def display(fun_dir, fs_dir, contrast):
mlab.figure(bgcolor=(1, 1, 1))
left_mesh = freesurfer.read_geometry(os.path.join(fs_dir, 'lh.inflated'))
right_mesh = freesurfer.read_geometry(os.path.join(fs_dir, 'rh.inflated'))
left_curv = os.path.join(fs_dir, 'lh.curv')
right_curv = os.path.join(fs_dir, 'rh.curv')
meshes = [left_mesh, right_mesh]
curves = [left_curv, right_curv]
for hemisphere, mesh_file, curv_file in zip(['lh', 'rh'], meshes, curves):
fun_file = os.path.join(fun_dir, '%s_z_map_%s.gii' % (
contrast, hemisphere))
coords, triangles = mesh_file
x, y, z = coords.T
if hemisphere == 'lh':
x -= 50
else:
x += 50
curv = freesurfer.read_morph_data(curv_file).astype(np.float)
tex = np.array([darrays.data for darrays in
read(fun_file).darrays]).ravel()
print fun_file, tex.min(), tex.max()
name = ''
cmin = -1
cmax = 1
mlab.triangular_mesh(x, y, z, triangles, transparent=True, opacity=1.,
name=name, scalars=curv, colormap="bone",
vmin=cmin, vmax=cmax)
func_mesh = mlab.pipeline.triangular_mesh_source(
x, y, z, triangles, scalars=tex)
thresh = mlab.pipeline.threshold(func_mesh, low=THRESHOLD)
mlab.pipeline.surface(thresh, colormap="hot", vmin=THRESHOLD, vmax=7)
def loadSurface(pathToSurface):
'''
This method loads the surface from a mgh file and returns it. Pretty simple
stuff
'''
print('Loading %s' % (pathToSurface))
surface = nfs.read_geometry(pathToSurface)
return surface
def load(self, meshfile, inflatedmeshpath=None, annotfile=None):
""" Load a FreeSurfer surface.
Parameters
----------
meshfile: str (mandatory)
the location of the file containing the FreeSurfer mesh to be
loaded.
inflatedmeshpath: str (optional, default None)
the location of the file containing the FreeSurfer inflated mesh
to be loaded.
annotfile: str (optional, default None)
the location of the file containing the FreeSurfer annotations to
be loaded.
Returns
-------
surf: TriSurface
a triangular surface representation.
"""
vertices, triangles = freesurfer.read_geometry(meshfile)
if inflatedmeshpath is not None:
inflated_vertices, _triangles = freesurfer.read_geometry(
inflatedmeshpath)
if not numpy.allclose(triangles, _triangles):
raise ValueError("'{0}' and '{1}' do not represent the same "
"surface.".format(meshfile, inflatedmeshpath))
else:
inflated_vertices = None
if annotfile is not None:
labels, ctab, regions = freesurfer.read_annot(
annotfile, orig_ids=False)
meta = dict(
(index, {"region": item[0], "color": item[1][:4].tolist()})
for index, item in enumerate(zip(regions, ctab)))
else:
labels = None
meta = None
return TriSurface(vertices=vertices, triangles=triangles,
labels=labels, metadata=meta,
inflated_vertices=inflated_vertices)
def surf_convert(fsdir, t1files, surffiles, output_directory=None,
rm_orig=False,
fsconfig="/i2bm/local/freesurfer/SetUpFreeSurfer.sh"):
""" Export FreeSurfer surfaces to the native space.
Note that all the vetices are given in the index coordinate system.
