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 create_mrtrix_recon_flow(config):
flow = pe.Workflow(name="reconstruction")
inputnode = pe.Node(interface=util.IdentityInterface(fields=["diffusion","diffusion_resampled","wm_mask_resampled"]),name="inputnode")
outputnode = pe.Node(interface=util.IdentityInterface(fields=["DWI","FA","eigVec","RF","grad"],mandatory_inputs=True),name="outputnode")
# Flip gradient table
flip_table = pe.Node(interface=flipTable(),name='flip_table')
flip_table.inputs.table = config.gradient_table
flip_table.inputs.flipping_axis = config.flip_table_axis
flip_table.inputs.delimiter = ' '
flip_table.inputs.header_lines = 0
flip_table.inputs.orientation = 'v'
flow.connect([
(flip_table,outputnode,[("table","grad")]),
])
# Tensor
mrtrix_tensor = pe.Node(interface=mrtrix.DWI2Tensor(),name='mrtrix_make_tensor')
flow.connect([
(inputnode, mrtrix_tensor,[('diffusion_resampled','in_file')]),
(flip_table,mrtrix_tensor,[("table","encoding_file")]),
])
# Tensor -> FA map
mrtrix_FA = pe.Node(interface=mrtrix.Tensor2FractionalAnisotropy(),name='mrtrix_FA')
convert_FA = pe.Node(interface=mrtrix.MRConvert(out_filename="FA.nii"),name='convert_FA')
flow.connect([
(mrtrix_tensor,mrtrix_FA,[('tensor','in_file')]),
(mrtrix_FA,convert_FA,[('FA','in_file')]),
(convert_FA,outputnode,[("converted","FA")])
])
# Tensor -> Eigenvectors
mrtrix_eigVectors = pe.Node(interface=mrtrix.Tensor2Vector(),name="mrtrix_eigenvectors")
flow.connect([
(mrtrix_tensor,mrtrix_eigVectors,[('tensor','in_file')]),
(mrtrix_eigVectors,outputnode,[('vector','eigVec')])
])
# Constrained Spherical Deconvolution
if config.local_model:
# Compute single fiber voxel mask
mrtrix_erode = pe.Node(interface=mrtrix.Erode(),name="mrtrix_erode")
mrtrix_erode.inputs.number_of_passes = 3
mrtrix_mul_eroded_FA = pe.Node(interface=MRtrix_mul(),name='mrtrix_mul_eroded_FA')
mrtrix_mul_eroded_FA.inputs.out_filename = "diffusion_resampled_tensor_FA_masked.mif"
mrtrix_thr_FA = pe.Node(interface=mrtrix.Threshold(),name='mrtrix_thr')
mrtrix_thr_FA.inputs.absolute_threshold_value = config.single_fib_thr
flow.connect([
(inputnode,mrtrix_erode,[("wm_mask_resampled",'in_file')]),
(mrtrix_erode,mrtrix_mul_eroded_FA,[('out_file','input2')]),
(mrtrix_FA,mrtrix_mul_eroded_FA,[('FA','input1')]),
(mrtrix_mul_eroded_FA,mrtrix_thr_FA,[('out_file','in_file')])
])
# Compute single fiber response function
mrtrix_rf = pe.Node(interface=mrtrix.EstimateResponseForSH(),name="mrtrix_rf")
if config.lmax_order != 'Auto':
mrtrix_rf.inputs.maximum_harmonic_order = config.lmax_order
mrtrix_rf.inputs.normalise = config.normalize_to_B0
flow.connect([
(inputnode,mrtrix_rf,[("diffusion_resampled","in_file")]),
(mrtrix_thr_FA,mrtrix_rf,[("out_file","mask_image")]),
(flip_table,mrtrix_rf,[("table","encoding_file")]),
])
# Perform spherical deconvolution
mrtrix_CSD = pe.Node(interface=mrtrix.ConstrainedSphericalDeconvolution(),name="mrtrix_CSD")
mrtrix_CSD.inputs.normalise = config.normalize_to_B0
flow.connect([
(inputnode,mrtrix_CSD,[('diffusion_resampled','in_file')]),
(mrtrix_rf,mrtrix_CSD,[('response','response_file')]),
(mrtrix_rf,outputnode,[('response','RF')]),
(inputnode,mrtrix_CSD,[("wm_mask_resampled",'mask_image')]),
(flip_table,mrtrix_CSD,[("table","encoding_file")]),
(mrtrix_CSD,outputnode,[('spherical_harmonics_image','DWI')])
])
else:
flow.connect([
(inputnode,outputnode,[('diffusion_resampled','DWI')])
])
return flow
def create_mrtrix_dti_pipeline(name="dtiproc",
tractography_type='probabilistic'):
"""Creates a pipeline that does the same diffusion processing as in the
:doc:`../../users/examples/dmri_mrtrix_dti` example script. Given a diffusion-weighted image,
b-values, and b-vectors, the workflow will return the tractography
computed from spherical deconvolution and probabilistic streamline tractography
Example
-------
>>> dti = create_mrtrix_dti_pipeline("mrtrix_dti")
>>> dti.inputs.inputnode.dwi = 'data.nii'
>>> dti.inputs.inputnode.bvals = 'bvals'
>>> dti.inputs.inputnode.bvecs = 'bvecs'
>>> dti.run() # doctest: +SKIP
Inputs::
inputnode.dwi
inputnode.bvecs
inputnode.bvals
Outputs::
outputnode.fa
outputnode.tdi
outputnode.tracts_tck
outputnode.tracts_trk
outputnode.csdeconv
"""
inputnode = pe.Node(
interface=util.IdentityInterface(fields=["dwi", "bvecs", "bvals"]),
name="inputnode")
bet = pe.Node(interface=fsl.BET(), name="bet")
bet.inputs.mask = True
fsl2mrtrix = pe.Node(interface=mrtrix.FSL2MRTrix(), name='fsl2mrtrix')
fsl2mrtrix.inputs.invert_y = True
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')
erode_mask_firstpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_firstpass')
erode_mask_secondpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_secondpass')
threshold_b0 = pe.Node(interface=mrtrix.Threshold(), name='threshold_b0')
threshold_FA = pe.Node(interface=mrtrix.Threshold(), name='threshold_FA')
threshold_FA.inputs.absolute_threshold_value = 0.7
threshold_wmmask = pe.Node(interface=mrtrix.Threshold(),
name='threshold_wmmask')
threshold_wmmask.inputs.absolute_threshold_value = 0.4
MRmultiply = pe.Node(interface=mrtrix.MRMultiply(), name='MRmultiply')
MRmult_merge = pe.Node(interface=util.Merge(2), name='MRmultiply_merge')
median3d = pe.Node(interface=mrtrix.MedianFilter3D(), name='median3D')
MRconvert = pe.Node(interface=mrtrix.MRConvert(), name='MRconvert')
MRconvert.inputs.extract_at_axis = 3
MRconvert.inputs.extract_at_coordinate = [0]
csdeconv = pe.Node(interface=mrtrix.ConstrainedSphericalDeconvolution(),
name='csdeconv')
gen_WM_mask = pe.Node(interface=mrtrix.GenerateWhiteMatterMask(),
name='gen_WM_mask')
estimateresponse = pe.Node(interface=mrtrix.EstimateResponseForSH(),
name='estimateresponse')
if tractography_type == 'probabilistic':
CSDstreamtrack = pe.Node(
interface=mrtrix.
