MRtrix's online documentation b-values and b-vectors stored in FSL's format are converted into a single encoding file for MRTrix. """ fsl2mrtrix = pe.Node(interface=mrtrix.FSL2MRTrix(),name='fsl2mrtrix') """ Tensors are fitted to each voxel in the diffusion-weighted image and from these three maps are created: * Major eigenvector in each voxel * Apparent diffusion coefficient * Fractional anisotropy """ gunzip = pe.Node(interface=misc.Gunzip(), name='gunzip') dwi2tensor = pe.Node(interface=mrtrix.DWI2Tensor(),name='dwi2tensor') tensor2vector = pe.Node(interface=mrtrix.Tensor2Vector(),name='tensor2vector') tensor2adc = pe.Node(interface=mrtrix.Tensor2ApparentDiffusion(),name='tensor2adc') tensor2fa = pe.Node(interface=mrtrix.Tensor2FractionalAnisotropy(),name='tensor2fa') """ These nodes are used to create a rough brain mask from the b0 image. The b0 image is extracted from the original diffusion-weighted image, put through a simple thresholding routine, and smoothed using a 3x3 median filter. """ MRconvert = pe.Node(interface=mrtrix.MRConvert(),name='MRconvert') MRconvert.inputs.extract_at_axis = 3 MRconvert.inputs.extract_at_coordinate = [0] threshold_b0 = pe.Node(interface=mrtrix.Threshold(),name='threshold_b0')
def FA_connectome(subject_list,base_directory,out_directory):
#==============================================================
# Loading required packages
import nipype.interfaces.io as nio
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
import nipype.interfaces.dipy as dipy
import nipype.interfaces.mrtrix as mrt
from own_nipype import DipyDenoise as denoise
from own_nipype import trk_Coreg as trkcoreg
from own_nipype import TXT2PCK as txt2pck
from own_nipype import FAconnectome as connectome
from own_nipype import Extractb0 as extract_b0
import nipype.interfaces.cmtk as cmtk
import nipype.interfaces.diffusion_toolkit as dtk
import nipype.algorithms.misc as misc
from nipype import SelectFiles
import os
registration_reference = os.environ['FSLDIR'] + '/data/standard/FMRIB58_FA_1mm.nii.gz'
nodes = list()
#====================================
# Defining the nodes for the workflow
# Utility nodes
gunzip = pe.Node(interface=misc.Gunzip(), name='gunzip')
gunzip2 = pe.Node(interface=misc.Gunzip(), name='gunzip2')
fsl2mrtrix = pe.Node(interface=mrt.FSL2MRTrix(invert_x=True),name='fsl2mrtrix')
# Getting the subject ID
infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']),name='infosource')
infosource.iterables = ('subject_id', subject_list)
# Getting the relevant diffusion-weighted data
templates = dict(dwi='{subject_id}/dwi/{subject_id}_dwi.nii.gz',
bvec='{subject_id}/dwi/{subject_id}_dwi.bvec',
bval='{subject_id}/dwi/{subject_id}_dwi.bval')
selectfiles = pe.Node(SelectFiles(templates),
name='selectfiles')
selectfiles.inputs.base_directory = os.path.abspath(base_directory)
# Denoising
denoise = pe.Node(interface=denoise(), name='denoise')
# Eddy-current and motion correction
eddycorrect = pe.Node(interface=fsl.epi.EddyCorrect(), name='eddycorrect')
eddycorrect.inputs.ref_num = 0
# Upsampling
resample = pe.Node(interface=dipy.Resample(interp=3,vox_size=(1.,1.,1.)), name='resample')
# Extract b0 image
extract_b0 = pe.Node(interface=extract_b0(),name='extract_b0')
# Fitting the diffusion tensor model
dwi2tensor = pe.Node(interface=mrt.DWI2Tensor(), name='dwi2tensor')
tensor2vector = pe.Node(interface=mrt.Tensor2Vector(), name='tensor2vector')
tensor2adc = pe.Node(interface=mrt.Tensor2ApparentDiffusion(), name='tensor2adc')
tensor2fa = pe.Node(interface=mrt.Tensor2FractionalAnisotropy(), name='tensor2fa')
# Create a brain mask
bet = pe.Node(interface=fsl.BET(frac=0.3,robust=False,mask=True),name='bet')
