def create_spherical_roi_volumes(node_size, coords, template_mask):
from pynets.nodemaker import get_sphere
mask_img = nib.load(template_mask)
mask_aff = mask_img.affine
print("%s%s" % ('Creating spherical ROI atlas with radius: ', node_size))
def mmToVox(nib_nifti, mmcoords):
return nib.affines.apply_affine(np.linalg.inv(nib_nifti.affine),
mmcoords)
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(mask_img, i))
coords_vox = list(set(list(tuple(x) for x in coords_vox)))
x_vox = np.diagonal(mask_img.affine[:3, 0:3])[0]
y_vox = np.diagonal(mask_img.affine[:3, 0:3])[1]
z_vox = np.diagonal(mask_img.affine[:3, 0:3])[2]
sphere_vol = np.zeros(mask_img.shape, dtype=bool)
parcel_list = []
i = 0
for coord in coords_vox:
inds = get_sphere(coord, node_size, (np.abs(x_vox), y_vox, z_vox),
mask_img.shape)
sphere_vol[tuple(inds.T)] = i * 1
parcel_list.append(
nib.Nifti1Image(sphere_vol.astype('int'), affine=mask_aff))
i = i + 1
par_max = len(coords)
parc = True
return parcel_list, par_max, node_size, parc
def extract_ts_coords_fast(node_size, conf, func_file, coords, dir_path):
import nibabel as nib
#import time
import subprocess
try:
from StringIO import StringIO
except ImportError:
from io import BytesIO as StringIO
from pynets.nodemaker import get_sphere
from pynets.graphestimation import generate_mask_from_voxels, normalize
#start_time=time.time()
data = nib.load(func_file)
activity_data = data.get_data()
volume_dims = np.shape(activity_data)[0:3]
ref_affine = data.get_qform()
ref_header = data.header
vox_dims = tuple(ref_header['pixdim'][1:4])
#print('Data loaded: t+'+str(time.time()-start_time)+'s')
label_mask = np.zeros(volume_dims)
label_file = "%s%s" % (dir_path, '/label_file_tmp.nii.gz')
[x_vox, y_vox, z_vox] = vox_dims
# finding sphere voxels
print(len(coords))
def mmToVox(mmcoords):
voxcoords = ['', '', '']
voxcoords[0] = int((round(int(mmcoords[0]) / x_vox)) + 45)
voxcoords[1] = int((round(int(mmcoords[1]) / y_vox)) + 63)
voxcoords[2] = int((round(int(mmcoords[2]) / z_vox)) + 36)
return voxcoords
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(i))
coords = list(tuple(x) for x in coords_vox)
for coord in range(len(coords)):
sphere_voxels = get_sphere(coords=coords[coord],
r=node_size,
vox_dims=vox_dims,
dims=volume_dims)
# creating mask from found voxels
sphere_mask = generate_mask_from_voxels(sphere_voxels, volume_dims)
label_mask = label_mask + (coord + 1) * sphere_mask
#print('Sphere voxels found: t+'+str(time.time()-start_time)+'s')
nib.save(nib.Nifti1Image(label_mask, ref_affine, header=ref_header),
label_file)
#print('Sphere mask saved: t+'+str(time.time()-start_time)+'s')
cmd = "%s%s%s%s" % ('fslmeants -i ', func_file, ' --label=', label_file)
stdout_extracted_ts = subprocess.check_output(cmd, shell=True)
ts_within_nodes = np.loadtxt(StringIO(stdout_extracted_ts))
ts_within_nodes = normalize(ts_within_nodes)
#print('Mean time series extracted: '+str(time.time()-start_time)+'s')
#print('Number of ROIs expected: '+str(len(coords)))
#print('Number of ROIs found: '+str(ts_within_nodes.shape[1]))
return (ts_within_nodes)
def create_spherical_roi_volumes(node_size, coords, template_mask):
"""
Create volume ROI mask of spheres from a given set of coordinates and radius.