ProbabilisticSphericallyDeconvolutedStreamlineTrack(),
name='CSDstreamtrack')
else:
CSDstreamtrack = pe.Node(
interface=mrtrix.SphericallyDeconvolutedStreamlineTrack(),
name='CSDstreamtrack')
CSDstreamtrack.inputs.desired_number_of_tracks = 15000
tracks2prob = pe.Node(interface=mrtrix.Tracks2Prob(), name='tracks2prob')
tracks2prob.inputs.colour = True
tck2trk = pe.Node(interface=mrtrix.MRTrix2TrackVis(), name='tck2trk')
workflow = pe.Workflow(name=name)
workflow.base_output_dir = name
workflow.connect([(inputnode, fsl2mrtrix, [("bvecs", "bvec_file"),
("bvals", "bval_file")])])
workflow.connect([(inputnode, dwi2tensor, [("dwi", "in_file")])])
workflow.connect([(fsl2mrtrix, dwi2tensor, [("encoding_file",
"encoding_file")])])
workflow.connect([
(dwi2tensor, tensor2vector, [['tensor', 'in_file']]),
(dwi2tensor, tensor2adc, [['tensor', 'in_file']]),
(dwi2tensor, tensor2fa, [['tensor', 'in_file']]),
])
workflow.connect([(inputnode, MRconvert, [("dwi", "in_file")])])
workflow.connect([(MRconvert, threshold_b0, [("converted", "in_file")])])
workflow.connect([(threshold_b0, median3d, [("out_file", "in_file")])])
workflow.connect([(median3d, erode_mask_firstpass, [("out_file", "in_file")
])])
workflow.connect([(erode_mask_firstpass, erode_mask_secondpass,
[("out_file", "in_file")])])
workflow.connect([(tensor2fa, MRmult_merge, [("FA", "in1")])])
workflow.connect([(erode_mask_secondpass, MRmult_merge, [("out_file",
"in2")])])
workflow.connect([(MRmult_merge, MRmultiply, [("out", "in_files")])])
workflow.connect([(MRmultiply, threshold_FA, [("out_file", "in_file")])])
workflow.connect([(threshold_FA, estimateresponse, [("out_file",
"mask_image")])])
workflow.connect([(inputnode, bet, [("dwi", "in_file")])])
workflow.connect([(inputnode, gen_WM_mask, [("dwi", "in_file")])])
workflow.connect([(bet, gen_WM_mask, [("mask_file", "binary_mask")])])
workflow.connect([(fsl2mrtrix, gen_WM_mask, [("encoding_file",
"encoding_file")])])
workflow.connect([(inputnode, estimateresponse, [("dwi", "in_file")])])
workflow.connect([(fsl2mrtrix, estimateresponse, [("encoding_file",
"encoding_file")])])
workflow.connect([(inputnode, csdeconv, [("dwi", "in_file")])])
workflow.connect([(gen_WM_mask, csdeconv, [("WMprobabilitymap",
"mask_image")])])
workflow.connect([(estimateresponse, csdeconv, [("response",
"response_file")])])
workflow.connect([(fsl2mrtrix, csdeconv, [("encoding_file",
"encoding_file")])])
workflow.connect([(gen_WM_mask, threshold_wmmask, [("WMprobabilitymap",
"in_file")])])
workflow.connect([(threshold_wmmask, CSDstreamtrack, [("out_file",
"seed_file")])])
workflow.connect([(csdeconv, CSDstreamtrack, [("spherical_harmonics_image",
"in_file")])])
if tractography_type == 'probabilistic':
workflow.connect([(CSDstreamtrack, tracks2prob, [("tracked", "in_file")
])])
workflow.connect([(inputnode, tracks2prob, [("dwi", "template_file")])
])
workflow.connect([(CSDstreamtrack, tck2trk, [("tracked", "in_file")])])
workflow.connect([(inputnode, tck2trk, [("dwi", "image_file")])])
output_fields = ["fa", "tracts_trk", "csdeconv", "tracts_tck"]
if tractography_type == 'probabilistic':
output_fields.append("tdi")
outputnode = pe.Node(
interface=util.IdentityInterface(fields=output_fields),
name="outputnode")
workflow.connect([
(CSDstreamtrack, outputnode, [("tracked", "tracts_tck")]),
(csdeconv, outputnode, [("spherical_harmonics_image", "csdeconv")]),
(tensor2fa, outputnode, [("FA", "fa")]),
(tck2trk, outputnode, [("out_file", "tracts_trk")])
])
if tractography_type == 'probabilistic':
workflow.connect([(tracks2prob, outputnode, [("tract_image", "tdi")])])
return workflow
#mrmult fa.mif wmmask.mif fa_corr.mif
mrmultNode = Node(fsl.BinaryMaths(), name = 'mrmult')
mrmultNode.inputs.operation = 'mul'
#Eigenvector (EV) map
#tensor2vector dt.mif ev.mif
tensor2vectorNode = Node(mrtrix.Tensor2Vector(), name = 'tensor_2_vector')
#Scale the EV map by the FA Image
#mrmult ev.mif fa_corr.mif ev_scaled.mif
scaleEvNode = Node(fsl.BinaryMaths(), name = 'scale_ev')
scaleEvNode.inputs.operation = 'mul'
#Mask of single-fibre voxels
#erode wmmask.mif -npass 1 - | mrmult fa_corr.mif - - | threshold - -abs 0.7 sf.mif
erodeNode = Node(mrtrix.Erode(), name = 'erode_wmmask')
erodeNode.inputs.number_of_passes = number_of_passes
cleanFaNode = Node(fsl.BinaryMaths(), name = 'multiplyFA_Mask')
cleanFaNode.inputs.operation = 'mul'
thresholdFANode = Node(mrtrix.Threshold(), name = 'threshold_FA')
thresholdFANode.inputs.absolute_threshold_value = absolute_threshold_value
#Response function coefficient
#estimate_response dwi.mif -grad btable.b -lmax ${lmax} sf.mif response.txt
estResponseNode = Node(mrtrix.EstimateResponseForSH(), name = 'estimate_deconv_response')
#CSD computation
#csdeconv dwi.mif -grad btable.b response.txt -lmax ${lmax} -mask wmmask.mif CSD8.mif
csdNode = Node(mrtrix.ConstrainedSphericalDeconvolution(), name = 'compute_CSD')
""" 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') median3d = pe.Node(interface=mrtrix.MedianFilter3D(),name='median3d') """ The brain mask is also used to help identify single-fiber voxels. This is done by passing the brain mask through two erosion steps, multiplying the remaining mask with the fractional anisotropy map, and thresholding the result to obtain some highly anisotropic within-brain voxels. """ erode_mask_firstpass = pe.Node(interface=mrtrix.Erode(),name='erode_mask_firstpass') erode_mask_secondpass = pe.Node(interface=mrtrix.Erode(),name='erode_mask_secondpass') MRmultiply = pe.Node(interface=mrtrix.MRMultiply(),name='MRmultiply') MRmult_merge = pe.Node(interface=util.Merge(2), name="MRmultiply_merge") threshold_FA = pe.Node(interface=mrtrix.Threshold(),name='threshold_FA') threshold_FA.inputs.absolute_threshold_value = 0.7 """ For whole-brain tracking we also require a broad white-matter seed mask. This is created by generating a white matter mask, given a brainmask, and thresholding it at a reasonably high level. """ bet = pe.Node(interface=fsl.BET(mask = True), name = 'bet_b0') gen_WM_mask = pe.Node(interface=mrtrix.GenerateWhiteMatterMask(),name='gen_WM_mask') threshold_wmmask = pe.Node(interface=mrtrix.Threshold(),name='threshold_wmmask')