The subjecy id in the t1 and surf files must appear in the -3 position:
xxx/subject_id/convert/t1.nii.gz
<unit>
<input name="fsdir" type="Directory" description="The
freesurfer working directory with all the subjects."/>
<input name="output_directory" type="Directory" description="The
conversion destination folder."/>
<input name="t1files" type="List_File" description="The t1 nifti
files."/>
<input name="surffiles" type="List_File" description="The surface
to be converted."/>
<input name="rm_orig" type="Bool" description="If true remove
the input surfaces."/>
<input name="fsconfig" type="File" description="The freesurfer
configuration batch."/>
<output name="csurffiles" type="List_File" description="The converted
surfaces in the native space."/>
</unit>
"""
# Create a t1 subject map
t1map = {}
for fname in t1files:
subject_id = fname.split("/")[-3]
if subject_id in t1map:
raise ("Can't map two t1 for subject '{0}'.".format(subject_id))
t1map[subject_id] = fname
# Convert all the surfaces
csurffiles = []
for fname in surffiles:
# Get the t1 reference image
subject_id = fname.split("/")[-3]
t1file = t1map[subject_id]
t1_image = nibabel.load(t1file)
# Compute the conformed space to the native anatomical deformation
asegfile = os.path.join(fsdir, subject_id, "mri", "aseg.mgz")
physical_to_index = numpy.linalg.inv(t1_image.get_affine())
translation = tkregister_translation(asegfile, fsconfig)
deformation = numpy.dot(physical_to_index, translation)
# Load and warp the mesh
# The mesh: a 2-uplet with vertex (x, y, z) coordinates and
# mesh triangles
mesh = freesurfer.read_geometry(fname)
surf = TriSurface(vertices=apply_affine_on_mesh(mesh[0], deformation),
triangles=mesh[1])
# Save the mesh in the native space
outputfile = fname + ".native"
surf.save(os.path.dirname(outputfile), os.path.basename(outputfile))
csurffiles.append(outputfile)
# Clean input surface if specified
if rm_orig:
os.remove(fname)
return csurffiles
def surf_convert(
fsdir,
t1files,
surffiles,
sidpos=-3,
rm_orig=False,
fsconfig=DEFAULT_FREESURFER_PATH):
""" Export FreeSurfer surfaces to the native space.
Note that all the returned vetices are given in the index coordinate
system.
The subject id in the t1 and surf files must appear in the 'sidpos'
position. For the default value '-3', the T1 path might look like
'xxx/subject_id/convert/t1.nii.gz'
Parameters
----------
fsdir: str (mandatory)
The FreeSurfer working directory with all the subjects.
t1files: str (mandatory)
The t1 nifti files.
surffiles:
The surfaces to be converted.
sidpos: int (optional, default -3)
The subject identifier position in the surface and T1 files.
rm_orig: bool (optional)
If True remove the input surfaces.
fsconfig: str (optional)
The FreeSurfer configuration batch.
Returns
-------
csurffiles:
The converted surfaces in the native space indexed coordinates.
"""
# Check input parameters
for path in t1files + surffiles:
if not os.path.isfile(path):
raise ValueError("'{0}' is not a valid file.".format(path))
if not os.path.isdir(fsdir):
raise ValueError("'{0}' is not a valid directory.".format(fsdir))
# Create a t1 subject map
t1map = {}
for fname in t1files:
subject_id = fname.split(os.path.sep)[sidpos]
if subject_id in t1map:
raise ValueError("Can't map two t1 for subject "
"'{0}'.".format(subject_id))
t1map[subject_id] = fname
# Convert all the surfaces
csurffiles = []
for fname in surffiles:
# Get the t1 reference image
subject_id = fname.split(os.path.sep)[sidpos]
t1file = t1map[subject_id]
t1_image = nibabel.load(t1file)
# Compute the conformed space to the native anatomical deformation
asegfile = os.path.join(fsdir, subject_id, "mri", "aseg.mgz")
physical_to_index = numpy.linalg.inv(t1_image.get_affine())
translation = tkregister_translation(asegfile, fsconfig)
deformation = numpy.dot(physical_to_index, translation)
# Load and warp the mesh
# The mesh: a 2-uplet with vertex (x, y, z) coordinates and
# mesh triangles
mesh = freesurfer.read_geometry(fname)
surf = TriSurface(vertices=apply_affine_on_mesh(mesh[0], deformation),
triangles=mesh[1])
# Save the mesh in the native space
outputfile = fname + ".native"
surf.save(outputfile)
csurffiles.append(outputfile)
# Construct the surfaces binarized volume
binarizedfile = os.path.join(outputfile + ".nii.gz")