# Eroding the brain mask
erode_mask_firstpass = pe.Node(interface=mrt.Erode(), name='erode_mask_firstpass')
erode_mask_secondpass = pe.Node(interface=mrt.Erode(), name='erode_mask_secondpass')
MRmultiply = pe.Node(interface=mrt.MRMultiply(), name='MRmultiply')
MRmult_merge = pe.Node(interface=util.Merge(2), name='MRmultiply_merge')
threshold_FA = pe.Node(interface=mrt.Threshold(absolute_threshold_value = 0.7), name='threshold_FA')
# White matter mask
gen_WM_mask = pe.Node(interface=mrt.GenerateWhiteMatterMask(), name='gen_WM_mask')
threshold_wmmask = pe.Node(interface=mrt.Threshold(absolute_threshold_value = 0.4), name='threshold_wmmask')
# CSD probabilistic tractography
estimateresponse = pe.Node(interface=mrt.EstimateResponseForSH(maximum_harmonic_order = 8), name='estimateresponse')
csdeconv = pe.Node(interface=mrt.ConstrainedSphericalDeconvolution(maximum_harmonic_order = 8), name='csdeconv')
# Tracking
probCSDstreamtrack = pe.Node(interface=mrt.ProbabilisticSphericallyDeconvolutedStreamlineTrack(), name='probCSDstreamtrack')
probCSDstreamtrack.inputs.inputmodel = 'SD_PROB'
probCSDstreamtrack.inputs.desired_number_of_tracks = 150000
tck2trk = pe.Node(interface=mrt.MRTrix2TrackVis(), name='tck2trk')
# smoothing the tracts
smooth = pe.Node(interface=dtk.SplineFilter(step_length=0.5), name='smooth')
# Co-registration with MNI space
mrconvert = pe.Node(mrt.MRConvert(extension='nii'), name='mrconvert')
flt = pe.Node(interface=fsl.FLIRT(reference=registration_reference, dof=12, cost_func='corratio'), name='flt')
# Moving tracts to common space
trkcoreg = pe.Node(interface=trkcoreg(reference=registration_reference),name='trkcoreg')
# calcuating the connectome matrix
calc_matrix = pe.Node(interface=connectome(ROI_file='/home/jb07/Desktop/aal.nii.gz'),name='calc_matrix')
# Converting the adjacency matrix from txt to pck format
txt2pck = pe.Node(interface=txt2pck(), name='txt2pck')
# Calculate graph theory measures with NetworkX and CMTK
nxmetrics = pe.Node(interface=cmtk.NetworkXMetrics(treat_as_weighted_graph = True), name='nxmetrics')
#====================================
# Setting up the workflow
fa_connectome = pe.Workflow(name='FA_connectome')
# Reading in files
fa_connectome.connect(infosource, 'subject_id', selectfiles, 'subject_id')
# Denoising
fa_connectome.connect(selectfiles, 'dwi', denoise, 'in_file')
# Eddy current and motion correction
fa_connectome.connect(denoise, 'out_file',eddycorrect, 'in_file')
fa_connectome.connect(eddycorrect, 'eddy_corrected', resample, 'in_file')
fa_connectome.connect(resample, 'out_file', extract_b0, 'in_file')
fa_connectome.connect(resample, 'out_file', gunzip,'in_file')
# Brain extraction
fa_connectome.connect(extract_b0, 'out_file', bet, 'in_file')
# Creating tensor maps
fa_connectome.connect(selectfiles,'bval',fsl2mrtrix,'bval_file')
fa_connectome.connect(selectfiles,'bvec',fsl2mrtrix,'bvec_file')
fa_connectome.connect(gunzip,'out_file',dwi2tensor,'in_file')
fa_connectome.connect(fsl2mrtrix,'encoding_file',dwi2tensor,'encoding_file')
fa_connectome.connect(dwi2tensor,'tensor',tensor2vector,'in_file')
fa_connectome.connect(dwi2tensor,'tensor',tensor2adc,'in_file')
fa_connectome.connect(dwi2tensor,'tensor',tensor2fa,'in_file')
fa_connectome.connect(tensor2fa,'FA', MRmult_merge, 'in1')
# Thresholding to create a mask of single fibre voxels
fa_connectome.connect(gunzip2, 'out_file', erode_mask_firstpass, 'in_file')
fa_connectome.connect(erode_mask_firstpass, 'out_file', erode_mask_secondpass, 'in_file')
fa_connectome.connect(erode_mask_secondpass,'out_file', MRmult_merge, 'in2')
fa_connectome.connect(MRmult_merge, 'out', MRmultiply, 'in_files')