def create_connectivity_pipeline(name="connectivity",
parcellation_name='scale500'):
inputnode_within = pe.Node(util.IdentityInterface(fields=[
"subject_id", "dwi", "bvecs", "bvals", "subjects_dir",
"resolution_network_file"
]),
name="inputnode_within")
FreeSurferSource = pe.Node(interface=nio.FreeSurferSource(),
name='fssource')
FreeSurferSourceLH = pe.Node(interface=nio.FreeSurferSource(),
name='fssourceLH')
FreeSurferSourceLH.inputs.hemi = 'lh'
FreeSurferSourceRH = pe.Node(interface=nio.FreeSurferSource(),
name='fssourceRH')
FreeSurferSourceRH.inputs.hemi = 'rh'
"""
Creating the workflow's nodes
=============================
"""
"""
Conversion nodes
----------------
"""
"""
A number of conversion operations are required to obtain NIFTI files from the FreesurferSource for each subject.
Nodes are used to convert the following:
* Original structural image to NIFTI
* Pial, white, inflated, and spherical surfaces for both the left and right hemispheres are converted to GIFTI for visualization in ConnectomeViewer
* Parcellated annotation files for the left and right hemispheres are also converted to GIFTI
"""
mri_convert_Brain = pe.Node(interface=fs.MRIConvert(),
name='mri_convert_Brain')
mri_convert_Brain.inputs.out_type = 'nii'
mri_convert_ROI_scale500 = mri_convert_Brain.clone(
'mri_convert_ROI_scale500')
mris_convertLH = pe.Node(interface=fs.MRIsConvert(), name='mris_convertLH')
mris_convertLH.inputs.out_datatype = 'gii'
mris_convertRH = mris_convertLH.clone('mris_convertRH')
mris_convertRHwhite = mris_convertLH.clone('mris_convertRHwhite')
mris_convertLHwhite = mris_convertLH.clone('mris_convertLHwhite')
mris_convertRHinflated = mris_convertLH.clone('mris_convertRHinflated')
mris_convertLHinflated = mris_convertLH.clone('mris_convertLHinflated')
mris_convertRHsphere = mris_convertLH.clone('mris_convertRHsphere')
mris_convertLHsphere = mris_convertLH.clone('mris_convertLHsphere')
mris_convertLHlabels = mris_convertLH.clone('mris_convertLHlabels')
mris_convertRHlabels = mris_convertLH.clone('mris_convertRHlabels')
"""
Diffusion processing nodes
--------------------------
.. seealso::
dmri_mrtrix_dti.py
Tutorial that focuses solely on the MRtrix diffusion processing
http://www.brain.org.au/software/mrtrix/index.html
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')
"""
Distortions induced by eddy currents are corrected prior to fitting the tensors.
The first image is used as a reference for which to warp the others.
"""
eddycorrect = create_eddy_correct_pipeline(name='eddycorrect')
eddycorrect.inputs.inputnode.ref_num = 1
"""
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
"""
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')
MRconvert_fa = pe.Node(interface=mrtrix.MRConvert(), name='MRconvert_fa')
MRconvert_fa.inputs.extension = 'nii'
"""
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')
median3d = pe.Node(interface=mrtrix.MedianFilter3D(), name='median3d')
"""
The brain mask is also used to help identify single-fiber voxels.
This is done by passing the brain mask through two erosion steps,
multiplying the remaining mask with the fractional anisotropy map, and
thresholding the result to obtain some highly anisotropic within-brain voxels.
"""
erode_mask_firstpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_firstpass')
erode_mask_secondpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_secondpass')
MRmultiply = pe.Node(interface=mrtrix.MRMultiply(), name='MRmultiply')
MRmult_merge = pe.Node(interface=util.Merge(2), name='MRmultiply_merge')
threshold_FA = pe.Node(interface=mrtrix.Threshold(), name='threshold_FA')
threshold_FA.inputs.absolute_threshold_value = 0.7
"""
For whole-brain tracking we also require a broad white-matter seed mask.
This is created by generating a white matter mask, given a brainmask, and
thresholding it at a reasonably high level.
"""
bet = pe.Node(interface=fsl.BET(mask=True), name='bet_b0')
gen_WM_mask = pe.Node(interface=mrtrix.GenerateWhiteMatterMask(),
name='gen_WM_mask')
threshold_wmmask = pe.Node(interface=mrtrix.Threshold(),
name='threshold_wmmask')
threshold_wmmask.inputs.absolute_threshold_value = 0.4
"""
The spherical deconvolution step depends on the estimate of the response function
in the highly anisotropic voxels we obtained above.
.. warning::
For damaged or pathological brains one should take care to lower the maximum harmonic order of these steps.
"""
estimateresponse = pe.Node(interface=mrtrix.EstimateResponseForSH(),
name='estimateresponse')
estimateresponse.inputs.maximum_harmonic_order = 6
csdeconv = pe.Node(interface=mrtrix.ConstrainedSphericalDeconvolution(),
name='csdeconv')
csdeconv.inputs.maximum_harmonic_order = 6
"""
Finally, we track probabilistically using the orientation distribution functions obtained earlier.
The tracts are then used to generate a tract-density image, and they are also converted to TrackVis format.
"""
probCSDstreamtrack = pe.Node(
interface=mrtrix.ProbabilisticSphericallyDeconvolutedStreamlineTrack(),
name='probCSDstreamtrack')
probCSDstreamtrack.inputs.inputmodel = 'SD_PROB'
probCSDstreamtrack.inputs.desired_number_of_tracks = 150000
tracks2prob = pe.Node(interface=mrtrix.Tracks2Prob(), name='tracks2prob')
tracks2prob.inputs.colour = True
MRconvert_tracks2prob = MRconvert_fa.clone(name='MRconvert_tracks2prob')
tck2trk = pe.Node(interface=mrtrix.MRTrix2TrackVis(), name='tck2trk')
"""
Structural segmentation nodes
-----------------------------
"""
"""
The following node identifies the transformation between the diffusion-weighted
image and the structural image. This transformation is then applied to the tracts
so that they are in the same space as the regions of interest.