overlay = numpy.zeros(t1_image.shape, dtype=numpy.uint)
indices = numpy.round(surf.vertices).astype(int).T
indices[0, numpy.where(indices[0] >= t1_image.shape[0])] = 0
indices[1, numpy.where(indices[1] >= t1_image.shape[1])] = 0
indices[2, numpy.where(indices[2] >= t1_image.shape[2])] = 0
overlay[indices.tolist()] = 1
overlay_image = nibabel.Nifti1Image(overlay, t1_image.get_affine())
nibabel.save(overlay_image, binarizedfile)
# Clean input surface if specified
if rm_orig:
os.remove(fname)
return csurffiles
def interface2surf(interface_image, surface_file, cortex_label, ref_mgz, out_file):
import os
import nibabel as nb
import nibabel.freesurfer as nbfs
import numpy as np
import scipy.spatial.distance as syd
# get image properties
interfaceImage = nb.load(interface_image)
interface_indexes = interfaceImage.get_data()
interface_shape = np.shape(interface_indexes)
reoriented_indexes = np.zeros(interface_shape)
affineMatrix = interfaceImage.get_affine()
# get surface and put it in voxel space
surface = nbfs.read_geometry(surface_file)
surface_coords = surface[0]
surface_coords[:, 0] = surface_coords[:, 0] + (interface_shape[0] / 2)
surface_coords[:, 1] = surface_coords[:, 1] + (interface_shape[1] / 2)
surface_coords[:, 2] = surface_coords[:, 2] + (interface_shape[2] / 2)
surf_array_dim = np.shape(surface_coords)
surf_length = surf_array_dim[0]
label_indices = np.loadtxt(cortex_label, delimiter=" ", dtype=long, skiprows=2, usecols=[0])
projected_index = np.zeros(surf_length)
projected_distance = np.zeros(surf_length) - 1
# get interface coordinates and put them in normal voxel space
voxelCoordList = []
for x, y, z in zip(*np.nonzero(interface_indexes)):
voxelCoord = [x, y, z]
if affineMatrix[0, 0] == -1:
voxelCoord[0] = interface_shape[0] - 1 - voxelCoord[0]
if affineMatrix[1, 1] == -1:
voxelCoord[1] = interface_shape[1] - 1 - voxelCoord[1]
if affineMatrix[2, 2] == -1:
voxelCoord[2] = interface_shape[2] - 1 - voxelCoord[2]
voxelCoordList.append(voxelCoord)
reoriented_indexes[voxelCoord[0], voxelCoord[1], voxelCoord[2]] = interface_indexes[x, y, z]
interface_voxels = np.array(voxelCoordList)
for i in label_indices:
surf_coord = surface_coords[i : i + 1, :]
surf_floor = np.floor(surf_coord)
local_index = reoriented_indexes[surf_floor[0, 0], surf_floor[0, 1], surf_floor[0, 2]]
"""
-if the vertex lays in an index voxel assign directly
-TO IMPLEMENT IF SLOW: check next in the 26-neighborhood
-otherwise, check distances to all index voxels and choose smallest
"""
if local_index != 0:
projected_index[i] = local_index
projected_distance[i] = 0.0
else:
all_dists = syd.cdist(surf_coord, interface_voxels + 0.5, "euclidean")
nearest_voxel_ID = np.argmin(all_dists)
nearest_dist = all_dists[0, nearest_voxel_ID]
projected_distance[i] = nearest_dist
projected_voxel_coords = interface_voxels[nearest_voxel_ID, :]
projected_index[i] = reoriented_indexes[
projected_voxel_coords[0], projected_voxel_coords[1], projected_voxel_coords[2]
]
"""
convert projected_index into a .mif file
"""
ref_mgz_file = nb.load(ref_mgz)
data = ref_mgz_file.get_data()
data[:, 0, 0] = projected_index
surface_projected_image = nb.MGHImage(data, ref_mgz_file.get_affine(), ref_mgz_file.get_header())
nb.save(surface_projected_image, out_file)
return os.path.abspath(out_file)
import pylab as pl
import nibabel.freesurfer as fs
# assuming cp -r $FREESURFER_HOME/subjects/fsaverage5 data/ folder,
here = os.path.dirname(os.path.abspath(__file__))
fname = lambda fn: os.path.join(here, '../data/fsaverage5', fn)
# load FS T1 (talairach.xfm is from -i vol.nii to T1.mgz ?)
img = fs.load(fname('mri/T1.mgz')) # type: fs.MGHImage
vol = img.get_data().transpose((0, 2, 1))
aff = img.affine
inv_aff = np.linalg.inv(aff)
# load left pial surface
verts, faces = fs.read_geometry(fname('surf/lh.pial'))
# choose sagittal slice by X coord
x = -32.0
i = int(inv_aff.dot(np.r_[x, 0.0, 0.0, 1.0])[0])
# mask vertices around chosen coord
vert_mask = np.c_[verts[:, 0] > (x - 2), verts[:, 0] < (x + 2)].all(axis=1)
in_slice_verts = isv_y, isv_z = verts[vert_mask, 1:].T
# plot slice & vertices in mask
fig = pl.figure(figsize=(15, 5))
pl.subplot(131)
pl.imshow(vol[i].T, cmap='gray', aspect='equal', extent=[-128.0, 128, -128.0, 128.0])
pl.plot(isv_y, isv_z, 'y.')