Parameters
----------
node_size : int
Spherical centroid node size in the case that coordinate-based centroids
are used as ROI's for tracking.
coords : list
List of (x, y, z) tuples in mm-space corresponding to a coordinate atlas used or
which represent the center-of-mass of each parcellation node..
template_mask : str
Path to binarized version of standard (MNI)-space template Nifti1Image file.
Returns
-------
parcel_list : list
List of 3D boolean numpy arrays or binarized Nifti1Images corresponding to ROI masks.
par_max : int
The maximum label intensity in the parcellation image.
node_size : int
Spherical centroid node size in the case that coordinate-based centroids
are used as ROI's for tracking.
parc : bool
Indicates whether to use the raw parcels as ROI nodes instead of coordinates at their center-of-mass.
"""
from pynets.nodemaker import get_sphere, mmToVox
mask_img = nib.load(template_mask)
mask_aff = mask_img.affine
print("%s%s" % ('Creating spherical ROI atlas with radius: ', node_size))
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(mask_aff, i))
coords_vox = list(set(list(tuple(x) for x in coords_vox)))
x_vox = np.diagonal(mask_img.affine[:3, 0:3])[0]
y_vox = np.diagonal(mask_img.affine[:3, 0:3])[1]
z_vox = np.diagonal(mask_img.affine[:3, 0:3])[2]
sphere_vol = np.zeros(mask_img.shape, dtype=bool)
parcel_list = []
i = 0
for coord in coords_vox:
inds = get_sphere(coord, node_size, (np.abs(x_vox), y_vox, z_vox),
mask_img.shape)
sphere_vol[tuple(inds.T)] = i * 1
parcel_list.append(
nib.Nifti1Image(sphere_vol.astype('int'), affine=mask_aff))
i = i + 1
par_max = len(coords)
parc = True
return parcel_list, par_max, node_size, parc
def coord_masker(mask, coords, label_names, error):
from nilearn import masking
x_vox = np.diagonal(masking._load_mask_img(mask)[1][:3, 0:3])[0]
y_vox = np.diagonal(masking._load_mask_img(mask)[1][:3, 0:3])[1]
z_vox = np.diagonal(masking._load_mask_img(mask)[1][:3, 0:3])[2]
def mmToVox(mmcoords):
voxcoords = ['', '', '']
voxcoords[0] = int((round(int(mmcoords[0]) / x_vox)) + 45)
voxcoords[1] = int((round(int(mmcoords[1]) / y_vox)) + 63)
voxcoords[2] = int((round(int(mmcoords[2]) / z_vox)) + 36)
return voxcoords
mask_data, _ = masking._load_mask_img(mask)
# mask_coords = list(zip(*np.where(mask_data == True)))
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(i))
coords_vox = list(tuple(x) for x in coords_vox)
bad_coords = []
for coord in coords_vox:
sphere_vol = np.zeros(mask_data.shape, dtype=bool)
sphere_vol[tuple(coord)] = 1
if (mask_data & sphere_vol).any():
print("%s%s" % (coord, ' falls within mask...'))
continue
inds = get_sphere(coord, error, (np.abs(x_vox), y_vox, z_vox),
mask_data.shape)
sphere_vol[tuple(inds.T)] = 1
if (mask_data & sphere_vol).any():
print("%s%s%.2f%s" % (coord, ' is within a + or - ', float(error),
' mm neighborhood...'))
