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')
def dwi_preproc(subject_list, base_directory, out_directory, template_directory):
# Loading required packages
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
import nipype.interfaces.dipy as dipy
from own_nipype import DipyDenoise as denoise
from own_nipype import AdditionalDTIMeasures
from own_nipype import ants_QuickSyN
from nipype.interfaces.ants.segmentation import CorticalThickness
from nipype import SelectFiles
import os
#====================================
# Defining the nodes for the workflow
# 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(T1='{subject_id}/anat/{subject_id}_T1w.nii.gz',
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)
#====================================
# Diffusion-data
# 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
fslroi = pe.Node(interface=fsl.ExtractROI(), name='extract_b0')
fslroi.inputs.t_min=0
fslroi.inputs.t_size=1
# Create a brain mask
bet = pe.Node(interface=fsl.BET(frac=0.3,robust=False,mask=True), name='bet')
# Fitting the diffusion tensor model
dtifit = pe.Node(interface=fsl.DTIFit(), name='dtifit')
# Getting AD and RD
get_rd = pe.Node(interface=AdditionalDTIMeasures(), name='get_rd')
# Calculating transform from subject to common space
quicksyn = pe.Node(interface=ants_QuickSyN(), name='quicksyn')
quicksyn.inputs.fixed_image = template_directory + '/T_template_BrainCerebellum.nii.gz'
quicksyn.inputs.image_dimensions = 3
quicksyn.inputs.output_prefix = 'NKIspace_'
quicksyn.inputs.transform_type = 's'
#====================================
# T1-weighted data
corticalthickness = pe.Node(interface=CorticalThickness(), name='corticalthickness')
corticalthickness.inputs.dimension = 3
corticalthickness.inputs.brain_template = template_directory + '/T_template.nii.gz'
corticalthickness.inputs.brain_probability_mask = template_directory + '/T_template_BrainCerebellumProbabilityMask.nii.gz'
corticalthickness.inputs.segmentation_priors = sorted([template_directory + '/Priors/' + prior for prior in os.listdir(template_directory + '/Priors/')])
corticalthickness.inputs.t1_registration_template = template_directory + '/T_template_BrainCerebellum.nii.gz'
#====================================
# Setting up the workflow
dwi_preproc = pe.Workflow(name='dwi_preproc')
dwi_preproc.connect(infosource, 'subject_id', selectfiles, 'subject_id')
# Diffusion data
dwi_preproc.connect(selectfiles, 'dwi', denoise, 'in_file')
dwi_preproc.connect(denoise, 'out_file', eddycorrect, 'in_file')
dwi_preproc.connect(eddycorrect, 'eddy_corrected', resample, 'in_file')
dwi_preproc.connect(resample, 'out_file', fslroi, 'in_file')
dwi_preproc.connect(fslroi, 'roi_file', bet, 'in_file')
dwi_preproc.connect(infosource, 'subject_id', dtifit, 'base_name')
dwi_preproc.connect(resample, 'out_file', dtifit, 'dwi')
dwi_preproc.connect(selectfiles, 'bvec', dtifit, 'bvecs')
dwi_preproc.connect(selectfiles, 'bval', dtifit, 'bvals')
dwi_preproc.connect(bet, 'mask_file', dtifit, 'mask')
dwi_preproc.connect(dtifit, 'L1', get_rd, 'L1')
dwi_preproc.connect(dtifit, 'L2', get_rd, 'L2')
dwi_preproc.connect(dtifit, 'L3', get_rd, 'L3')
dwi_preproc.connect(dtifit, 'FA', quicksyn, 'moving_image')
# T1w data
dwi_preproc.connect(selectfiles, 'T1', corticalthickness, 'anatomical_image')
#====================================
# Running the workflow
dwi_preproc.base_dir = os.path.abspath(out_directory)
dwi_preproc.write_graph()
dwi_preproc.run(plugin='PBSGraph')
