetition time units not specified - assuming seconds')
from nilearn.input_data import NiftiMasker
from nilearn.plotting import cm
if not report_mask:
nifti_masker = NiftiMasker(mask_strategy='epi')
nifti_masker.fit(index_img(in_nii, range(2)))
mask_img = nifti_masker.mask_img_
else:
mask_img = nb.load(report_mask)
mask_sl = []
for j in range(3):
mask_sl.append(transform_to_2d(mask_img.get_data(), j))
timeseries = np.loadtxt(os.path.join(melodic_dir, "melodic_mix"))
power = np.loadtxt(os.path.join(melodic_dir, "melodic_FTmix"))
stats = np.loadtxt(os.path.join(melodic_dir, "melodic_ICstats"))
n_components = stats.shape[0]
Fs = 1.0 / tr
Ny = Fs / 2
f = Ny * (np.array(list(range(1, power.shape[0] + 1)))) / (power.shape[0])
# Set default colors
color_title = 'k'
color_time = current_palette[0]
color_power = current_palette[1]
classified_colors = None
warning_row = 0 # Do not allocate warning row
# Only if the components file has been provided, a warning banner will
# be issued if all or none of the components were classified as noise
if noise_components_file:
noise_components = np.loadtxt(noise_components_file,
dtype=int, delimiter=',', ndmin=1)
# Activate warning row if pertinent
warning_row = int(noise_components.size == 0 or
noise_components.size == n_components)
classified_colors = {True: 'r', False: 'g'}
n_rows = int((n_components + (n_components % 2)) / 2)
fig = plt.figure(figsize=(6.5 * 1.5, (n_rows + warning_row) * 0.85))
gs = GridSpec(n_rows * 2 + warning_row, 9,
width_ratios=[1, 1, 1, 4, 0.001, 1, 1, 1, 4, ],
height_ratios=[5] * warning_row + [1.1, 1] * n_rows)
if warning_row:
ax = fig.add_subplot(gs[0, :])
ncomps = 'NONE of the'
if noise_components.size == n_components:
ncomps = 'ALL'
ax.annotate(
'WARNING: {} components were classified as noise'.format(ncomps),
xy=(0.0, 0.5), xycoords='axes fraction',
xytext=(0.01, 0.5), textcoords='axes fraction',
size=12, color='#ea8800',
bbox=dict(boxstyle="round",
fc='#f7dcb7',
ec='#FC990E'))
ax.axes.get_xaxis().set_visible(False)
ax.axes.get_yaxis().set_visible(False)
titlefmt = "C{id:d}{noise}: Tot. var. expl. {var:.2g}%".format
for i, img in enumerate(
iter_img(os.path.join(melodic_dir, "melodic_IC.nii.gz"))):
col = i % 2
row = i // 2
l_row = row * 2 + warning_row
is_noise = False
if classified_colors:
# If a noise components list is provided, assign red/green
is_noise = (i + 1) in noise_components
color_title = color_time = color_power = classified_colors[is_noise]
data = img.get_data()
for j in range(3):
ax1 = fig.add_subplot(gs[l_row:l_row + 2, j + col * 5])
sl = transform_to_2d(data, j)
m = np.abs(sl).max()
ax1.imshow(sl, vmin=-m, vmax=+m, cmap=cm.cold_white_hot,
interpolation="nearest")
ax1.contour(mask_sl[j], levels=[0.5], colors='k', linewidths=0.5)
plt.axis("off")
ax1.autoscale_view('tight')
if j == 0:
ax1.set_title(
titlefmt(id=i + 1,
noise=' [noise]' * is_noise,
var=stats[i, 1]),
x=0, y=1.18, fontsize=7,
horizontalalignment='left',
verticalalignment='top',
color=color_title)
ax2 = fig.add_subplot(gs[l_row, 3 + col * 5])
ax3 = fig.add_subplot(gs[l_row + 1, 3 + col * 5])
ax2.plot(np.arange(len(timeseries[:, i])) * tr, timeseries[:, i],
linewidth=min(200 / len(timeseries[:, i]), 1.0),
color=color_time)
ax2.set_xlim([0, len(timeseries[:, i]) * tr])
ax2.axes.get_yaxis().set_visible(False)
ax2.autoscale_view('tight')
ax2.tick_params(axis='both', which='major', pad=0)
sns.despine(left=True, bottom=True)
for tick in ax2.xaxis.get_major_ticks():
tick.label.set_fontsize(6)
tick.label.set_color(color_time)
ax3.plot(f[0:], power[0:, i], color=color_power,
linewidth=min(100 / len(power[0:, i]), 1.0))
ax3.set_xlim([f[0], f.max()])
ax3.axes.get_yaxis().set_visible(False)
ax3.autoscale_view('tight')
ax3.tick_params(axis='both', which='major', pad=0)
for tick in ax3.xaxis.get_major_ticks():
tick.label.set_fontsize(6)
tick.label.set_color(color_power)
sns.despine(left=True, bottom=True)
plt.subplots_adjust(hspace=0.5)
image_buf = StringIO()
fig.savefig(image_buf, dpi=300, format='svg', transparent=True,
bbox_inches='tight', pad_inches=0.01)
fig.clf()
image_svg = image_buf.getvalue()
if compress is True or compress == 'auto':
image_svg = svg_compress(image_svg, compress)
image_svg = re.sub(' height="[0-9]+[a-z]*"', '', image_svg, count=1)
image_svg = re.sub(' width="[0-9]+[a-z]*"', '', image_svg, count=1)
image_svg = re.sub(' viewBox',
' preseveAspectRation="xMidYMid meet" viewBox',
image_svg, count=1)
Path(out_file).write_text(image_svg)
canica = CanICA(n_components=20, smoothing_fwhm=6.,
memory="nilearn_cache", memory_level=5,
threshold=3., verbose=10, random_state=0)
canica.fit(func_filenames)
# Retrieve the independent components in brain space
components_img = canica.masker_.inverse_transform(canica.components_)
# components_img is a Nifti Image object, and can be saved to a file with
# the following line:
components_img.to_filename('canica_resting_state.nii.gz')
####################################################################
# To visualize we plot the outline of all components on one figure
from nilearn.plotting import plot_prob_atlas
# Plot all ICA components together
plot_prob_atlas(components_img, title='All ICA components')
####################################################################
# Finally, we plot the map for each ICA component separately
from nilearn.image import iter_img
from nilearn.plotting import plot_stat_map, show
for i, cur_img in enumerate(iter_img(components_img)):
plot_stat_map(cur_img, display_mode="z", title="IC %d" % i,
cut_coords=1, colorbar=False)
show()