fa_connectome.connect(MRmultiply, 'out_file', threshold_FA, 'in_file')
# Create seed mask
fa_connectome.connect(gunzip, 'out_file', gen_WM_mask, 'in_file')
fa_connectome.connect(bet, 'mask_file', gunzip2, 'in_file')
fa_connectome.connect(gunzip2, 'out_file', gen_WM_mask, 'binary_mask')
fa_connectome.connect(fsl2mrtrix, 'encoding_file', gen_WM_mask, 'encoding_file')
fa_connectome.connect(gen_WM_mask, 'WMprobabilitymap', threshold_wmmask, 'in_file')
# Estimate response
fa_connectome.connect(gunzip, 'out_file', estimateresponse, 'in_file')
fa_connectome.connect(fsl2mrtrix, 'encoding_file', estimateresponse, 'encoding_file')
fa_connectome.connect(threshold_FA, 'out_file', estimateresponse, 'mask_image')
# CSD calculation
fa_connectome.connect(gunzip, 'out_file', csdeconv, 'in_file')
fa_connectome.connect(gen_WM_mask, 'WMprobabilitymap', csdeconv, 'mask_image')
fa_connectome.connect(estimateresponse, 'response', csdeconv, 'response_file')
fa_connectome.connect(fsl2mrtrix, 'encoding_file', csdeconv, 'encoding_file')
# Running the tractography
fa_connectome.connect(threshold_wmmask, "out_file", probCSDstreamtrack, "seed_file")
fa_connectome.connect(csdeconv, "spherical_harmonics_image", probCSDstreamtrack, "in_file")
fa_connectome.connect(gunzip, "out_file", tck2trk, "image_file")
fa_connectome.connect(probCSDstreamtrack, "tracked", tck2trk, "in_file")
# Smoothing the trackfile
fa_connectome.connect(tck2trk, 'out_file',smooth,'track_file')
# Co-registering FA with FMRIB58_FA_1mm standard space
fa_connectome.connect(MRmultiply,'out_file',mrconvert,'in_file')
fa_connectome.connect(mrconvert,'converted',flt,'in_file')
fa_connectome.connect(smooth,'smoothed_track_file',trkcoreg,'in_file')
fa_connectome.connect(mrconvert,'converted',trkcoreg,'FA_file')
fa_connectome.connect(flt,'out_matrix_file',trkcoreg,'transfomation_matrix')
# Calculating the FA connectome
fa_connectome.connect(trkcoreg,'transformed_track_file',calc_matrix,'trackfile')
fa_connectome.connect(flt,'out_file',calc_matrix,'FA_file')
# Calculating graph measures
fa_connectome.connect(calc_matrix,'out_file',txt2pck,'in_file')
fa_connectome.connect(txt2pck,'out_file',nxmetrics,'in_file')
#====================================
# Running the workflow
fa_connectome.base_dir = os.path.abspath(out_directory)
fa_connectome.write_graph()
fa_connectome.run('PBSGraph')
get_session_informations.inputs.regressors = REGRESSORS
workflow.connect(datasource, 'events', get_session_informations, 'events_files')
workflow.connect(datasource, 'confounds_regressors', get_session_informations, 'confounds_regressors')
workflow.connect(datasource, 'stim_regressors', get_session_informations, 'stim_regressors')
# contrasts of interest
contrasts_of_interest = pe.Node(niu.Function(inputnames=['subject_id',
'conditions'],
output_names=['contrasts'],
function=_specify_contrast),
name='contrasts_of_interest')
contrasts_of_interest.inputs.conditions = CONDITIONS
workflow.connect(infosource, 'subject_id', contrasts_of_interest, 'subject_id')
# fmri model specifications
unzip_source = pe.MapNode(misc.Gunzip(),
iterfield=['in_file'],
name='unzip_source')
workflow.connect(datasource, 'func', unzip_source, 'in_file')
smooth = pe.Node(interface=spm.Smooth(fwhm=[8, 8, 8]),
name='smooth')
workflow.connect(unzip_source, 'out_file', smooth, 'in_files')
modelspec = pe.Node(interface=modelgen.SpecifySPMModel(),
name='modelspec')
modelspec.inputs.input_units = 'secs'
modelspec.inputs.output_units = 'secs'
modelspec.inputs.time_repetition = TR
modelspec.inputs.high_pass_filter_cutoff = HIGHPASS_CUTOFF
workflow.connect(get_session_informations, 'informations', modelspec, 'subject_info')