"""
coregister = pe.Node(interface=fsl.FLIRT(dof=6), name='coregister')
coregister.inputs.cost = ('normmi')
"""
Parcellation is performed given the aparc+aseg image from Freesurfer.
The CMTK Parcellation step subdivides these regions to return a higher-resolution parcellation scheme.
The parcellation used here is entitled "scale500" and returns 1015 regions.
"""
parcellate = pe.Node(interface=cmtk.Parcellate(), name="Parcellate")
parcellate.inputs.parcellation_name = parcellation_name
"""
The CreateMatrix interface takes in the remapped aparc+aseg image as well as the label dictionary and fiber tracts
and outputs a number of different files. The most important of which is the connectivity network itself, which is stored
as a 'gpickle' and can be loaded using Python's NetworkX package (see CreateMatrix docstring). Also outputted are various
NumPy arrays containing detailed tract information, such as the start and endpoint regions, and statistics on the mean and
standard deviation for the fiber length of each connection. These matrices can be used in the ConnectomeViewer to plot the
specific tracts that connect between user-selected regions.
Here we choose the Lausanne2008 parcellation scheme, since we are incorporating the CMTK parcellation step.
"""
creatematrix = pe.Node(interface=cmtk.CreateMatrix(), name="CreateMatrix")
creatematrix.inputs.count_region_intersections = True
"""
Next we define the endpoint of this tutorial, which is the CFFConverter node, as well as a few nodes which use
the Nipype Merge utility. These are useful for passing lists of the files we want packaged in our CFF file.
The inspect.getfile command is used to package this script into the resulting CFF file, so that it is easy to
look back at the processing parameters that were used.
"""
CFFConverter = pe.Node(interface=cmtk.CFFConverter(), name="CFFConverter")
CFFConverter.inputs.script_files = op.abspath(
inspect.getfile(inspect.currentframe()))
giftiSurfaces = pe.Node(interface=util.Merge(8), name="GiftiSurfaces")
giftiLabels = pe.Node(interface=util.Merge(2), name="GiftiLabels")
niftiVolumes = pe.Node(interface=util.Merge(3), name="NiftiVolumes")
fiberDataArrays = pe.Node(interface=util.Merge(4), name="FiberDataArrays")
"""
We also create a node to calculate several network metrics on our resulting file, and another CFF converter
which will be used to package these networks into a single file.
"""
networkx = create_networkx_pipeline(name='networkx')
cmats_to_csv = create_cmats_to_csv_pipeline(name='cmats_to_csv')
nfibs_to_csv = pe.Node(interface=misc.Matlab2CSV(), name='nfibs_to_csv')
merge_nfib_csvs = pe.Node(interface=misc.MergeCSVFiles(),
name='merge_nfib_csvs')
merge_nfib_csvs.inputs.extra_column_heading = 'Subject'
merge_nfib_csvs.inputs.out_file = 'fibers.csv'
NxStatsCFFConverter = pe.Node(interface=cmtk.CFFConverter(),
name="NxStatsCFFConverter")
NxStatsCFFConverter.inputs.script_files = op.abspath(
inspect.getfile(inspect.currentframe()))
"""
Connecting the workflow
=======================
Here we connect our processing pipeline.
"""
"""
Connecting the inputs, FreeSurfer nodes, and conversions
--------------------------------------------------------
"""
mapping = pe.Workflow(name='mapping')
"""
First, we connect the input node to the FreeSurfer input nodes.
"""
mapping.connect([(inputnode_within, FreeSurferSource, [("subjects_dir",
"subjects_dir")])])
mapping.connect([(inputnode_within, FreeSurferSource, [("subject_id",
"subject_id")])])
mapping.connect([(inputnode_within, FreeSurferSourceLH,
[("subjects_dir", "subjects_dir")])])
mapping.connect([(inputnode_within, FreeSurferSourceLH, [("subject_id",
"subject_id")])])
mapping.connect([(inputnode_within, FreeSurferSourceRH,
[("subjects_dir", "subjects_dir")])])
mapping.connect([(inputnode_within, FreeSurferSourceRH, [("subject_id",
"subject_id")])])
mapping.connect([(inputnode_within, parcellate, [("subjects_dir",
"subjects_dir")])])
mapping.connect([(inputnode_within, parcellate, [("subject_id",
"subject_id")])])
mapping.connect([(parcellate, mri_convert_ROI_scale500, [('roi_file',
'in_file')])])
"""
Nifti conversion for subject's stripped brain image from Freesurfer:
"""
mapping.connect([(FreeSurferSource, mri_convert_Brain, [('brain',
'in_file')])])
"""
Surface conversions to GIFTI (pial, white, inflated, and sphere for both hemispheres)
"""
mapping.connect([(FreeSurferSourceLH, mris_convertLH, [('pial', 'in_file')
])])
mapping.connect([(FreeSurferSourceRH, mris_convertRH, [('pial', 'in_file')
])])
mapping.connect([(FreeSurferSourceLH, mris_convertLHwhite, [('white',
'in_file')])])
mapping.connect([(FreeSurferSourceRH, mris_convertRHwhite, [('white',
'in_file')])])
mapping.connect([(FreeSurferSourceLH, mris_convertLHinflated,
[('inflated', 'in_file')])])
mapping.connect([(FreeSurferSourceRH, mris_convertRHinflated,
[('inflated', 'in_file')])])
mapping.connect([(FreeSurferSourceLH, mris_convertLHsphere,
[('sphere', 'in_file')])])
mapping.connect([(FreeSurferSourceRH, mris_convertRHsphere,
[('sphere', 'in_file')])])
"""
The annotation files are converted using the pial surface as a map via the MRIsConvert interface.
One of the functions defined earlier is used to select the lh.aparc.annot and rh.aparc.annot files
specifically (rather than e.g. rh.aparc.a2009s.annot) from the output list given by the FreeSurferSource.
