def apply_mask_and_get_affinity(seeds,
niimg,
radius,
allow_overlap,
n_jobs=1,
mask_img=None):
import time
start = time.time()
seeds = list(seeds)
affine = niimg.affine
# Compute world coordinates of all in-mask voxels.
mask_img = check_niimg_3d(mask_img)
mask_img = image.resample_img(mask_img,
target_affine=affine,
target_shape=niimg.shape[:3],
interpolation='nearest')
mask, _ = masking._load_mask_img(mask_img)
mask_coords = list(zip(*np.where(mask != 0)))
X = masking._apply_mask_fmri(niimg, mask_img)
# For each seed, get coordinates of nearest voxel
nearests = joblib.Parallel(n_jobs=n_jobs)(
joblib.delayed(seed_nearest)(seed_chunk, affine, mask_coords)
for thread_id, seed_chunk in enumerate(np.array_split(seeds, n_jobs)))
nearests = [i for j in nearests for i in j]
mask_coords = np.asarray(list(zip(*mask_coords)))
mask_coords = coord_transform(mask_coords[0], mask_coords[1],
mask_coords[2], affine)
mask_coords = np.asarray(mask_coords).T
clf = neighbors.NearestNeighbors(radius=radius)
A = clf.fit(mask_coords).radius_neighbors_graph(seeds)
A = A.tolil()
for i, nearest in enumerate(nearests):
if nearest is None:
continue
A[i, nearest] = True
# Include the voxel containing the seed itself if not masked
mask_coords = mask_coords.astype(int).tolist()
for i, seed in enumerate(seeds):
try:
A[i, mask_coords.index(seed)] = True
except ValueError:
# seed is not in the mask
pass
if not allow_overlap:
if np.any(A.sum(axis=0) >= 2):
raise ValueError('Overlap detected between spheres')
return X, A
def _mask_stat_map(stat_map_img, threshold=None):
""" Load a stat map and apply a threshold.
Returns: mask_img, stat_map_img, data, threshold
"""
# Load stat map
stat_map_img = check_niimg_3d(stat_map_img, dtype="auto")
data = _safe_get_data(stat_map_img, ensure_finite=True)
# threshold the stat_map
if threshold is not None:
data, mask, threshold = _threshold_data(data, threshold)
mask_img = new_img_like(stat_map_img, mask, stat_map_img.affine)
else:
mask_img = new_img_like(stat_map_img, np.zeros(data.shape),
stat_map_img.affine)
return mask_img, stat_map_img, data, threshold
def view_img_on_surf(stat_map_img,
surf_mesh='fsaverage5',
threshold=None,
cmap=cm.cold_hot,
black_bg=False,
vmax=None,
vmin=None,
symmetric_cmap=True,
colorbar=True,
colorbar_height=.5,
colorbar_fontsize=25,
title=None,
title_fontsize=25,
vol_to_surf_kwargs={}):
"""Insert a surface plot of a statistical map into an HTML page.
Parameters
----------
stat_map_img : Niimg-like object, 3D
See http://nilearn.github.io/manipulating_images/input_output.html
surf_mesh : str or dict, optional.
if 'fsaverage5', use fsaverage5 mesh from nilearn.datasets
if 'fsaverage', use fsaverage mesh from nilearn.datasets
if a dictionary, it should have the same structure as those returned by
nilearn.datasets.fetch_surf_fsaverage, i.e. keys should be 'infl_left',
'pial_left', 'sulc_left', 'infl_right', 'pial_right', and 'sulc_right',
containing inflated and pial meshes, and sulcal depth values for left
and right hemispheres. Default='fsaverage5'.
threshold : str, number or None, optional
If None, no thresholding.
If it is a number only values of amplitude greater
than threshold will be shown.
If it is a string it must finish with a percent sign,
e.g. "25.3%", and only values of amplitude above the
given percentile will be shown.
cmap : str or matplotlib colormap, optional
Colormap to use. Default=cm.cold_hot.
black_bg : bool, optional
If True, image is plotted on a black background. Otherwise on a
white background. Default=False.
vmax : float or None, optional
upper bound for the colorbar. if None, use the absolute max of the
brain map.
vmin : float or None, optional
min value for mapping colors.
If `symmetric_cmap` is `True`, `vmin` is always equal to `-vmax` and
cannot be chosen.