continue
bad_coords.append(coord)
bad_coords = [x for x in bad_coords if x is not None]
indices = []
for bad_coord in bad_coords:
indices.append(coords_vox.index(bad_coord))
label_names = list(label_names)
coords = list(tuple(x) for x in coords)
for ix in sorted(indices, reverse=True):
print("%s%s%s%s" % ('Removing: ', label_names[ix], ' at ', coords[ix]))
label_names.pop(ix)
coords.pop(ix)
return coords, label_names
def get_node_membership(network, func_file, coords, label_names, parc, parcel_list):
from nilearn.image import resample_img
from pynets.nodemaker import get_sphere
import pkg_resources
import pandas as pd
##For parcel membership determination, specify overlap thresh and error cushion in mm voxels
perc_overlap = 0.75 ##Default is >=90% overlap
error = 2
##Load subject func data
bna_img = nib.load(func_file)
x_vox = np.diagonal(bna_img.affine[:3,0:3])[0]
y_vox = np.diagonal(bna_img.affine[:3,0:3])[1]
z_vox = np.diagonal(bna_img.affine[:3,0:3])[2]
##Determine whether input is from 17-networks or 7-networks
seven_nets = [ 'Vis', 'SomMot', 'DorsAttn', 'SalVentAttn', 'Limbic', 'Cont', 'Default' ]
seventeen_nets = ['VisCent', 'VisPeri', 'SomMotA', 'SomMotB', 'DorsAttnA', 'DorsAttnB', 'SalVentAttnA', 'SalVentAttnB', 'LimbicOFC', 'LimbicTempPole', 'ContA', 'ContB', 'ContC', 'DefaultA', 'DefaultB', 'DefaultC', 'TempPar']
if network in seventeen_nets:
if x_vox <= 1 and y_vox <= 1 and z_vox <=1:
par_file = pkg_resources.resource_filename("pynets", "rsnrefs/BIGREF1mm.nii.gz")
else:
par_file = pkg_resources.resource_filename("pynets", "rsnrefs/BIGREF2mm.nii.gz")
##Grab RSN reference file
nets_ref_txt = pkg_resources.resource_filename("pynets", "rsnrefs/Schaefer2018_1000_17nets_ref.txt")
elif network in seven_nets:
if x_vox <= 1 and y_vox <= 1 and z_vox <=1:
par_file = pkg_resources.resource_filename("pynets", "rsnrefs/SMALLREF1mm.nii.gz")
else:
par_file = pkg_resources.resource_filename("pynets", "rsnrefs/SMALLREF2mm.nii.gz")
##Grab RSN reference file
nets_ref_txt = pkg_resources.resource_filename("pynets", "rsnrefs/Schaefer2018_1000_7nets_ref.txt")
else:
nets_ref_txt = None
if not nets_ref_txt:
raise ValueError('Network: ' + str(network) + ' not found!\nSee valid network names using the --help flag with pynets_run.py')
##Create membership dictionary
dict_df = pd.read_csv(nets_ref_txt, sep="\t", header=None, names=["Index", "Region", "X", "Y", "Z"])
dict_df.Region.unique().tolist()
ref_dict = {v: k for v, k in enumerate(dict_df.Region.unique().tolist())}
par_img = nib.load(par_file)
par_data = par_img.get_data()
RSN_ix=list(ref_dict.keys())[list(ref_dict.values()).index(network)]
RSNmask = par_data[:,:,:,RSN_ix]
def mmToVox(mmcoords):
voxcoords = ['','','']
voxcoords[0] = int((round(int(mmcoords[0])/x_vox))+45)
voxcoords[1] = int((round(int(mmcoords[1])/y_vox))+63)
voxcoords[2] = int((round(int(mmcoords[2])/z_vox))+36)
return voxcoords
def VoxTomm(voxcoords):
mmcoords = ['','','']
mmcoords[0] = int((round(int(voxcoords[0])-45)*x_vox))
mmcoords[1] = int((round(int(voxcoords[1])-63)*y_vox))
mmcoords[2] = int((round(int(voxcoords[2])-36)*z_vox))
return mmcoords
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(i))
coords_vox = list(tuple(x) for x in coords_vox)
if parc == False:
i = -1
RSN_parcels = None
RSN_coords_vox = []
net_label_names = []
for coord in coords_vox:
sphere_vol = np.zeros(RSNmask.shape, dtype=bool)
sphere_vol[tuple(coord)] = 1
i = i + 1
if (RSNmask.astype('bool') & sphere_vol).any():
print(str(coord) + ' coord falls within ' + network + '...')