def dwi_preproc_minimal(subject_list,base_directory,out_directory): """ This function implements the dwi preprocessing workflow. The function takes a list of subject IDs and their parent directory - the data is expected to be stored according to the Brain Imaging Data Structure (BIDS). It then performs the preprocessing steps: denoising with non-local means (http://nipy.org/dipy/examples_built/denoise_nlmeans.html), FSL eddy_correct to correct for eddy current and participant motion, resampling to 1mm isotropic resolution with trilinear interpolation, extraction of the first b0 volume, brain extraction with FSL bet, and fitting of the diffusion tensor model with FSL dtifit inputs: subject list: python list of string with the subject IDs base_directory: directory in which the raw data is stored (diffusion weighted volume, bval and bvecs file) out_directory: directory where is output will be stored written by Joe Bathelt,PhD MRC Cognition & Brain Sciences Unit [email protected] """ #============================================================== # 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 from own_nipype import DipyDenoise as denoise from nipype import SelectFiles import os nodes = list() #==================================== # Defining the nodes for the workflow # 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) nodes.append(selectfiles) # Denoising denoise = pe.Node(interface=denoise(), name='denoise') nodes.append(denoise) # Eddy-current and motion correction eddycorrect = pe.Node(interface=fsl.epi.EddyCorrect(), name='eddycorrect') eddycorrect.inputs.ref_num = 0 nodes.append(eddycorrect) # Extract b0 image fslroi = pe.Node(interface=fsl.ExtractROI(),name='extract_b0') fslroi.inputs.t_min=0 fslroi.inputs.t_size=1 nodes.append(fslroi) # Create a brain mask bet = pe.Node(interface=fsl.BET(frac=0.3,robust=False,mask=True),name='bet') nodes.append(bet) # Erode brain mask erode = pe.Node(interface=fsl.maths.ErodeImage(),name='erode') nodes.append(erode) # Fitting the diffusion tensor model dtifit = pe.Node(interface=fsl.DTIFit(),name='dtifit') nodes.append(dtifit) #==================================== # Setting up the workflow dwi_preproc_minimal = pe.Workflow(name='dwi_preproc_minimal') dwi_preproc_minimal.add_nodes(nodes) dwi_preproc_minimal.connect(infosource, 'subject_id', selectfiles, 'subject_id') dwi_preproc_minimal.connect(selectfiles, 'dwi', eddycorrect, 'in_file') dwi_preproc_minimal.connect(eddycorrect, 'eddy_corrected', fslroi, 'in_file') dwi_preproc_minimal.connect(fslroi, 'roi_file', bet, 'in_file') dwi_preproc_minimal.connect(infosource, 'subject_id',dtifit,'base_name') dwi_preproc_minimal.connect(eddycorrect, 'eddy_corrected', dtifit,'dwi') dwi_preproc_minimal.connect(selectfiles, 'bvec',dtifit,'bvecs') dwi_preproc_minimal.connect(selectfiles, 'bval',dtifit,'bvals') dwi_preproc_minimal.connect(bet,'mask_file',dtifit,'mask') dwi_preproc_minimal.connect(bet,'mask_file',erode,'in_file') #==================================== # Running the workflow dwi_preproc_minimal.base_dir = os.path.abspath(out_directory) dwi_preproc_minimal.write_graph() dwi_preproc_minimal.run()
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 FAconnectome as connectome
from own_nipype import Extractb0 as extract_b0
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/MNI152_T1_1mm_brain.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')
#====================================
# 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')
#====================================