pl.xlabel('+Y Anterior')
def get_geometry(subject, side, surface_type="inflated"):
mesh_file = get_surface_file(subject, side, surface_type)
vertices, triangles = read_geometry(mesh_file)
x, y, z = vertices.T
return x, y, z, triangles
def find_parcel_centroids(*,
lhannot,
rhannot,
method='surface',
version='fsaverage',
surf='sphere',
drop_labels=None):
"""
Returns vertex coords corresponding to centroids of parcels in annotations
Note that using any other `surf` besides the default of 'sphere' may result
in centroids that are not directly within the parcels themselves due to
sulcal folding patterns.
Parameters
----------
{lh,rh}annot : str
Path to .annot file containing labels of parcels on the {left,right}
hemisphere. These must be specified as keyword arguments to avoid
accidental order switching.
method : {'average', 'surface', 'geodesic'}, optional
Method for calculation of parcel centroid. See Notes for more
information. Default: 'surface'
version : str, optional
Specifies which version of `fsaverage` provided annotation files
correspond to. Must be one of {'fsaverage', 'fsaverage3', 'fsaverage4',
'fsaverage5', 'fsaverage6'}. Default: 'fsaverage'
surf : str, optional
Specifies which surface projection of fsaverage to use for finding
parcel centroids. Default: 'sphere'
drop_labels : list, optional
Specifies regions in {lh,rh}annot for which the parcel centroid should
not be calculated. If not specified, centroids for parcels defined in
`netneurotools.freesurfer.FSIGNORE` are not calculated. Default: None
Returns
-------
centroids : (N, 3) numpy.ndarray
xyz coordinates of vertices closest to the centroid of each parcel
defined in `lhannot` and `rhannot`
hemiid : (N,) numpy.ndarray
Array denoting hemisphere designation of coordinates in `centroids`,
where `hemiid=0` denotes the left and `hemiid=1` the right hemisphere
Notes
-----
The following methods can be used for finding parcel centroids:
1. ``method='average'``
Uses the arithmetic mean of the coordinates for the vertices in each
parcel. Note that in this case the calculated centroids will not act
actually fall on the surface of `surf`.
2. ``method='surface'``
Calculates the 'average' coordinates and then finds the closest vertex
on `surf`, where closest is defined as the vertex with the minimum
Euclidean distance.
3. ``method='geodesic'``
Uses the coordinates of the vertex with the minimum average geodesic
distance to all other vertices in the parcel. Note that this is slightly
more time-consuming than the other two methods, especially for
high-resolution meshes.
"""
methods = ['average', 'surface', 'geodesic']
if method not in methods:
raise ValueError('Provided method for centroid calculation {} is '
'invalid. Must be one of {}'.format(methods, methods))
if drop_labels is None:
drop_labels = FSIGNORE
drop_labels = _decode_list(drop_labels)
surfaces = fetch_fsaverage(version)[surf]
centroids, hemiid = [], []
for n, (annot, surf) in enumerate(zip([lhannot, rhannot], surfaces)):
vertices, faces = read_geometry(surf)
labels, ctab, names = read_annot(annot)
names = _decode_list(names)
for lab in np.unique(labels):
if names[lab] in drop_labels:
continue
if method in ['average', 'surface']:
roi = np.atleast_2d(vertices[labels == lab].mean(axis=0))
if method == 'surface': # find closest vertex on the sphere
roi = vertices[np.argmin(cdist(vertices, roi), axis=0)[0]]
elif method == 'geodesic':
inds, = np.where(labels == lab)
roi = _geodesic_parcel_centroid(vertices, faces, inds)
centroids.append(roi)
hemiid.append(n)
return np.row_stack(centroids), np.asarray(hemiid)
def surf_convert(fsdir,
t1files,
surffiles,
sidpos=-3,
rm_orig=False,
fsconfig=DEFAULT_FREESURFER_PATH):
""" Export FreeSurfer surfaces to the native space.