"""
mapping.connect([(FreeSurferSourceLH, mris_convertLHlabels,
[('pial', 'in_file')])])
mapping.connect([(FreeSurferSourceRH, mris_convertRHlabels,
[('pial', 'in_file')])])
mapping.connect([(FreeSurferSourceLH, mris_convertLHlabels,
[(('annot', select_aparc_annot), 'annot_file')])])
mapping.connect([(FreeSurferSourceRH, mris_convertRHlabels,
[(('annot', select_aparc_annot), 'annot_file')])])
"""
Diffusion Processing
--------------------
Now we connect the tensor computations:
"""
mapping.connect([(inputnode_within, fsl2mrtrix, [("bvecs", "bvec_file"),
("bvals", "bval_file")])])
mapping.connect([(inputnode_within, eddycorrect, [("dwi",
"inputnode.in_file")])])
mapping.connect([(eddycorrect, dwi2tensor, [("outputnode.eddy_corrected",
"in_file")])])
mapping.connect([(fsl2mrtrix, dwi2tensor, [("encoding_file",
"encoding_file")])])
mapping.connect([
(dwi2tensor, tensor2vector, [['tensor', 'in_file']]),
(dwi2tensor, tensor2adc, [['tensor', 'in_file']]),
(dwi2tensor, tensor2fa, [['tensor', 'in_file']]),
])
mapping.connect([(tensor2fa, MRmult_merge, [("FA", "in1")])])
mapping.connect([(tensor2fa, MRconvert_fa, [("FA", "in_file")])])
"""
This block creates the rough brain mask to be multiplied, mulitplies it with the
fractional anisotropy image, and thresholds it to get the single-fiber voxels.
"""
mapping.connect([(eddycorrect, MRconvert, [("outputnode.eddy_corrected",
"in_file")])])
mapping.connect([(MRconvert, threshold_b0, [("converted", "in_file")])])
mapping.connect([(threshold_b0, median3d, [("out_file", "in_file")])])
mapping.connect([(median3d, erode_mask_firstpass, [("out_file", "in_file")
])])
mapping.connect([(erode_mask_firstpass, erode_mask_secondpass,
[("out_file", "in_file")])])
mapping.connect([(erode_mask_secondpass, MRmult_merge, [("out_file", "in2")
])])
mapping.connect([(MRmult_merge, MRmultiply, [("out", "in_files")])])
mapping.connect([(MRmultiply, threshold_FA, [("out_file", "in_file")])])
"""
Here the thresholded white matter mask is created for seeding the tractography.
"""
mapping.connect([(eddycorrect, bet, [("outputnode.eddy_corrected",
"in_file")])])
mapping.connect([(eddycorrect, gen_WM_mask, [("outputnode.eddy_corrected",
"in_file")])])
mapping.connect([(bet, gen_WM_mask, [("mask_file", "binary_mask")])])
mapping.connect([(fsl2mrtrix, gen_WM_mask, [("encoding_file",
"encoding_file")])])
mapping.connect([(gen_WM_mask, threshold_wmmask, [("WMprobabilitymap",
"in_file")])])
"""
Next we estimate the fiber response distribution.
"""
mapping.connect([(eddycorrect, estimateresponse,
[("outputnode.eddy_corrected", "in_file")])])
mapping.connect([(fsl2mrtrix, estimateresponse, [("encoding_file",
"encoding_file")])])
mapping.connect([(threshold_FA, estimateresponse, [("out_file",
"mask_image")])])
"""
Run constrained spherical deconvolution.
"""
mapping.connect([(eddycorrect, csdeconv, [("outputnode.eddy_corrected",
"in_file")])])
mapping.connect([(gen_WM_mask, csdeconv, [("WMprobabilitymap",
"mask_image")])])
mapping.connect([(estimateresponse, csdeconv, [("response",
"response_file")])])
mapping.connect([(fsl2mrtrix, csdeconv, [("encoding_file", "encoding_file")
])])
"""
Connect the tractography and compute the tract density image.
"""
mapping.connect([(threshold_wmmask, probCSDstreamtrack, [("out_file",
"seed_file")])])
mapping.connect([(csdeconv, probCSDstreamtrack,
[("spherical_harmonics_image", "in_file")])])
mapping.connect([(probCSDstreamtrack, tracks2prob, [("tracked", "in_file")
])])
mapping.connect([(eddycorrect, tracks2prob, [("outputnode.eddy_corrected",
"template_file")])])
mapping.connect([(tracks2prob, MRconvert_tracks2prob, [("tract_image",
"in_file")])])
"""
Structural Processing
---------------------
First, we coregister the diffusion image to the structural image
"""
mapping.connect([(eddycorrect, coregister, [("outputnode.eddy_corrected",
"in_file")])])
mapping.connect([(mri_convert_Brain, coregister, [('out_file', 'reference')
])])
"""
The MRtrix-tracked fibers are converted to TrackVis format (with voxel and data dimensions grabbed from the DWI).
The connectivity matrix is created with the transformed .trk fibers and the parcellation file.
"""
mapping.connect([(eddycorrect, tck2trk, [("outputnode.eddy_corrected",
"image_file")])])
mapping.connect([(mri_convert_Brain, tck2trk,
[("out_file", "registration_image_file")])])
mapping.connect([(coregister, tck2trk, [("out_matrix_file", "matrix_file")
])])
mapping.connect([(probCSDstreamtrack, tck2trk, [("tracked", "in_file")])])
mapping.connect([(tck2trk, creatematrix, [("out_file", "tract_file")])])
mapping.connect(inputnode_within, 'resolution_network_file', creatematrix,
'resolution_network_file')
mapping.connect([(inputnode_within, creatematrix, [("subject_id",
"out_matrix_file")])])
mapping.connect([(inputnode_within, creatematrix,
[("subject_id", "out_matrix_mat_file")])])
mapping.connect([(parcellate, creatematrix, [("roi_file", "roi_file")])])
"""
The merge nodes defined earlier are used here to create lists of the files which are
destined for the CFFConverter.
"""
mapping.connect([(mris_convertLH, giftiSurfaces, [("converted", "in1")])])
mapping.connect([(mris_convertRH, giftiSurfaces, [("converted", "in2")])])
mapping.connect([(mris_convertLHwhite, giftiSurfaces, [("converted", "in3")
])])
mapping.connect([(mris_convertRHwhite, giftiSurfaces, [("converted", "in4")
])])
mapping.connect([(mris_convertLHinflated, giftiSurfaces, [("converted",
"in5")])])
mapping.connect([(mris_convertRHinflated, giftiSurfaces, [("converted",
"in6")])])
mapping.connect([(mris_convertLHsphere, giftiSurfaces, [("converted",
"in7")])])
mapping.connect([(mris_convertRHsphere, giftiSurfaces, [("converted",
"in8")])])
mapping.connect([(mris_convertLHlabels, giftiLabels, [("converted", "in1")
])])
mapping.connect([(mris_convertRHlabels, giftiLabels, [("converted", "in2")
])])
mapping.connect([(parcellate, niftiVolumes, [("roi_file", "in1")])])
mapping.connect([(eddycorrect, niftiVolumes, [("outputnode.eddy_corrected",
"in2")])])
mapping.connect([(mri_convert_Brain, niftiVolumes, [("out_file", "in3")])])
mapping.connect([(creatematrix, fiberDataArrays, [("endpoint_file", "in1")
])])
mapping.connect([(creatematrix, fiberDataArrays, [("endpoint_file_mm",
"in2")])])
mapping.connect([(creatematrix, fiberDataArrays, [("fiber_length_file",
"in3")])])
mapping.connect([(creatematrix, fiberDataArrays, [("fiber_label_file",
"in4")])])
"""
This block actually connects the merged lists to the CFF converter. We pass the surfaces
and volumes that are to be included, as well as the tracts and the network itself. The currently
running pipeline (dmri_connectivity_advanced.py) is also scraped and included in the CFF file. This
makes it easy for the user to examine the entire processing pathway used to generate the end
product.