If `symmetric_cmap` is `False`, `vmin` defaults to the min of the
image, or 0 when a threshold is used.
symmetric_cmap : bool, optional
Make colormap symmetric (ranging from -vmax to vmax).
You can set it to False if you are plotting only positive values.
Default=True.
colorbar : bool, optional
Add a colorbar or not. Default=True.
colorbar_height : float, optional
Height of the colorbar, relative to the figure height. Default=0.5.
colorbar_fontsize : int, optional
Fontsize of the colorbar tick labels. Default=25.
title : str, optional
Title for the plot.
title_fontsize : int, optional
Fontsize of the title. Default=25.
vol_to_surf_kwargs : dict, optional
Dictionary of keyword arguments that are passed on to
:func:`nilearn.surface.vol_to_surf` when extracting a surface from
the input image. See the function documentation for details.This
parameter is especially useful when plotting an atlas. See
https://nilearn.github.io/auto_examples/01_plotting/plot_3d_map_to_surface_projection.html
Returns
-------
SurfaceView : plot of the stat map.
It can be saved as an html page or rendered (transparently) by the
Jupyter notebook. Useful methods are :
- 'resize' to resize the plot displayed in a Jupyter notebook
- 'save_as_html' to save the plot to a file
- 'open_in_browser' to save the plot and open it in a web browser.
See Also
--------
nilearn.plotting.view_surf: plot from a surface map on a cortical mesh.
"""
stat_map_img = check_niimg_3d(stat_map_img)
info = full_brain_info(volume_img=stat_map_img,
mesh=surf_mesh,
threshold=threshold,
cmap=cmap,
black_bg=black_bg,
vmax=vmax,
vmin=vmin,
symmetric_cmap=symmetric_cmap,
vol_to_surf_kwargs=vol_to_surf_kwargs)
info['colorbar'] = colorbar
info['cbar_height'] = colorbar_height
info['cbar_fontsize'] = colorbar_fontsize
info['title'] = title
info['title_fontsize'] = title_fontsize
return _fill_html_template(info, embed_js=True)
def _apply_mask_and_get_affinity(seeds,
niimg,
radius,
allow_overlap,
mask_img=None):
seeds = list(seeds)
aff = niimg.get_affine()
# Compute world coordinates of all in-mask voxels.
if mask_img is not None:
mask_img = check_niimg_3d(mask_img)
mask_img = image.resample_img(mask_img,
target_affine=aff,
target_shape=niimg.shape[:3],
interpolation='nearest')
mask, _ = masking._load_mask_img(mask_img)
mask_coords = list(zip(*np.where(mask != 0)))
# X = masking._apply_mask_fmri(niimg, mask_img)
else:
mask_coords = list(np.ndindex(niimg.shape[:3]))
# For each seed, get coordinates of nearest voxel
nearests = []
for sx, sy, sz in seeds:
nearest = np.round(coord_transform(sx, sy, sz, np.linalg.inv(aff)))
nearest = nearest.astype(int)
nearest = (nearest[0], nearest[1], nearest[2])
try:
nearests.append(mask_coords.index(nearest))
except ValueError:
nearests.append(None)
mask_coords = np.asarray(list(zip(*mask_coords)))
mask_coords = coord_transform(mask_coords[0], mask_coords[1],
mask_coords[2], aff)
mask_coords = np.asarray(mask_coords).T
if (radius is not None
and LooseVersion(sklearn.__version__) < LooseVersion('0.16')):
# Fix for scikit learn versions below 0.16. See
# https://github.com/scikit-learn/scikit-learn/issues/4072
radius += 1e-6
clf = neighbors.NearestNeighbors(radius=radius)
A = clf.fit(mask_coords).radius_neighbors_graph(seeds)
A = A.tolil()
for i, nearest in enumerate(nearests):
if nearest is None:
continue
A[i, nearest] = True
# Include the voxel containing the seed itself if not masked
mask_coords = mask_coords.astype(int).tolist()
for i, seed in enumerate(seeds):
try:
A[i, mask_coords.index(seed)] = True
except ValueError:
# seed is not in the mask
pass
if not allow_overlap:
if np.any(A.sum(axis=0) >= 2):
raise ValueError('Overlap detected between spheres')
return A
def create_spherical_vois(ref_img, seeds, radius=1):
"""
Utility to create spherical masks for voi extraction.
