def connect_afni_centrality_workflow(workflow, c, strat, num_strat,
resample_functional_to_template,
template,
merge_node,
method_option, threshold_option,
threshold):
# Import packages
from CPAC.network_centrality.afni_network_centrality \
import create_afni_centrality_wf
import CPAC.network_centrality.utils as cent_utils
# Init variables
# Set method_options variables
if method_option == 'degree':
out_list = 'deg_list'
elif method_option == 'eigenvector':
out_list = 'eig_list'
elif method_option == 'lfcd':
out_list = 'lfcd_list'
# Init workflow name and resource limits
wf_name = 'afni_centrality_%d_%s' % (num_strat, method_option)
num_threads = c.maxCoresPerParticipant
memory = c.memoryAllocatedForDegreeCentrality
# Format method and threshold options properly and check for
# errors
method_option, threshold_option = \
cent_utils.check_centrality_params(method_option,
threshold_option,
threshold)
# Change sparsity thresholding to % to work with afni
if threshold_option == 'sparsity':
threshold = threshold * 100
# Init the workflow
afni_centrality_wf = \
create_afni_centrality_wf(wf_name, method_option,
threshold_option,
threshold, num_threads, memory)
# Connect pipeline resources to workflow
workflow.connect(resample_functional_to_template, 'out_file',
afni_centrality_wf, 'inputspec.in_file')
# Mask
workflow.connect(template, 'local_path',
afni_centrality_wf, 'inputspec.template')
# Connect outputs to merge node
workflow.connect(afni_centrality_wf,
'outputspec.outfile_list',
merge_node,
out_list)
def connect_centrality_workflow(workflow, c, resample_functional_to_template,
template_node, template_out, merge_node,
method_option, pipe_num):
template = c.network_centrality['template_specification_file']
# Set method_options variables
if method_option == 'degree_centrality':
out_list = 'deg_list'
elif method_option == 'eigenvector_centrality':
out_list = 'eig_list'
elif method_option == 'local_functional_connectivity_density':
out_list = 'lfcd_list'
threshold_option = c.network_centrality[method_option][
'correlation_threshold_option']
threshold = c.network_centrality[method_option]['correlation_threshold']
# Init workflow name and resource limits
wf_name = f'afni_centrality_{method_option}_{pipe_num}'
num_threads = c.pipeline_setup['system_config'][
'max_cores_per_participant']
memory = c.network_centrality['memory_allocation']
# Format method and threshold options properly and check for
# errors
method_option, threshold_option = check_centrality_params(
method_option, threshold_option, threshold)
# Change sparsity thresholding to % to work with afni
if threshold_option == 'sparsity':
threshold = threshold * 100
afni_centrality_wf = \
create_centrality_wf(wf_name, method_option,
c.network_centrality[method_option][
'weight_options'], threshold_option,
threshold, num_threads, memory)
workflow.connect(resample_functional_to_template, 'out_file',
afni_centrality_wf, 'inputspec.in_file')
workflow.connect(template_node, template_out, afni_centrality_wf,
'inputspec.template')
workflow.connect(afni_centrality_wf, 'outputspec.outfile_list', merge_node,
out_list)
def create_centrality_wf(wf_name, method_option, threshold_option,
threshold, num_threads=1, memory_gb=1.0):
"""
Function to create the afni-based centrality workflow
Parameters
----------
wf_name : string
the name of the workflow
method_option : string
'degree', 'eigenvector', or 'lfcd'
threshold_option : string
'significance', 'sparsity', or 'correlation'
threshold : float
the threshold value for thresholding the similarity matrix
num_threads : integer (optional); default=1
the number of threads to utilize for centrality computation
memory_gb : float (optional); default=1.0
the amount of memory the centrality calculation will take (GB)
Returns
-------
centrality_wf : nipype Workflow
the initialized nipype workflow for the afni centrality command