# Running the workflow
fa_connectome.base_dir = os.path.abspath(out_directory)
fa_connectome.write_graph()
fa_connectome.run(plugin='MultiProc')
def CSD_probablistic_tractography_MRTrix(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
import nipype.interfaces.diffusion_toolkit as dtk
import nipype.algorithms.misc as misc
from nipype import SelectFiles
import os
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)
nodes.append(selectfiles)
# Denoising
denoise = pe.Node(interface=denoise(), name='denoise')
nodes.append(denoise)
# Eddy-current and motion correction
eddycorrect = pe.Node(interface=fsl.epi.EddyCorrect(), name='eddycorrect')
eddycorrect.inputs.ref_num = 0
nodes.append(eddycorrect)
# Extract b0 image
fslroi = pe.Node(interface=fsl.ExtractROI(),name='extract_b0')
fslroi.inputs.t_min=0
fslroi.inputs.t_size=1
nodes.append(fslroi)
# 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')
nodes.append(bet)
# Eroding the brain mask
threshold_b0 = pe.Node(interface=mrt.Threshold(), name='threshold_b0')
median3d = pe.Node(interface=mrt.MedianFilter3D(), name='median3d')
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')
nodes.append(smooth)
#====================================
# Setting up the workflow
csd_prob = pe.Workflow(name='CSD_probablistic_tractography')
csd_prob.add_nodes(nodes)
# Reading in files
csd_prob.connect(infosource, 'subject_id', selectfiles, 'subject_id')
# Denoising
csd_prob.connect(selectfiles, 'dwi', denoise, 'in_file')
# Eddy current and motion correction
csd_prob.connect(denoise, 'out_file',eddycorrect, 'in_file')
csd_prob.connect(eddycorrect, 'eddy_corrected', fslroi, 'in_file')
# Brain extraction
csd_prob.connect(fslroi, 'roi_file', bet, 'in_file')
# Creating tensor maps
csd_prob.connect(selectfiles,'bval',fsl2mrtrix,'bval_file')
csd_prob.connect(selectfiles,'bvec',fsl2mrtrix,'bvec_file')
csd_prob.connect(eddycorrect,'eddy_corrected',gunzip,'in_file')
csd_prob.connect(gunzip,'out_file',dwi2tensor,'in_file')
csd_prob.connect(fsl2mrtrix,'encoding_file',dwi2tensor,'encoding_file')
csd_prob.connect(dwi2tensor,'tensor',tensor2vector,'in_file')
csd_prob.connect(dwi2tensor,'tensor',tensor2adc,'in_file')
csd_prob.connect(dwi2tensor,'tensor',tensor2fa,'in_file')
csd_prob.connect(tensor2fa,'FA', MRmult_merge, 'in1')
# Thresholding to create a mask of single fibre voxels
csd_prob.connect(gunzip, 'out_file', threshold_b0, 'in_file')
csd_prob.connect(threshold_b0, 'out_file', median3d, 'in_file')
csd_prob.connect(median3d, 'out_file', erode_mask_firstpass, 'in_file')
csd_prob.connect(erode_mask_firstpass, 'out_file', erode_mask_secondpass, 'in_file')
csd_prob.connect(erode_mask_secondpass,'out_file', MRmult_merge, 'in2')
csd_prob.connect(MRmult_merge, 'out', MRmultiply, 'in_files')
csd_prob.connect(MRmultiply, 'out_file', threshold_FA, 'in_file')
# Create seed mask
csd_prob.connect(gunzip, 'out_file', gen_WM_mask, 'in_file')
csd_prob.connect(bet, 'mask_file', gunzip2, 'in_file')
csd_prob.connect(gunzip2, 'out_file', gen_WM_mask, 'binary_mask')
csd_prob.connect(fsl2mrtrix, 'encoding_file', gen_WM_mask, 'encoding_file')
csd_prob.connect(gen_WM_mask, 'WMprobabilitymap', threshold_wmmask, 'in_file')
# Estimate response
csd_prob.connect(gunzip, 'out_file', estimateresponse, 'in_file')
csd_prob.connect(fsl2mrtrix, 'encoding_file', estimateresponse, 'encoding_file')
csd_prob.connect(threshold_FA, 'out_file', estimateresponse, 'mask_image')
# CSD calculation
csd_prob.connect(gunzip, 'out_file', csdeconv, 'in_file')
csd_prob.connect(gen_WM_mask, 'WMprobabilitymap', csdeconv, 'mask_image')