RSN_coords_vox.append(coord)
net_label_names.append(label_names[i])
continue
else:
inds = get_sphere(coord, error, (np.abs(x_vox), y_vox, z_vox), RSNmask.shape)
sphere_vol[tuple(inds.T)] = 1
if (RSNmask.astype('bool') & sphere_vol).any():
print(str(coord) + ' coord is within a + or - ' + str(error) + ' mm neighborhood of ' + network + '...')
RSN_coords_vox.append(coord)
net_label_names.append(label_names[i])
coords_mm = []
for i in RSN_coords_vox:
coords_mm.append(VoxTomm(i))
coords_mm = list(set(list(tuple(x) for x in coords_mm)))
else:
i = 0
RSN_parcels = []
coords_with_parc = []
net_label_names = []
for parcel in parcel_list:
parcel_vol = np.zeros(RSNmask.shape, dtype=bool)
parcel_data_reshaped = resample_img(parcel, target_affine=par_img.affine,
target_shape=RSNmask.shape).get_data()
parcel_vol[parcel_data_reshaped==1] = 1
##Count number of unique voxels where overlap of parcel and mask occurs
overlap_count = len(np.unique(np.where((RSNmask.astype('uint8')==1) & (parcel_vol.astype('uint8')==1))))
##Count number of total unique voxels within the parcel
total_count = len(np.unique(np.where(((parcel_vol.astype('uint8')==1)))))
##Calculate % overlap
try:
overlap = float(overlap_count/total_count)
except:
overlap = float(0)
if overlap >=perc_overlap:
print(str(round(100*overlap,1)) + '% of parcel ' + str(label_names[i]) + ' falls within ' + str(network) + ' mask...')
RSN_parcels.append(parcel)
coords_with_parc.append(coords[i])
net_label_names.append(label_names[i])
i = i + 1
coords_mm = list(set(list(tuple(x) for x in coords_with_parc)))
return(coords_mm, RSN_parcels, net_label_names, network)
def coords_masker(roi, coords, label_names, mask, error):
from nilearn import masking
if mask and roi == mask:
error = 0
mask_data, mask_aff = masking._load_mask_img(roi)
x_vox = np.diagonal(mask_aff[:3, 0:3])[0]
y_vox = np.diagonal(mask_aff[:3, 0:3])[1]
z_vox = np.diagonal(mask_aff[:3, 0:3])[2]
def mmToVox(mask_aff, mmcoords):
return nib.affines.apply_affine(np.linalg.inv(mask_aff), mmcoords)
# mask_coords = list(zip(*np.where(mask_data == True)))
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(mask_aff, i))
coords_vox = list(
tuple(map(lambda y: isinstance(y, float) and int(round(y, 0)), x))
for x in coords_vox)
bad_coords = []
for coords in coords_vox:
sphere_vol = np.zeros(mask_data.shape, dtype=bool)
sphere_vol[tuple(coords)] = 1
if (mask_data & sphere_vol).any():
print("%s%s" % (coords, ' falls within roi mask...'))
continue
inds = get_sphere(coords, error, (np.abs(x_vox), y_vox, z_vox),
mask_data.shape)
sphere_vol[tuple(inds.T)] = 1
if (mask_data & sphere_vol).any():
print("%s%s%.2f%s" % (coords, ' is within a + or - ', float(error),
' mm neighborhood...'))
continue
bad_coords.append(coords)
bad_coords = [x for x in bad_coords if x is not None]
indices = []
for bad_coords in bad_coords:
indices.append(coords_vox.index(bad_coords))
label_names = list(label_names)
coords = list(tuple(x) for x in coords_vox)
try:
for ix in sorted(indices, reverse=True):
print("%s%s%s%s" %
('Removing: ', label_names[ix], ' at ', coords[ix]))
label_names.pop(ix)
coords.pop(ix)
except RuntimeError:
print(
'ERROR: Restrictive masking. No coords remain after masking with brain mask/roi...'