"""
mapping.connect([(giftiSurfaces, CFFConverter, [("out", "gifti_surfaces")])
])
mapping.connect([(giftiLabels, CFFConverter, [("out", "gifti_labels")])])
mapping.connect([(creatematrix, CFFConverter, [("matrix_files",
"gpickled_networks")])])
mapping.connect([(niftiVolumes, CFFConverter, [("out", "nifti_volumes")])])
mapping.connect([(fiberDataArrays, CFFConverter, [("out", "data_files")])])
mapping.connect([(creatematrix, CFFConverter, [("filtered_tractography",
"tract_files")])])
mapping.connect([(inputnode_within, CFFConverter, [("subject_id", "title")
])])
"""
The graph theoretical metrics which have been generated are placed into another CFF file.
"""
mapping.connect([(inputnode_within, networkx,
[("subject_id", "inputnode.extra_field")])])
mapping.connect([(creatematrix, networkx, [("intersection_matrix_file",
"inputnode.network_file")])])
mapping.connect([(networkx, NxStatsCFFConverter,
[("outputnode.network_files", "gpickled_networks")])])
mapping.connect([(giftiSurfaces, NxStatsCFFConverter,
[("out", "gifti_surfaces")])])
mapping.connect([(giftiLabels, NxStatsCFFConverter, [("out",
"gifti_labels")])])
mapping.connect([(niftiVolumes, NxStatsCFFConverter, [("out",
"nifti_volumes")])])
mapping.connect([(fiberDataArrays, NxStatsCFFConverter, [("out",
"data_files")])])
mapping.connect([(inputnode_within, NxStatsCFFConverter, [("subject_id",
"title")])])
mapping.connect([(inputnode_within, cmats_to_csv,
[("subject_id", "inputnode.extra_field")])])
mapping.connect([(creatematrix, cmats_to_csv, [
("matlab_matrix_files", "inputnode.matlab_matrix_files")
])])
mapping.connect([(creatematrix, nfibs_to_csv, [("stats_file", "in_file")])
])
mapping.connect([(nfibs_to_csv, merge_nfib_csvs, [("csv_files", "in_files")
])])
mapping.connect([(inputnode_within, merge_nfib_csvs, [("subject_id",
"extra_field")])])
"""
Create a higher-level workflow
--------------------------------------
Finally, we create another higher-level workflow to connect our mapping workflow with the info and datagrabbing nodes
declared at the beginning. Our tutorial can is now extensible to any arbitrary number of subjects by simply adding
their names to the subject list and their data to the proper folders.
"""
inputnode = pe.Node(interface=util.IdentityInterface(
fields=["subject_id", "dwi", "bvecs", "bvals", "subjects_dir"]),
name="inputnode")
outputnode = pe.Node(interface=util.IdentityInterface(fields=[
"fa", "struct", "tracts", "tracks2prob", "connectome", "nxstatscff",
"nxmatlab", "nxcsv", "fiber_csv", "cmatrices_csv", "nxmergedcsv",
"cmatrix", "networks", "filtered_tracts", "rois", "odfs", "tdi",
"mean_fiber_length", "median_fiber_length", "fiber_length_std"
]),
name="outputnode")
connectivity = pe.Workflow(name="connectivity")
connectivity.base_output_dir = name
connectivity.base_dir = name
connectivity.connect([(inputnode, mapping, [
("dwi", "inputnode_within.dwi"), ("bvals", "inputnode_within.bvals"),
("bvecs", "inputnode_within.bvecs"),
("subject_id", "inputnode_within.subject_id"),
("subjects_dir", "inputnode_within.subjects_dir")
])])
connectivity.connect([(mapping, outputnode, [
("tck2trk.out_file", "tracts"),
("CFFConverter.connectome_file", "connectome"),
("NxStatsCFFConverter.connectome_file", "nxstatscff"),
("CreateMatrix.matrix_mat_file", "cmatrix"),
("CreateMatrix.mean_fiber_length_matrix_mat_file",
"mean_fiber_length"),
("CreateMatrix.median_fiber_length_matrix_mat_file",
"median_fiber_length"),
("CreateMatrix.fiber_length_std_matrix_mat_file", "fiber_length_std"),
("CreateMatrix.matrix_files", "networks"),
("CreateMatrix.filtered_tractographies", "filtered_tracts"),
("merge_nfib_csvs.csv_file", "fiber_csv"),
("mri_convert_ROI_scale500.out_file", "rois"),
("csdeconv.spherical_harmonics_image", "odfs"),
("mri_convert_Brain.out_file", "struct"),
("MRconvert_fa.converted", "fa"),
("MRconvert_tracks2prob.converted", "tracks2prob")
])])
connectivity.connect([(cmats_to_csv, outputnode, [("outputnode.csv_file",
"cmatrices_csv")])])
connectivity.connect([(networkx, outputnode, [("outputnode.csv_files",
"nxcsv")])])
return connectivity
def create_precoth_pipeline_step1(name="precoth_step1", reg_pet_T1=True, auto_reorient=True):
inputnode = pe.Node(
interface=util.IdentityInterface(fields=["subjects_dir",
"subject_id",
"dwi",
"bvecs",
"bvals",
"fdgpet"]),
name="inputnode")
nonlinfit_interface = util.Function(input_names=["dwi", "bvecs", "bvals", "base_name"],
output_names=["tensor", "FA", "MD", "evecs", "evals", "rgb_fa", "norm", "mode", "binary_mask", "b0_masked"], function=nonlinfit_fn)
nonlinfit_node = pe.Node(interface=nonlinfit_interface, name="nonlinfit_node")
erode_mask_firstpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_firstpass')
erode_mask_firstpass.inputs.out_filename = "b0_mask_median3D_erode.nii.gz"
erode_mask_secondpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_secondpass')
erode_mask_secondpass.inputs.out_filename = "b0_mask_median3D_erode_secondpass.nii.gz"
threshold_FA = pe.Node(interface=fsl.ImageMaths(), name='threshold_FA')
threshold_FA.inputs.op_string = "-thr 0.8 -uthr 0.99"
threshold_mode = pe.Node(interface=fsl.ImageMaths(), name='threshold_mode')
threshold_mode.inputs.op_string = "-thr 0.9 -fmedian -fmedian"
make_termination_mask = pe.Node(interface=fsl.ImageMaths(), name='make_termination_mask')
make_termination_mask.inputs.op_string = "-bin"
fast_seg_T1 = pe.Node(interface=fsl.FAST(), name='fast_seg_T1')