Note that all the returned vetices are given in the index coordinate
system.
The subject id in the t1 and surf files must appear in the 'sidpos'
position. For the default value '-3', the T1 path might look like:
xxx/subject_id/convert/t1.nii.gz
Parameters
----------
fsdir: str (mandatory)
The FreeSurfer working directory with all the subjects.
t1files: str (mandatory)
The t1 nifti files.
surffiles:
The surfaces to be converted.
sidpos: int (optional, default -3)
The subject identifier position in the surface and T1 files.
rm_orig: bool (optional)
If True remove the input surfaces.
fsconfig: str (optional)
The FreeSurfer configuration batch.
Returns
-------
csurffiles:
The converted surfaces in the native space indexed coordinates.
"""
# Check input parameters
for path in t1files + surffiles:
if not os.path.isfile(path):
raise ValueError("'{0}' is not a valid file.".format(path))
if not os.path.isdir(fsdir):
raise ValueError("'{0}' is not a valid directory.".format(fsdir))
# Create a t1 subject map
t1map = {}
for fname in t1files:
subject_id = fname.split(os.path.sep)[sidpos]
if subject_id in t1map:
raise ValueError("Can't map two t1 for subject "
"'{0}'.".format(subject_id))
t1map[subject_id] = fname
# Convert all the surfaces
csurffiles = []
for fname in surffiles:
# Get the t1 reference image
subject_id = fname.split(os.path.sep)[sidpos]
t1file = t1map[subject_id]
t1_image = nibabel.load(t1file)
# Compute the conformed space to the native anatomical deformation
asegfile = os.path.join(fsdir, subject_id, "mri", "aseg.mgz")
physical_to_index = numpy.linalg.inv(t1_image.get_affine())
translation = tkregister_translation(asegfile, fsconfig)
deformation = numpy.dot(physical_to_index, translation)
# Load and warp the mesh
# The mesh: a 2-uplet with vertex (x, y, z) coordinates and
# mesh triangles
mesh = freesurfer.read_geometry(fname)
surf = TriSurface(vertices=apply_affine_on_mesh(mesh[0], deformation),
triangles=mesh[1])
# Save the mesh in the native space
outputfile = fname + ".native"
surf.save(outputfile)
csurffiles.append(outputfile)
# Construct the surfaces binarized volume
binarizedfile = os.path.join(outputfile + ".nii.gz")
overlay = numpy.zeros(t1_image.shape, dtype=numpy.uint)
indices = numpy.round(surf.vertices).astype(int).T
indices[0, numpy.where(indices[0] >= t1_image.shape[0])] = 0
indices[1, numpy.where(indices[1] >= t1_image.shape[1])] = 0
indices[2, numpy.where(indices[2] >= t1_image.shape[2])] = 0
overlay[indices.tolist()] = 1
overlay_image = nibabel.Nifti1Image(overlay, t1_image.get_affine())
nibabel.save(overlay_image, binarizedfile)
# Clean input surface if specified
if rm_orig:
os.remove(fname)
return csurffiles
def read_cortex_surface_segmentation(fsdir, physical_to_index, fsconfig,
affine=None):
""" Read the cortex gyri surface segmentatation of freesurfer.
Give access to the right and left hemisphere segmentations that can be
projected on the cortical and inflated cortical surfaces.
The vertex are expressed in the voxel coordinates.
Parameters
----------
fsdir: str( mandatory)
the subject freesurfer segmentation directory.
physical_to_index: array (mandatory)
the transformation to project a physical point in an array.
fsconfig: str (mandatory)
the freesurfer configuration file.
affine: array (optional, default None)
an affine transformation in voxel coordinates that will be applied on
the output vertex of the cortex surface.
Returns
-------
segmentation: dict
contain the two hemisphere 'lh' and 'rh' triangular surfaces and
inflated surfaces represented in a TriSurface structure.