)
if len(coords) <= 1:
raise ValueError(
'\nERROR: ROI mask was likely too restrictive and yielded < 2 remaining coords'
)
return coords, label_names
def get_node_membership(network,
infile,
coords,
label_names,
parc,
parcel_list,
perc_overlap=0.75,
error=2):
from nilearn.image import resample_img
from pynets.nodemaker import get_sphere
import pkg_resources
import pandas as pd
# Determine whether input is from 17-networks or 7-networks
seven_nets = [
'Vis', 'SomMot', 'DorsAttn', 'SalVentAttn', 'Limbic', 'Cont', 'Default'
]
seventeen_nets = [
'VisCent', 'VisPeri', 'SomMotA', 'SomMotB', 'DorsAttnA', 'DorsAttnB',
'SalVentAttnA', 'SalVentAttnB', 'LimbicOFC', 'LimbicTempPole', 'ContA',
'ContB', 'ContC', 'DefaultA', 'DefaultB', 'DefaultC', 'TempPar'
]
# Load subject func data
bna_img = nib.load(infile)
x_vox = np.diagonal(bna_img.affine[:3, 0:3])[0]
y_vox = np.diagonal(bna_img.affine[:3, 0:3])[1]
z_vox = np.diagonal(bna_img.affine[:3, 0:3])[2]
if network in seventeen_nets:
if x_vox <= 1 and y_vox <= 1 and z_vox <= 1:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/BIGREF1mm.nii.gz")
else:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/BIGREF2mm.nii.gz")
# Grab RSN reference file
nets_ref_txt = pkg_resources.resource_filename(
"pynets", "rsnrefs/Schaefer2018_1000_17nets_ref.txt")
elif network in seven_nets:
if x_vox <= 1 and y_vox <= 1 and z_vox <= 1:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/SMALLREF1mm.nii.gz")
else:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/SMALLREF2mm.nii.gz")
# Grab RSN reference file
nets_ref_txt = pkg_resources.resource_filename(
"pynets", "rsnrefs/Schaefer2018_1000_7nets_ref.txt")
else:
nets_ref_txt = None
if not nets_ref_txt:
raise ValueError(
"%s%s%s" %
('Network: ', str(network),
' not found!\nSee valid network names using the --help '
'flag with pynets_run.py'))
# Create membership dictionary
dict_df = pd.read_csv(nets_ref_txt,
sep="\t",
header=None,
names=["Index", "Region", "X", "Y", "Z"])
dict_df.Region.unique().tolist()
ref_dict = {v: k for v, k in enumerate(dict_df.Region.unique().tolist())}
par_img = nib.load(par_file)
par_data = par_img.get_fdata()
RSN_ix = list(ref_dict.keys())[list(ref_dict.values()).index(network)]
RSNmask = par_data[:, :, :, RSN_ix]
def mmToVox(nib_nifti, mmcoords):
return nib.affines.apply_affine(np.linalg.inv(nib_nifti.affine),
mmcoords)
def VoxTomm(nib_nifti, voxcoords):
return nib.affines.apply_affine(nib_nifti.affine, voxcoords)
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(bna_img, i))
coords_vox = list(
tuple(map(lambda y: isinstance(y, float) and int(round(y, 0)), x))
for x in coords_vox)
if parc is False:
i = -1
RSN_parcels = None
RSN_coords_vox = []
net_label_names = []
for coords in coords_vox:
sphere_vol = np.zeros(RSNmask.shape, dtype=bool)
sphere_vol[tuple(coords)] = 1
i = i + 1
if (RSNmask.astype('bool') & sphere_vol).any():
print("%s%s%s%s" %
(coords, ' coords falls within ', network, '...'))
RSN_coords_vox.append(coords)
net_label_names.append(label_names[i])
continue
else:
inds = get_sphere(coords, error, (np.abs(x_vox), y_vox, z_vox),
RSNmask.shape)
sphere_vol[tuple(inds.T)] = 1
if (RSNmask.astype('bool') & sphere_vol).any():
print("%s%s%.2f%s%s%s" %
(coords, ' coords is within a + or - ', float(error),
' mm neighborhood of ', network, '...'))