csd_prob.connect(estimateresponse, 'response', csdeconv, 'response_file')
csd_prob.connect(fsl2mrtrix, 'encoding_file', csdeconv, 'encoding_file')
# Running the tractography
csd_prob.connect(threshold_wmmask, "out_file", probCSDstreamtrack, "seed_file")
csd_prob.connect(csdeconv, "spherical_harmonics_image", probCSDstreamtrack, "in_file")
csd_prob.connect(gunzip, "out_file", tck2trk, "image_file")
csd_prob.connect(probCSDstreamtrack, "tracked", tck2trk, "in_file")
# Smoothing the trackfile
csd_prob.connect(tck2trk, 'out_file',smooth,'track_file')
#====================================
# Running the workflow
csd_prob.base_dir = os.path.abspath(out_directory)
csd_prob.write_graph()
csd_prob.run()
def CSD_deterministic_tractography(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
from own_nipype import CSDdet as csdet
from own_nipype import DipyDenoise as denoise
import nipype.interfaces.diffusion_toolkit as dtk
from nipype import SelectFiles
import os
nodes = list()
#====================================
# Defining the nodes for the workflow
# 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)
nodes.append(selectfiles)
# Denoising
denoise = pe.Node(interface=denoise(), name='denoise')
nodes.append(denoise)
# Eddy-current and motion correction
eddycorrect = pe.Node(interface=fsl.epi.EddyCorrect(), name='eddycorrect')
eddycorrect.inputs.ref_num = 0
nodes.append(eddycorrect)
# Upsampling
resample = pe.Node(interface=dipy.Resample(interp=3,vox_size=(1.,1.,1.)), name='resample')
nodes.append(resample)
# Extract b0 image
fslroi = pe.Node(interface=fsl.ExtractROI(),name='extract_b0')
fslroi.inputs.t_min=0
fslroi.inputs.t_size=1
nodes.append(fslroi)
# Create a brain mask
bet = pe.Node(interface=fsl.BET(frac=0.3,robust=False,mask=True),name='bet')
nodes.append(bet)
# Erode brain mask
erode = pe.Node(interface=fsl.maths.ErodeImage(),name='erode')
nodes.append(erode)
# Fitting the diffusion tensor model
dtifit = pe.Node(interface=fsl.DTIFit(),name='dtifit')
nodes.append(dtifit)
# CSD deterministic tractography
csdet = pe.Node(interface=csdet(),name='csdet')
nodes.append(csdet)
# smoothing the tracts
smooth = pe.Node(interface=dtk.SplineFilter(step_length=0.5), name='smooth')
nodes.append(smooth)
#====================================
# Setting up the workflow
csd_det = pe.Workflow(name='dwi_preproc_minimal')
csd_det.add_nodes(nodes)
csd_det.connect(infosource, 'subject_id', selectfiles, 'subject_id')
csd_det.connect(selectfiles, 'dwi', denoise, 'in_file')
csd_det.connect(denoise, 'out_file',eddycorrect, 'in_file')
csd_det.connect(eddycorrect, 'eddy_corrected', resample, 'in_file')
csd_det.connect(resample, 'out_file', fslroi, 'in_file')
csd_det.connect(fslroi, 'roi_file', bet, 'in_file')
csd_det.connect(infosource, 'subject_id',dtifit,'base_name')
csd_det.connect(resample, 'out_file', dtifit,'dwi')
csd_det.connect(selectfiles, 'bvec',dtifit,'bvecs')
csd_det.connect(selectfiles, 'bval',dtifit,'bvals')
csd_det.connect(bet,'mask_file',dtifit,'mask')
csd_det.connect(bet,'mask_file',erode,'in_file')
csd_det.connect(erode,'out_file',csdet,'brain_mask')
csd_det.connect(dtifit,'FA',csdet,'FA_file')
csd_det.connect(selectfiles,'bval',csdet,'bval')
csd_det.connect(selectfiles,'bvec',csdet,'bvec')
csd_det.connect(eddycorrect, 'eddy_corrected',csdet,'in_file')
csd_det.connect(csdet, 'out_file',smooth,'track_file')
#====================================
# Running the workflow
csd_det.base_dir = os.path.abspath(out_directory)
csd_det.write_graph()
csd_det.run()