"""
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import CPAC.network_centrality.utils as utils
test_thresh = threshold
if threshold_option == 'sparsity':
test_thresh = threshold / 100.0
method_option, threshold_option = \
utils.check_centrality_params(method_option, threshold_option, test_thresh)
centrality_wf = pe.Workflow(name=wf_name)
input_node = pe.Node(util.IdentityInterface(fields=['in_file',
'template',
'threshold']),
name='inputspec')
input_node.inputs.threshold = threshold
# Degree centrality
if method_option == 'degree':
afni_centrality_node = \
pe.Node(DegreeCentrality(environ={'OMP_NUM_THREADS' : str(num_threads)}),
name='afni_centrality', mem_gb=memory_gb)
afni_centrality_node.inputs.out_file = 'degree_centrality_merged.nii.gz'
out_names = ('degree_centrality_binarize', 'degree_centrality_weighted')
# Eigenvector centrality
elif method_option == 'eigenvector':
afni_centrality_node = \
pe.Node(ECM(environ={'OMP_NUM_THREADS': str(num_threads)}),
name='afni_centrality', mem_gb=memory_gb)
afni_centrality_node.inputs.out_file = 'eigenvector_centrality_merged.nii.gz'
afni_centrality_node.inputs.memory = memory_gb # 3dECM input only
out_names = ('eigenvector_centrality_binarize',
'eigenvector_centrality_weighted')
# lFCD
elif method_option == 'lfcd':
afni_centrality_node = \
pe.Node(LFCD(environ={'OMP_NUM_THREADS': str(num_threads)}),
name='afni_centrality', mem_gb=memory_gb)
afni_centrality_node.inputs.out_file = 'lfcd_merged.nii.gz'
out_names = ('lfcd_binarize', 'lfcd_weighted')
afni_centrality_node.interface.num_threads = num_threads
# Connect input image and mask tempalte
centrality_wf.connect(input_node, 'in_file',
afni_centrality_node, 'in_file')
centrality_wf.connect(input_node, 'template',
afni_centrality_node, 'mask')
# If we're doing significan thresholding, convert to correlation
if threshold_option == 'significance':
# Check and (possibly) conver threshold
convert_thr_node = pe.Node(util.Function(input_names=['datafile',
'p_value',
'two_tailed'],
output_names=['rvalue_threshold'],
function=utils.convert_pvalue_to_r),
name='convert_threshold')
# Wire workflow to connect in conversion node
centrality_wf.connect(input_node, 'in_file',
convert_thr_node, 'datafile')
centrality_wf.connect(input_node, 'threshold',
convert_thr_node, 'p_value')
centrality_wf.connect(convert_thr_node, 'rvalue_threshold',
afni_centrality_node, 'thresh')
# Sparsity thresholding
elif threshold_option == 'sparsity':
# Check to make sure it's not lFCD
if method_option == 'lfcd':
raise Exception('Sparsity thresholding is not supported for lFCD')
# Otherwise, connect threshold to sparsity input
centrality_wf.connect(input_node, 'threshold',
afni_centrality_node, 'sparsity')
# Correlation thresholding
elif threshold_option == 'correlation':
centrality_wf.connect(input_node, 'threshold',
afni_centrality_node, 'thresh')
# Need to seprate sub-briks
sep_subbriks_node = \
pe.Node(util.Function(input_names=['nifti_file', 'out_names'],
output_names=['output_niftis'],
function=utils.sep_nifti_subbriks),
name='sep_nifti_subbriks')
sep_subbriks_node.inputs.out_names = out_names
centrality_wf.connect(afni_centrality_node, 'out_file',
sep_subbriks_node, 'nifti_file')
output_node = pe.Node(util.IdentityInterface(fields=['outfile_list',
'oned_output']),
name='outputspec')
centrality_wf.connect(sep_subbriks_node, 'output_niftis',
output_node, 'outfile_list')
return centrality_wf
def create_afni_centrality_wf(wf_name, method_option, threshold_option, threshold, num_threads=1, memory_gb=1.0):
"""
Function to create the afni-based centrality workflow
Parameters
----------
wf_name : string
the name of the workflow
method_option : string
'degree', 'eigenvector', or 'lfcd'
threshold_option : string
'significance', 'sparsity', or 'correlation'
threshold : float
the threshold value for thresholding the similarity matrix