RSN_coords_vox.append(coords)
net_label_names.append(label_names[i])
coords_mm = []
for i in RSN_coords_vox:
coords_mm.append(VoxTomm(bna_img, i))
coords_mm = list(set(list(tuple(x) for x in coords_mm)))
else:
i = 0
RSN_parcels = []
coords_with_parc = []
net_label_names = []
for parcel in parcel_list:
parcel_vol = np.zeros(RSNmask.shape, dtype=bool)
parcel_data_reshaped = resample_img(
parcel,
target_affine=par_img.affine,
target_shape=RSNmask.shape).get_fdata()
parcel_vol[parcel_data_reshaped == 1] = 1
# Count number of unique voxels where overlap of parcel and mask occurs
overlap_count = len(
np.unique(
np.where((RSNmask.astype('uint8') == 1)
& (parcel_vol.astype('uint8') == 1))))
# Count number of total unique voxels within the parcel
total_count = len(
np.unique(np.where((parcel_vol.astype('uint8') == 1))))
# Calculate % overlap
try:
overlap = float(overlap_count / total_count)
except RuntimeWarning:
print('\nWarning: No overlap with roi mask!\n')
overlap = float(0)
if overlap >= perc_overlap:
print("%.2f%s%s%s%s%s" %
(100 * overlap, '% of parcel ', label_names[i],
' falls within ', str(network), ' mask...'))
RSN_parcels.append(parcel)
coords_with_parc.append(coords[i])
net_label_names.append(label_names[i])
i = i + 1
coords_mm = list(set(list(tuple(x) for x in coords_with_parc)))
bna_img.uncache()
if len(coords_mm) <= 1:
raise ValueError(
"%s%s%s" %
('\nERROR: No coords from the specified atlas found within ',
network, ' network.'))
return coords_mm, RSN_parcels, net_label_names, network
def coords_masker(roi, coords, labels, error):
"""
Evaluate the affinity of any arbitrary list of coordinate nodes for a user-specified ROI mask.
Parameters
----------
roi : str
File path to binarized/boolean region-of-interest Nifti1Image file.
coords : list
List of (x, y, z) tuples in mm-space corresponding to a coordinate atlas used or
which represent the center-of-mass of each parcellation node.
labels : list
List of string labels corresponding to ROI nodes.
error : int
Rounded euclidean distance, in units of voxel number, to use as a spatial error cushion in the case of
evaluating the spatial affinity of a given list of coordinates to the given ROI mask.
Returns
-------
coords : list
Filtered list of (x, y, z) tuples in mm-space with a spatial affinity for the specified ROI mask.
labels : list
Filtered list of string labels corresponding to ROI nodes with a spatial affinity for the specified ROI mask.
"""
from nilearn import masking
from pynets.nodemaker import mmToVox
mask_data, mask_aff = masking._load_mask_img(roi)
x_vox = np.diagonal(mask_aff[:3, 0:3])[0]
y_vox = np.diagonal(mask_aff[:3, 0:3])[1]
z_vox = np.diagonal(mask_aff[:3, 0:3])[2]
# mask_coords = list(zip(*np.where(mask_data == True)))
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(mask_aff, i))
coords_vox = list(
tuple(map(lambda y: isinstance(y, float) and int(round(y, 0)), x))
for x in coords_vox)
bad_coords = []
for coords in coords_vox:
sphere_vol = np.zeros(mask_data.shape, dtype=bool)
sphere_vol[tuple(coords)] = 1
if (mask_data & sphere_vol).any():
print("%s%s" % (coords, ' falls within mask...'))
continue
inds = get_sphere(coords, error, (np.abs(x_vox), y_vox, z_vox),
mask_data.shape)
sphere_vol[tuple(inds.T)] = 1
if (mask_data & sphere_vol).any():
print("%s%s%.2f%s" % (coords, ' is within a + or - ', float(error),
' mm neighborhood...'))
continue
bad_coords.append(coords)
bad_coords = [x for x in bad_coords if x is not None]
indices = []
for bad_coords in bad_coords:
indices.append(coords_vox.index(bad_coords))
labels = list(labels)
coords = list(tuple(x) for x in coords_vox)
try:
for ix in sorted(indices, reverse=True):
print("%s%s%s%s" % ('Removing: ', labels[ix], ' at ', coords[ix]))
labels.pop(ix)
coords.pop(ix)
except RuntimeError:
print(
'ERROR: Restrictive masking. No coords remain after masking with brain mask/roi...'