"""
# Construct the path to the surface segmentation results and associated
# labels
meshdir = os.path.join(fsdir, "surf")
labeldir = os.path.join(fsdir, "label")
segfile = os.path.join(fsdir, "mri")
# Get deformation between the ras and ras-tkregister spaces
asegfile = os.path.join(segfile, "aseg.mgz")
translation = tkregister_translation(asegfile, fsconfig)
# Construct the deformation to apply on the cortex mesh
if affine is None:
affine = numpy.identity(4)
deformation = numpy.dot(affine, numpy.dot(physical_to_index, translation))
# Create an dictionary to contain all the surfaces and labels
segmentation = {}
# Select the hemisphere
for hemi in ["lh", "rh"]:
# Get annotation id at each vertex (if a vertex does not belong
# to any label and orig_ids=False, its id will be set to -1) and
# the names of the labels
annotfile = os.path.join(labeldir, "{0}.aparc.annot".format(hemi))
labels, ctab, regions = freesurfer.read_annot(
annotfile, orig_ids=False)
meta = dict((index, {"region": item[0], "color": item[1][:4].tolist()})
for index, item in enumerate(zip(regions, ctab)))
# Select the surface type
hemisegmentation = {}
for surf in ["white", "inflated"]:
# Load the mesh: a 2-uplet with vertex (x, y, z) coordinates and
# mesh triangles
meshfile = os.path.join(meshdir, "{0}.{1}".format(hemi, surf))
mesh = freesurfer.read_geometry(meshfile)
hemisegmentation[surf] = {
"vertices": apply_affine_on_mesh(mesh[0], deformation),
"triangles": mesh[1]
}
# Save the segmentation result
segmentation[hemi] = TriSurface(
vertices=hemisegmentation["white"]["vertices"],
inflated_vertices=hemisegmentation["inflated"]["vertices"],
triangles=hemisegmentation["white"]["triangles"],
labels=labels,
metadata=meta)
return segmentation
def interface2surf(interface_image, surface_file, cortex_label, ref_mgz, out_file):
import os
import nibabel as nb
import nibabel.freesurfer as nbfs
import numpy as np
import scipy.spatial.distance as syd
# get image properties
interfaceImage = nb.load(interface_image)
interface_indexes = interfaceImage.get_data()
interface_shape = np.shape(interface_indexes)
reoriented_indexes = np.zeros(interface_shape)
affineMatrix = interfaceImage.get_affine()
# get surface and put it in voxel space
surface = nbfs.read_geometry(surface_file)
surface_coords = surface[0]
surface_coords[:,0] = surface_coords[:,0] + (interface_shape[0]/2)
surface_coords[:,1] = surface_coords[:,1] + (interface_shape[1]/2)
surface_coords[:,2] = surface_coords[:,2] + (interface_shape[2]/2)
surf_array_dim = np.shape(surface_coords)
surf_length = surf_array_dim[0]
label_indices = np.loadtxt(cortex_label, delimiter=' ', dtype=long, skiprows=2, usecols=[0])
projected_index=np.zeros(surf_length)
projected_distance=np.zeros(surf_length)-1
# get interface coordinates and put them in normal voxel space
voxelCoordList=[]
for x, y, z in zip(*np.nonzero(interface_indexes)):
voxelCoord = [x,y,z]
if(affineMatrix[0,0]==-1):
voxelCoord[0]=interface_shape[0]-1-voxelCoord[0]
if(affineMatrix[1,1]==-1):
voxelCoord[1]=interface_shape[1]-1-voxelCoord[1]
if(affineMatrix[2,2]==-1):
voxelCoord[2]=interface_shape[2]-1-voxelCoord[2]
voxelCoordList.append(voxelCoord)
reoriented_indexes[voxelCoord[0],voxelCoord[1],voxelCoord[2]]=interface_indexes[x,y,z]
interface_voxels = np.array(voxelCoordList)
for i in label_indices:
surf_coord = surface_coords[i:i+1,:]
surf_floor = np.floor(surf_coord)
local_index = reoriented_indexes[surf_floor[0,0],surf_floor[0,1],surf_floor[0,2]]
"""
-if the vertex lays in an index voxel assign directly
-TO IMPLEMENT IF SLOW: check next in the 26-neighborhood
-otherwise, check distances to all index voxels and choose smallest
"""
if( local_index != 0):
projected_index[i] = local_index
projected_distance[i] = 0.0
else:
all_dists = syd.cdist(surf_coord, interface_voxels + 0.5, 'euclidean')
nearest_voxel_ID = np.argmin(all_dists)
nearest_dist = all_dists[0,nearest_voxel_ID]
projected_distance[i] = nearest_dist
projected_voxel_coords=interface_voxels[nearest_voxel_ID,:]
projected_index[i] = reoriented_indexes[ projected_voxel_coords[0],projected_voxel_coords[1],projected_voxel_coords[2] ]
"""
convert projected_index into a .mif file
"""
ref_mgz_file = nb.load(ref_mgz)
data=ref_mgz_file.get_data()
data[:,0,0]=projected_index
surface_projected_image = nb.MGHImage(data, ref_mgz_file.get_affine(), ref_mgz_file.get_header())
nb.save(surface_projected_image, out_file)
return os.path.abspath(out_file)
def map_to_average_brain(coords, left_pial, right_pial, left_sphere,
right_sphere):
"""
Maps a set of Freesurfer surface coordinates in an individual brain to the equivalent coordinates on the average
brain.