num_threads : integer (optional); default=1
the number of threads to utilize for centrality computation
memory_gb : float (optional); default=1.0
the amount of memory the centrality calculation will take (GB)
Returns
-------
centrality_wf : nipype Workflow
the initialized nipype workflow for the afni centrality command
"""
# Import packages
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import CPAC.network_centrality.utils as utils
# Check the centrality parameters
test_thresh = threshold
if threshold_option == "sparsity":
test_thresh = threshold / 100.0
method_option, threshold_option = utils.check_centrality_params(method_option, threshold_option, test_thresh)
# Init variables
centrality_wf = pe.Workflow(name=wf_name)
# Create inputspec node
input_node = pe.Node(util.IdentityInterface(fields=["in_file", "template", "threshold"]), name="inputspec")
# Input threshold
input_node.inputs.threshold = threshold
# Define main input/function node
# Degree centrality
if method_option == "degree":
afni_centrality_node = pe.Node(
DegreeCentrality(environ={"OMP_NUM_THREADS": str(num_threads)}), name="afni_centrality"
)
afni_centrality_node.inputs.out_file = "degree_centrality_merged.nii.gz"
out_names = ("degree_centrality_binarize", "degree_centrality_weighted")
# Eigenvector centrality
elif method_option == "eigenvector":
afni_centrality_node = pe.Node(ECM(environ={"OMP_NUM_THREADS": str(num_threads)}), name="afni_centrality")
afni_centrality_node.inputs.out_file = "eigenvector_centrality_merged.nii.gz"
afni_centrality_node.inputs.memory = memory_gb # 3dECM input only
out_names = ("eigenvector_centrality_binarize", "eigenvector_centrality_weighted")
# lFCD
elif method_option == "lfcd":
afni_centrality_node = pe.Node(LFCD(environ={"OMP_NUM_THREADS": str(num_threads)}), name="afni_centrality")
afni_centrality_node.inputs.out_file = "lfcd_merged.nii.gz"
out_names = ("lfcd_binarize", "lfcd_weighted")
# Limit its num_threads and memory via MultiProc plugin
afni_centrality_node.interface.num_threads = num_threads
afni_centrality_node.interface.estimated_memory_gb = memory_gb
# Connect input image and mask tempalte
centrality_wf.connect(input_node, "in_file", afni_centrality_node, "in_file")
centrality_wf.connect(input_node, "template", afni_centrality_node, "mask")
# If we're doing significan thresholding, convert to correlation
if threshold_option == "significance":
# Check and (possibly) conver threshold
convert_thr_node = pe.Node(
util.Function(
input_names=["datafile", "p_value", "two_tailed"],
output_names=["rvalue_threshold"],
function=utils.convert_pvalue_to_r,
),
name="convert_threshold",
)
# Wire workflow to connect in conversion node
centrality_wf.connect(input_node, "in_file", convert_thr_node, "datafile")
centrality_wf.connect(input_node, "threshold", convert_thr_node, "p_value")
centrality_wf.connect(convert_thr_node, "rvalue_threshold", afni_centrality_node, "thresh")
# Sparsity thresholding
elif threshold_option == "sparsity":
# Check to make sure it's not lFCD
if method_option == "lfcd":
err_msg = "Sparsity thresholding is not supported for lFCD"
raise Exception(err_msg)
# Otherwise, connect threshold to sparsity input
centrality_wf.connect(input_node, "threshold", afni_centrality_node, "sparsity")
# Correlation thresholding
elif threshold_option == "correlation":
centrality_wf.connect(input_node, "threshold", afni_centrality_node, "thresh")
# Need to seprate sub-briks
sep_subbriks_node = pe.Node(
util.Function(
input_names=["nifti_file", "out_names"], output_names=["output_niftis"], function=utils.sep_nifti_subbriks
),
name="sep_nifti_subbriks",
)
sep_subbriks_node.inputs.out_names = out_names
# Connect the degree centrality output image to seperate subbriks node
centrality_wf.connect(afni_centrality_node, "out_file", sep_subbriks_node, "nifti_file")