fast_seg_T1.inputs.segments = True
fast_seg_T1.inputs.probability_maps = True
fix_wm_mask = pe.Node(interface=fsl.MultiImageMaths(), name='fix_wm_mask')
fix_wm_mask.inputs.op_string = "-mul %s"
fix_termination_mask = pe.Node(interface=fsl.MultiImageMaths(), name='fix_termination_mask')
fix_termination_mask.inputs.op_string = "-binv -mul %s"
wm_mask_interface = util.Function(input_names=["in_file", "out_filename"],
output_names=["out_file"],
function=wm_labels_only)
make_wm_mask = pe.Node(interface=wm_mask_interface, name='make_wm_mask')
MRmultiply = pe.Node(interface=mrtrix.MRMultiply(), name='MRmultiply')
MRmultiply.inputs.out_filename = "Eroded_FA.nii.gz"
MultFAbyMode = pe.Node(interface=mrtrix.MRMultiply(), name='MultFAbyMode')
MRmult_merge = pe.Node(interface=util.Merge(2), name='MRmultiply_merge')
MultFAbyMode_merge = pe.Node(interface=util.Merge(2), name='MultFAbyMode_merge')
median3d = pe.Node(interface=mrtrix.MedianFilter3D(), name='median3D')
FreeSurferSource = pe.Node(
interface=nio.FreeSurferSource(), name='fssource')
mri_convert_Brain = pe.Node(
interface=fs.MRIConvert(), name='mri_convert_Brain')
mri_convert_Brain.inputs.out_type = 'nii'
mri_convert_Brain.inputs.no_change = True
mri_convert_Ribbon = mri_convert_Brain.clone("mri_convert_Ribbon")
mri_convert_ROIs = mri_convert_Brain.clone("mri_convert_ROIs")
mri_convert_T1 = mri_convert_Brain.clone("mri_convert_T1")
mni_for_reg = op.join(os.environ["FSL_DIR"],"data","standard","MNI152_T1_1mm.nii.gz")
if auto_reorient:
reorientBrain = pe.Node(interface=fsl.FLIRT(dof=6), name = 'reorientBrain')
reorientBrain.inputs.reference = mni_for_reg
reorientROIs = pe.Node(interface=fsl.ApplyXfm(), name = 'reorientROIs')
reorientROIs.inputs.interp = "nearestneighbour"
reorientROIs.inputs.reference = mni_for_reg
reorientRibbon = reorientROIs.clone("reorientRibbon")
reorientRibbon.inputs.interp = "nearestneighbour"
reorientT1 = reorientROIs.clone("reorientT1")
reorientT1.inputs.interp = "trilinear"
if reg_pet_T1:
reg_pet_T1 = pe.Node(interface=fsl.FLIRT(dof=6), name = 'reg_pet_T1')
reg_pet_T1.inputs.cost = ('corratio')
reslice_fdgpet = mri_convert_Brain.clone("reslice_fdgpet")
reslice_fdgpet.inputs.no_change = True
extract_PreCoTh_interface = util.Function(input_names=["in_file", "out_filename"],
output_names=["out_file"],
function=extract_PreCoTh)
thalamus2precuneus2cortex_ROIs = pe.Node(
interface=extract_PreCoTh_interface, name='thalamus2precuneus2cortex_ROIs')
workflow = pe.Workflow(name=name)
workflow.base_output_dir = name
workflow.connect(
[(inputnode, FreeSurferSource, [("subjects_dir", "subjects_dir")])])
workflow.connect(
[(inputnode, FreeSurferSource, [("subject_id", "subject_id")])])
workflow.connect(
[(FreeSurferSource, mri_convert_T1, [('T1', 'in_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_Brain, [('brain', 'in_file')])])
if auto_reorient:
workflow.connect(
[(mri_convert_T1, reorientT1, [('out_file', 'in_file')])])
workflow.connect(
[(mri_convert_Brain, reorientBrain, [('out_file', 'in_file')])])
workflow.connect(
[(reorientBrain, reorientROIs, [('out_matrix_file', 'in_matrix_file')])])
workflow.connect(
[(reorientBrain, reorientRibbon, [('out_matrix_file', 'in_matrix_file')])])
workflow.connect(
[(reorientBrain, reorientT1, [('out_matrix_file', 'in_matrix_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_ROIs, [(('aparc_aseg', select_aparc), 'in_file')])])
if auto_reorient:
workflow.connect(
[(mri_convert_ROIs, reorientROIs, [('out_file', 'in_file')])])
workflow.connect(
[(reorientROIs, make_wm_mask, [('out_file', 'in_file')])])
workflow.connect(
[(reorientROIs, thalamus2precuneus2cortex_ROIs, [("out_file", "in_file")])])
else:
workflow.connect(
[(mri_convert_ROIs, make_wm_mask, [('out_file', 'in_file')])])
workflow.connect(
[(mri_convert_ROIs, thalamus2precuneus2cortex_ROIs, [("out_file", "in_file")])])
workflow.connect(
[(FreeSurferSource, mri_convert_Ribbon, [(('ribbon', select_ribbon), 'in_file')])])
if auto_reorient:
workflow.connect(
[(mri_convert_Ribbon, reorientRibbon, [('out_file', 'in_file')])])
workflow.connect(
[(reorientRibbon, make_termination_mask, [('out_file', 'in_file')])])
else:
workflow.connect(
[(mri_convert_Ribbon, make_termination_mask, [('out_file', 'in_file')])])
if auto_reorient:
workflow.connect(
[(reorientBrain, fast_seg_T1, [('out_file', 'in_files')])])
else:
workflow.connect(
[(mri_convert_Brain, fast_seg_T1, [('out_file', 'in_files')])])
workflow.connect(
[(inputnode, fast_seg_T1, [("subject_id", "out_basename")])])
workflow.connect([(fast_seg_T1, fix_termination_mask, [(('tissue_class_files', select_CSF), 'in_file')])])
workflow.connect([(fast_seg_T1, fix_wm_mask, [(('tissue_class_files', select_WM), 'in_file')])])
workflow.connect(
[(make_termination_mask, fix_termination_mask, [('out_file', 'operand_files')])])
workflow.connect(
[(make_wm_mask, fix_wm_mask, [('out_file', 'operand_files')])])
workflow.connect(inputnode, 'dwi', nonlinfit_node, 'dwi')
workflow.connect(inputnode, 'subject_id', nonlinfit_node, 'base_name')
workflow.connect(inputnode, 'bvecs', nonlinfit_node, 'bvecs')
workflow.connect(inputnode, 'bvals', nonlinfit_node, 'bvals')
if reg_pet_T1:
workflow.connect([(inputnode, reg_pet_T1, [("fdgpet", "in_file")])])
if auto_reorient:
workflow.connect(
[(reorientBrain, reg_pet_T1, [("out_file", "reference")])])
workflow.connect(
[(reorientROIs, reslice_fdgpet, [("out_file", "reslice_like")])])