Method taken from the iElvis project (http://ielvis.pbworks.com), which implemented the same function in MATLAB:
https://github.com/iELVis/iELVis/blob/master/iELVis_MAIN/iELVis_MATLAB/ELEC_LOC/sub2AvgBrain.m
:param coords: {np.ndarray} Coordinates in the individual Freesurfer space
:param subject_surf_dir: {str} Path to the directory containing the subject's surface meshes
:param avg_surf_dir: {str} Path to the directory containing the fsaverage surface meshes
:return: {np.ndarray} The matching coordinates in the average brain
:return: {np.ndarray} The corresponding atlas labels in the average brain
"""
hemispheres = [
'left', 'right'
] # For all surfaces, we append the right hemisphere to the left hemisphere
fsavg_subj_dir = osp.join(
paths.rhino_root,
'data',
'eeg',
'freesurfer',
'subjects',
'fsaverage',
)
files = {
'left_pial': left_pial,
'right_pial': right_pial,
'left_sphere': left_sphere,
'right_sphere': right_sphere,
'left_avg_sphere': osp.join(fsavg_subj_dir, 'surf', 'lh.sphere.reg'),
'right_avg_sphere': osp.join(fsavg_subj_dir, 'surf', 'rh.sphere.reg'),
'left_avg_pial': osp.join(fsavg_subj_dir, 'surf', 'lh.pial'),
'right_avg_pial': osp.join(fsavg_subj_dir, 'surf', 'rh.pial'),
'left_avg_annot': osp.join(fsavg_subj_dir, 'label', 'lh.aparc.annot'),
'right_avg_annot': osp.join(fsavg_subj_dir, 'label', 'rh.aparc.annot')
}
# Find vertex indices on subject's pial surface
pial_verts = [read_geometry(files['%s_pial' % h])[0] for h in hemispheres]
distances = [dist.cdist(v, coords) for v in pial_verts]
hemisphere = np.min(distances[0], 0) < np.min(distances[1], 0)
pial_indices = [np.argmin(d, 0) for d in distances]
# Take those vertices in sphere.reg
sphere_verts = [
read_geometry(files['%s_sphere' % h])[0] for h in hemispheres
]
electrode_sphere_verts = [
sv[pi] for (sv, pi) in zip(sphere_verts, pial_indices)
]
# Find indices of nearest vertices in fsaverage.?h.sphere.reg
avg_sphere_verts = [
read_geometry(files['%s_avg_sphere' % h])[0] for h in hemispheres
]
avg_sphere_indices = [
np.argmin(dist.cdist(asv, esv), axis=0)
for (asv, esv) in zip(avg_sphere_verts, electrode_sphere_verts)
]
# Take those vertices on average pial surface
avg_pial_verts = [
read_geometry(files['%s_avg_pial' % h])[0] for h in hemispheres
]
avg_pial_inds, _, avg_pial_labels = zip(
*[read_annot(files['%s_avg_annot' % h]) for h in hemispheres])
avg_pial_labels = [np.array(x) for x in avg_pial_labels]
new_pial_verts = np.where(
hemisphere[:, None],
*[apv[asi] for apv, asi in zip(avg_pial_verts, avg_sphere_indices)])
new_pial_labels = np.where(
hemisphere, *[
np.array(apl)[(api[asi])] for apl, api, asi in zip(
avg_pial_labels, avg_pial_inds, avg_sphere_indices)
])
print(new_pial_verts.shape)
print(new_pial_labels.shape)
return new_pial_verts, new_pial_labels
def find_parcel_centroids(*,
lhannot,
rhannot,
version='fsaverage',
surf='sphere',
drop=None):
"""
Returns vertex coords corresponding to centroids of parcels in annotations
Note that using any other `surf` besides the default of 'sphere' may result
in centroids that are not directly within the parcels themselves due to
sulcal folding patterns.