)
if len(coords) <= 1:
raise ValueError(
'\nERROR: ROI mask was likely too restrictive and yielded < 2 remaining coords'
)
return coords, labels
def get_node_membership(network,
infile,
coords,
labels,
parc,
parcel_list,
perc_overlap=0.75,
error=4):
"""
Evaluate the affinity of any arbitrary list of coordinate or parcel nodes for a user-specified RSN based on
Yeo-7 or Yeo-17 definitions.
Parameters
----------
network : str
Resting-state network based on Yeo-7 and Yeo-17 naming (e.g. 'Default') used to filter nodes in the study of
brain subgraphs.
infile : str
File path to Nifti1Image object whose affine will provide sampling reference for evaluation spatial proximity.
coords : list
List of (x, y, z) tuples in mm-space corresponding to a coordinate atlas used or
which represent the center-of-mass of each parcellation node.
labels : list
List of string labels corresponding to ROI nodes.
parc : bool
Indicates whether to use parcels instead of coordinates as ROI nodes.
parcel_list : list
List of 3D boolean numpy arrays or binarized Nifti1Images corresponding to ROI masks.
perc_overlap : float
Value 0-1 indicating a threshold of spatial overlap to use as a spatial error cushion in the case of
evaluating RSN membership from a given list of parcel masks. Default is 0.75.
error : int
Rounded euclidean distance, in units of voxel number, to use as a spatial error cushion in the case of
evaluating RSN membership from a given list of coordinates. Default is 4.
Returns
-------
coords_mm : list
Filtered list of (x, y, z) tuples in mm-space with a spatial affinity for the specified RSN.
RSN_parcels : list
Filtered list of 3D boolean numpy arrays or binarized Nifti1Images corresponding to ROI masks with a spatial
affinity for the specified RSN.
net_labels : list
Filtered list of string labels corresponding to ROI nodes with a spatial affinity for the specified RSN.
network : str
Resting-state network based on Yeo-7 and Yeo-17 naming (e.g. 'Default') used to filter nodes in the study of
brain subgraphs.
"""
from nilearn.image import resample_img
from pynets.nodemaker import get_sphere, mmToVox, VoxTomm
import pkg_resources
import pandas as pd
# Determine whether input is from 17-networks or 7-networks
seven_nets = [
'Vis', 'SomMot', 'DorsAttn', 'SalVentAttn', 'Limbic', 'Cont', 'Default'
]
seventeen_nets = [
'VisCent', 'VisPeri', 'SomMotA', 'SomMotB', 'DorsAttnA', 'DorsAttnB',
'SalVentAttnA', 'SalVentAttnB', 'LimbicOFC', 'LimbicTempPole', 'ContA',
'ContB', 'ContC', 'DefaultA', 'DefaultB', 'DefaultC', 'TempPar'
]
# Load subject func data
bna_img = nib.load(infile)
x_vox = np.diagonal(bna_img.affine[:3, 0:3])[0]
y_vox = np.diagonal(bna_img.affine[:3, 0:3])[1]
z_vox = np.diagonal(bna_img.affine[:3, 0:3])[2]
if network in seventeen_nets:
if x_vox <= 1 and y_vox <= 1 and z_vox <= 1:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/BIGREF1mm.nii.gz")
else:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/BIGREF2mm.nii.gz")
# Grab RSN reference file
nets_ref_txt = pkg_resources.resource_filename(
"pynets", "rsnrefs/Schaefer2018_1000_17nets_ref.txt")
elif network in seven_nets:
if x_vox <= 1 and y_vox <= 1 and z_vox <= 1:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/SMALLREF1mm.nii.gz")