# Define outputs node
output_node = pe.Node(util.IdentityInterface(fields=["outfile_list", "oned_output"]), name="outputspec")
centrality_wf.connect(sep_subbriks_node, "output_niftis", output_node, "outfile_list")
# Return the centrality workflow
return centrality_wf
def create_afni_centrality_wf(wf_name, method_option, threshold_option,
threshold, num_threads=1, memory_gb=1.0):
'''
Function to create the afni-based centrality workflow
Parameters
----------
wf_name : string
the name of the workflow
method_option : string
'degree', 'eigenvector', or 'lfcd'
threshold_option : string
'significance', 'sparsity', or 'correlation'
threshold : float
the threshold value for thresholding the similarity matrix
num_threads : integer (optional); default=1
the number of threads to utilize for centrality computation
memory_gb : float (optional); default=1.0
the amount of memory the centrality calculation will take (GB)
Returns
-------
centrality_wf : nipype Workflow
the initialized nipype workflow for the afni centrality command
'''
# Import packages
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import CPAC.network_centrality.utils as utils
# Check the centrality parameters
test_thresh = threshold
if threshold_option == 'sparsity':
test_thresh = threshold/100.0
method_option, threshold_option = \
utils.check_centrality_params(method_option, threshold_option, test_thresh)
# Init variables
centrality_wf = pe.Workflow(name=wf_name)
# Create inputspec node
input_node = pe.Node(util.IdentityInterface(fields=['in_file',
'template',
'threshold']),
name='inputspec')
# Input threshold
input_node.inputs.threshold = threshold
# Define main input/function node
# Degree centrality
if method_option == 'degree':
afni_centrality_node = \
pe.Node(DegreeCentrality(environ={'OMP_NUM_THREADS' : str(num_threads)}),
name='afni_centrality', mem_gb=memory_gb)
afni_centrality_node.inputs.out_file = 'degree_centrality_merged.nii.gz'
out_names = ('degree_centrality_binarize', 'degree_centrality_weighted')
# Eigenvector centrality
elif method_option == 'eigenvector':
afni_centrality_node = \
pe.Node(ECM(environ={'OMP_NUM_THREADS' : str(num_threads)}),
name='afni_centrality', mem_gb=memory_gb)
afni_centrality_node.inputs.out_file = 'eigenvector_centrality_merged.nii.gz'
afni_centrality_node.inputs.memory = memory_gb # 3dECM input only
out_names = ('eigenvector_centrality_binarize',
'eigenvector_centrality_weighted')
# lFCD
elif method_option == 'lfcd':
afni_centrality_node = \
pe.Node(LFCD(environ={'OMP_NUM_THREADS' : str(num_threads)}),
name='afni_centrality', mem_gb=memory_gb)
afni_centrality_node.inputs.out_file = 'lfcd_merged.nii.gz'
out_names = ('lfcd_binarize', 'lfcd_weighted')
# Limit its num_threads and memory via MultiProc plugin
afni_centrality_node.interface.num_threads = num_threads
# Connect input image and mask tempalte
centrality_wf.connect(input_node, 'in_file',
afni_centrality_node, 'in_file')
centrality_wf.connect(input_node, 'template',
afni_centrality_node, 'mask')
# If we're doing significan thresholding, convert to correlation
if threshold_option == 'significance':
# Check and (possibly) conver threshold
convert_thr_node = pe.Node(util.Function(input_names=['datafile',
'p_value',
'two_tailed'],
output_names=['rvalue_threshold'],
function=utils.convert_pvalue_to_r),
name='convert_threshold')
# Wire workflow to connect in conversion node
centrality_wf.connect(input_node, 'in_file',
convert_thr_node, 'datafile')
centrality_wf.connect(input_node, 'threshold',
convert_thr_node, 'p_value')
centrality_wf.connect(convert_thr_node, 'rvalue_threshold',
afni_centrality_node, 'thresh')
# Sparsity thresholding
elif threshold_option == 'sparsity':
# Check to make sure it's not lFCD
if method_option == 'lfcd':
err_msg = 'Sparsity thresholding is not supported for lFCD'
raise Exception(err_msg)
# Otherwise, connect threshold to sparsity input
centrality_wf.connect(input_node, 'threshold',