Careful, differing from NiftiSpheresMasker this function
does not check whether vois are overlapping. The function
puts out single masks for each coordinate. These can then
be used with e.g. the NiftiMasker. Importantly note, that
this function is just a "remix" of nilearn's
NiftiSpheresMasker! So check it out!
Parameters
----------
ref_img : 3D nifti image, which serves as the reference
for VOI creation. Output masks will have the same
dimensions and affine as ref_img.
seeds : a list of lists or tuples of size 3, defining
the seed coordinates in MNI-space around which the
vois will be centered.
radius : the radius of the VOI in mm, defaults to 1.
Returns
-------
voi_masks : A list of length(seeds), containing
a spherical mask for each seed in the dimensions
of the ref_img.
"""
niimg = check_niimg_3d(ref_img)
affine = niimg.affine
img_shape = niimg.shape
X = niimg.get_data().reshape([-1, 1]).T
mask_coords = list(np.ndindex(img_shape[:3]))
voi_masks = []
nearests = []
for sx, sy, sz in seeds:
nearest = np.round(coord_transform(sx, sy, sz, np.linalg.inv(affine)))
nearest = nearest.astype(int)
nearest = (nearest[0], nearest[1], nearest[2])
try:
nearests.append(mask_coords.index(nearest))
except ValueError:
nearests.append(None)
mask_coords = np.asarray(list(zip(*mask_coords)))
mask_coords = coord_transform(mask_coords[0], mask_coords[1],
mask_coords[2], affine)
mask_coords = np.asarray(mask_coords).T
clf = neighbors.NearestNeighbors(radius=radius)
A = clf.fit(mask_coords).radius_neighbors_graph(seeds)
A = A.tolil()
clf.fit(mask_coords)
for i, nearest in enumerate(nearests):
if nearest is None:
continue
A[i, nearest] = True
voi_mask = new_img_like(niimg, A[i].toarray().reshape(img_shape[:3]))
voi_masks.append(voi_mask)
return voi_masks
def _apply_mask_and_get_affinity(seeds,
niimg,
radius,
allow_overlap,
mask_img=None):
seeds = list(seeds)
affine = niimg.affine
# Compute world coordinates of all in-mask voxels.
if mask_img is not None:
mask_img = check_niimg_3d(mask_img)
mask_img = image.resample_img(mask_img,
target_affine=affine,
target_shape=niimg.shape[:3],
interpolation='nearest')
mask, _ = masking._load_mask_img(mask_img)
mask_coords = list(zip(*np.where(mask != 0)))
X = masking._apply_mask_fmri(niimg, mask_img)
else:
if np.isnan(np.sum(_safe_get_data(niimg))):
warnings.warn('The imgs you have fed into fit_transform() contains'
' NaN values which will be converted to zeroes ')
X = _safe_get_data(niimg, True).reshape([-1, niimg.shape[3]]).T
else:
X = _safe_get_data(niimg).reshape([-1, niimg.shape[3]]).T
mask_coords = list(np.ndindex(niimg.shape[:3]))
# For each seed, get coordinates of nearest voxel
nearests = []
for sx, sy, sz in seeds:
nearest = np.round(coord_transform(sx, sy, sz, np.linalg.inv(affine)))
nearest = nearest.astype(int)
nearest = (nearest[0], nearest[1], nearest[2])
try:
nearests.append(mask_coords.index(nearest))
except ValueError:
nearests.append(None)
mask_coords = np.asarray(list(zip(*mask_coords)))
mask_coords = coord_transform(mask_coords[0], mask_coords[1],
mask_coords[2], affine)
mask_coords = np.asarray(mask_coords).T
clf = neighbors.NearestNeighbors(radius=radius)
A = clf.fit(mask_coords).radius_neighbors_graph(seeds)
A = A.tolil()
for i, nearest in enumerate(nearests):
if nearest is None:
continue
A[i, nearest] = True
# Include the voxel containing the seed itself if not masked
mask_coords = mask_coords.astype(int).tolist()
for i, seed in enumerate(seeds):
try:
A[i, mask_coords.index(seed)] = True
except ValueError:
# seed is not in the mask
pass
if not allow_overlap:
if np.any(A.sum(axis=0) >= 2):
raise ValueError('Overlap detected between spheres')
return X, A