else:
par_file = pkg_resources.resource_filename(
"pynets", "rsnrefs/SMALLREF2mm.nii.gz")
# Grab RSN reference file
nets_ref_txt = pkg_resources.resource_filename(
"pynets", "rsnrefs/Schaefer2018_1000_7nets_ref.txt")
else:
nets_ref_txt = None
if not nets_ref_txt:
raise ValueError(
"%s%s%s" %
('Network: ', str(network),
' not found!\nSee valid network names using the --help '
'flag with pynets_run.py'))
# Create membership dictionary
dict_df = pd.read_csv(nets_ref_txt,
sep="\t",
header=None,
names=["Index", "Region", "X", "Y", "Z"])
dict_df.Region.unique().tolist()
ref_dict = {v: k for v, k in enumerate(dict_df.Region.unique().tolist())}
par_img = nib.load(par_file)
par_data = par_img.get_fdata()
RSN_ix = list(ref_dict.keys())[list(ref_dict.values()).index(network)]
RSNmask = par_data[:, :, :, RSN_ix]
bna_aff = bna_img.affine
coords_vox = []
for i in coords:
coords_vox.append(mmToVox(bna_aff, i))
coords_vox = list(
tuple(map(lambda y: isinstance(y, float) and int(round(y, 0)), x))
for x in coords_vox)
if parc is False:
i = -1
RSN_parcels = None
RSN_coords_vox = []
net_labels = []
for coords in coords_vox:
sphere_vol = np.zeros(RSNmask.shape, dtype=bool)
sphere_vol[tuple(coords)] = 1
i = i + 1
if (RSNmask.astype('bool') & sphere_vol).any():
print("%s%s%s%s" %
(coords, ' coords falls within ', network, '...'))
RSN_coords_vox.append(coords)
net_labels.append(labels[i])
continue
else:
inds = get_sphere(coords, error, (np.abs(x_vox), y_vox, z_vox),
RSNmask.shape)
sphere_vol[tuple(inds.T)] = 1
if (RSNmask.astype('bool') & sphere_vol).any():
print("%s%s%.2f%s%s%s" %
(coords, ' coords is within a + or - ', float(error),
' mm neighborhood of ', network, '...'))
RSN_coords_vox.append(coords)
net_labels.append(labels[i])
coords_mm = []
for i in RSN_coords_vox:
coords_mm.append(VoxTomm(bna_aff, i))
coords_mm = list(set(list(tuple(x) for x in coords_mm)))
else:
i = 0
RSN_parcels = []
coords_with_parc = []
net_labels = []
for parcel in parcel_list:
parcel_vol = np.zeros(RSNmask.shape, dtype=bool)
parcel_data_reshaped = resample_img(
parcel,
target_affine=par_img.affine,
target_shape=RSNmask.shape).get_fdata()
parcel_vol[parcel_data_reshaped == 1] = 1
# Count number of unique voxels where overlap of parcel and mask occurs
overlap_count = len(
np.unique(
np.where((RSNmask.astype('uint8') == 1)
& (parcel_vol.astype('uint8') == 1))))
# Count number of total unique voxels within the parcel
total_count = len(
np.unique(np.where((parcel_vol.astype('uint8') == 1))))
# Calculate % overlap
try:
overlap = float(overlap_count / total_count)
except RuntimeWarning:
print('\nWarning: No overlap with roi mask!\n')
overlap = float(0)
if overlap >= perc_overlap:
print("%.2f%s%s%s%s%s" %
(100 * overlap, '% of parcel ', labels[i],
' falls within ', str(network), ' mask...'))
RSN_parcels.append(parcel)
coords_with_parc.append(coords[i])
net_labels.append(labels[i])
i = i + 1
coords_mm = list(set(list(tuple(x) for x in coords_with_parc)))
bna_img.uncache()
if len(coords_mm) <= 1:
raise ValueError(
"%s%s%s" %
('\nERROR: No coords from the specified atlas found within ',
network, ' network.'))
return coords_mm, RSN_parcels, net_labels, network