Parameters
----------
{lh,rh}annot : str
Path to .annot file containing labels of parcels on the {left,right}
hemisphere. These must be specified as keyword arguments to avoid
accidental order switching.
version : str, optional
Specifies which version of `fsaverage` provided annotation files
correspond to. Must be one of {'fsaverage', 'fsaverage3', 'fsaverage4',
'fsaverage5', 'fsaverage6'}. Default: 'fsaverage'
surf : str, optional
Specifies which surface projection of fsaverage to use for finding
parcel centroids. Default: 'sphere'
drop : list, optional
Specifies regions in {lh,rh}annot for which the parcel centroid should
not be calculated. If not specified, centroids for 'unknown' and
'corpuscallosum' are not calculated. Default: None
Returns
-------
centroids : (N, 3) numpy.ndarray
xyz coordinates of vertices closest to the centroid of each parcel
defined in `lhannot` and `rhannot`
hemiid : (N,) numpy.ndarray
Array denoting hemisphere designation of coordinates in `centroids`,
where `hemiid=0` denotes the left and `hemiid=1` the right hemisphere
"""
if drop is None:
drop = [
'unknown',
'corpuscallosum', # default FreeSurfer
'Background+FreeSurfer_Defined_Medial_Wall' # common alternative
]
drop = _decode_list(drop)
surfaces = fetch_fsaverage(version)[surf]
centroids, hemiid = [], []
for n, (annot, surf) in enumerate(zip([lhannot, rhannot], surfaces)):
vertices, faces = read_geometry(surf)
labels, ctab, names = read_annot(annot)
names = _decode_list(names)
for lab in np.unique(labels):
if names[lab] in drop:
continue
coords = np.atleast_2d(vertices[labels == lab].mean(axis=0))
roi = vertices[np.argmin(cdist(vertices, coords), axis=0)[0]]
centroids.append(roi)
hemiid.append(n)
return np.row_stack(centroids), np.asarray(hemiid)
def surf_convert(fsdir,
output_directory,
t1files,
surffiles,
rm_orig=False,
fsconfig="/i2bm/local/freesurfer/SetUpFreeSurfer.sh"):
""" Export FreeSurfer surfaces to the native space.
Note that all the vetices are given in the index coordinate system.
The subjecy id in the t1 and surf files must appear in the -3 position:
xxx/subject_id/convert/t1.nii.gz
<unit>
<input name="fsdir" type="Directory" description="The
freesurfer working directory with all the subjects."/>
<input name="output_directory" type="Directory" description="The
conversion destination folder."/>
<input name="t1files" type="List_File" description="The t1 nifti
files."/>
<input name="surffiles" type="List_File" description="The surface
to be converted."/>
<input name="rm_orig" type="Bool" description="If true remove
the input surfaces."/>
<input name="fsconfig" type="File" description="The freesurfer
configuration batch."/>
<output name="csurffiles" type="List_File" description="The converted
surfaces in the native space."/>
</unit>
"""
# Create a t1 subject map
t1map = {}
for fname in t1files:
subject_id = fname.split("/")[-3]
if subject_id in t1map:
raise ("Can't map two t1 for subject '{0}'.".format(subject_id))
t1map[subject_id] = fname
# Convert all the surfaces
csurffiles = []
for fname in surffiles:
# Get the t1 reference image
subject_id = fname.split("/")[-3]
t1file = t1map[subject_id]
t1_image = nibabel.load(t1file)
# Compute the conformed space to the native anatomical deformation
asegfile = os.path.join(fsdir, subject_id, "mri", "aseg.mgz")
physical_to_index = numpy.linalg.inv(t1_image.get_affine())
translation = tkregister_translation(asegfile, fsconfig)
deformation = numpy.dot(physical_to_index, translation)
# Load and warp the mesh
# The mesh: a 2-uplet with vertex (x, y, z) coordinates and
# mesh triangles
mesh = freesurfer.read_geometry(fname)
surf = TriSurface(vertices=apply_affine_on_mesh(mesh[0], deformation),
triangles=mesh[1])
# Save the mesh in the native space
outputfile = fname + ".native"
surf.save(os.path.dirname(outputfile), os.path.basename(outputfile))
csurffiles.append(outputfile)
# Clean input surface if specified
if rm_orig:
os.remove(fname)
return csurffiles