afni_centrality_node, 'sparsity')
# Correlation thresholding
elif threshold_option == 'correlation':
centrality_wf.connect(input_node, 'threshold',
afni_centrality_node, 'thresh')
# Need to seprate sub-briks
sep_subbriks_node = \
pe.Node(util.Function(input_names=['nifti_file', 'out_names'],
output_names=['output_niftis'],
function=utils.sep_nifti_subbriks),
name='sep_nifti_subbriks')
sep_subbriks_node.inputs.out_names = out_names
# Connect the degree centrality output image to seperate subbriks node
centrality_wf.connect(afni_centrality_node, 'out_file',
sep_subbriks_node, 'nifti_file')
# Define outputs node
output_node = pe.Node(util.IdentityInterface(fields=['outfile_list',
'oned_output']),
name='outputspec')
centrality_wf.connect(sep_subbriks_node, 'output_niftis',
output_node, 'outfile_list')
# Return the centrality workflow
return centrality_wf
def calc_centrality(in_file, template, method_option, threshold_option,
threshold, allocated_memory):
'''
Function to calculate centrality and map them to a nifti file
Parameters
----------
in_file : string (nifti file)
path to subject data file
template : string (nifti file)
path to mask/parcellation unit
method_option : string
accepted values are 'degree centrality', 'eigenvector centrality', and
'lfcd'
threshold_option : string
accepted values are: 'significance', 'sparsity', and 'correlation'
threshold : float
pvalue/sparsity_threshold/threshold value
allocated_memory : string
amount of memory allocated to degree centrality
Returns
-------
out_list : list
list containing out mapped centrality images
'''
# Import packages
from CPAC.network_centrality import load,\
get_centrality_by_rvalue,\
get_centrality_by_sparsity,\
get_centrality_fast,\
map_centrality_matrix,\
calc_blocksize,\
convert_pvalue_to_r
from CPAC.network_centrality.utils import check_centrality_params
from CPAC.cwas.subdist import norm_cols
# First check input parameters and get proper formatted method/thr options
method_option, threshold_option = \
check_centrality_params(method_option, threshold_option, threshold)
# Init variables
out_list = []
ts, aff, mask, t_type, scans = load(in_file, template)
# If we're doing degree sparsity
if method_option == 'degree' and threshold_option == 'sparsity':
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
sparsity_thresh=threshold)
# Otherwise
elif method_option == 'eigenvector':
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
include_full_matrix=True)
# Otherwise, compute blocksize with regards to available memory
else:
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
include_full_matrix=False)
# Normalize the timeseries for easy dot-product correlation calc.
ts_normd = norm_cols(ts.T)
# P-value threshold centrality
if threshold_option == 'significance':
r_value = convert_pvalue_to_r(in_file, threshold, two_tailed=False)
centrality_matrix = get_centrality_by_rvalue(ts_normd,
mask,
method_option,
r_value,
block_size)
# Sparsity threshold
elif threshold_option == 'sparsity':
centrality_matrix = get_centrality_by_sparsity(ts_normd,
method_option,
threshold,
block_size)
# R-value threshold centrality
elif threshold_option == 'correlation':
centrality_matrix = get_centrality_by_rvalue(ts_normd,
mask,
method_option,
threshold,
block_size)
# For fast approach (no thresholding)
elif threshold_option == 3:
centrality_matrix = get_centrality_fast(ts, method_option)
# Otherwise, incorrect input for threshold_option
else:
err_msg = 'Threshold option: %s not supported for network centrality '\
'measure: %s; fix this in the pipeline config'\
% (str(threshold_option), str(method_option))
raise Exception(err_msg)
# Map the arrays back to images
for mat in centrality_matrix:
centrality_image = map_centrality_matrix(mat, aff, mask, t_type)
out_list.append(centrality_image)
# Finally return
return out_list