else:
workflow.connect(
[(mri_convert_Brain, reg_pet_T1, [("out_file", "reference")])])
workflow.connect(
[(mri_convert_ROIs, reslice_fdgpet, [("out_file", "reslice_like")])])
workflow.connect(
[(reg_pet_T1, reslice_fdgpet, [("out_file", "in_file")])])
else:
workflow.connect([(inputnode, reslice_fdgpet, [("fdgpet", "in_file")])])
if auto_reorient:
workflow.connect(
[(reorientROIs, reslice_fdgpet, [("out_file", "reslice_like")])])
else:
workflow.connect(
[(mri_convert_ROIs, reslice_fdgpet, [("out_file", "reslice_like")])])
workflow.connect([(nonlinfit_node, median3d, [("binary_mask", "in_file")])])
workflow.connect(
[(median3d, erode_mask_firstpass, [("out_file", "in_file")])])
workflow.connect(
[(erode_mask_firstpass, erode_mask_secondpass, [("out_file", "in_file")])])
workflow.connect([(nonlinfit_node, MRmult_merge, [("FA", "in1")])])
workflow.connect(
[(erode_mask_secondpass, MRmult_merge, [("out_file", "in2")])])
workflow.connect([(MRmult_merge, MRmultiply, [("out", "in_files")])])
workflow.connect([(MRmultiply, threshold_FA, [("out_file", "in_file")])])
workflow.connect([(nonlinfit_node, threshold_mode, [("mode", "in_file")])])
workflow.connect([(threshold_mode, MultFAbyMode_merge, [("out_file", "in1")])])
workflow.connect([(threshold_FA, MultFAbyMode_merge, [("out_file", "in2")])])
workflow.connect([(MultFAbyMode_merge, MultFAbyMode, [("out", "in_files")])])
workflow.connect([(inputnode, MultFAbyMode, [(('subject_id', add_subj_name_to_sfmask), 'out_filename')])])
workflow.connect([(inputnode, reslice_fdgpet, [(('subject_id', add_subj_name_to_fdgpet), 'out_file')])])
workflow.connect([(inputnode, make_wm_mask, [(('subject_id', add_subj_name_to_wmmask), 'out_filename')])])
workflow.connect([(inputnode, fix_wm_mask, [(('subject_id', add_subj_name_to_wmmask), 'out_file')])])
workflow.connect([(inputnode, fix_termination_mask, [(('subject_id', add_subj_name_to_termmask), 'out_file')])])
workflow.connect([(inputnode, thalamus2precuneus2cortex_ROIs, [(('subject_id', add_subj_name_to_rois), 'out_filename')])])
if auto_reorient:
workflow.connect([(inputnode, reorientT1, [(('subject_id', add_subj_name_to_T1), 'out_file')])])
workflow.connect([(inputnode, reorientBrain, [(('subject_id', add_subj_name_to_T1brain), 'out_file')])])
else:
workflow.connect([(inputnode, mri_convert_T1, [(('subject_id', add_subj_name_to_T1), 'out_file')])])
workflow.connect([(inputnode, mri_convert_Brain, [(('subject_id', add_subj_name_to_T1brain), 'out_file')])])
output_fields = ["single_fiber_mask", "fa", "rgb_fa", "md", "t1", "t1_brain",
"wm_mask", "term_mask", "fdgpet", "rois","mode", "tissue_class_files", "probability_maps"]
outputnode = pe.Node(
interface=util.IdentityInterface(fields=output_fields),
name="outputnode")
workflow.connect([(fast_seg_T1, outputnode, [("tissue_class_files", "tissue_class_files")])])
workflow.connect([(fast_seg_T1, outputnode, [("probability_maps", "probability_maps")])])
workflow.connect([
(nonlinfit_node, outputnode, [("FA", "fa")]),
(nonlinfit_node, outputnode, [("rgb_fa", "rgb_fa")]),
(nonlinfit_node, outputnode, [("MD", "md")]),
(nonlinfit_node, outputnode, [("mode", "mode")]),
(MultFAbyMode, outputnode, [("out_file", "single_fiber_mask")]),
(fix_wm_mask, outputnode, [("out_file", "wm_mask")]),
(fix_termination_mask, outputnode, [("out_file", "term_mask")]),
(reslice_fdgpet, outputnode, [("out_file", "fdgpet")]),
(thalamus2precuneus2cortex_ROIs, outputnode, [("out_file", "rois")]),
])
if auto_reorient:
workflow.connect([
(reorientBrain, outputnode, [("out_file", "t1_brain")]),
(reorientT1, outputnode, [("out_file", "t1")]),
])
else:
workflow.connect([
(mri_convert_Brain, outputnode, [("out_file", "t1_brain")]),
(mri_convert_T1, outputnode, [("out_file", "t1")]),
])
return workflow
def create_precoth_pipeline(name="precoth", tractography_type='probabilistic', reg_pet_T1=True):
inputnode = pe.Node(
interface=util.IdentityInterface(fields=["subjects_dir",
"subject_id",
"dwi",
"bvecs",
"bvals",
"fdgpet",
"dose",
"weight",
"delay",
"glycemie",
"scan_time"]),
name="inputnode")
nonlinfit_interface = util.Function(input_names=["dwi", "bvecs", "bvals", "base_name"],
output_names=["tensor", "FA", "MD", "evecs", "evals", "rgb_fa", "norm", "mode", "binary_mask", "b0_masked"], function=nonlinfit_fn)
nonlinfit_node = pe.Node(interface=nonlinfit_interface, name="nonlinfit_node")
coregister = pe.Node(interface=fsl.FLIRT(dof=12), name = 'coregister')
coregister.inputs.cost = ('normmi')
invertxfm = pe.Node(interface=fsl.ConvertXFM(), name = 'invertxfm')
invertxfm.inputs.invert_xfm = True
WM_to_FA = pe.Node(interface=fsl.ApplyXfm(), name = 'WM_to_FA')
WM_to_FA.inputs.interp = 'nearestneighbour'
TermMask_to_FA = WM_to_FA.clone("TermMask_to_FA")
mni_for_reg = op.join(os.environ["FSL_DIR"],"data","standard","MNI152_T1_1mm.nii.gz")
reorientBrain = pe.Node(interface=fsl.FLIRT(dof=6), name = 'reorientBrain')
reorientBrain.inputs.reference = mni_for_reg
reorientROIs = pe.Node(interface=fsl.ApplyXfm(), name = 'reorientROIs')
reorientROIs.inputs.interp = "nearestneighbour"
reorientROIs.inputs.reference = mni_for_reg
reorientRibbon = reorientROIs.clone("reorientRibbon")
reorientRibbon.inputs.interp = "nearestneighbour"
reorientT1 = reorientROIs.clone("reorientT1")
reorientT1.inputs.interp = "trilinear"
fsl2mrtrix = pe.Node(interface=mrtrix.FSL2MRTrix(), name='fsl2mrtrix')
fsl2mrtrix.inputs.invert_y = True
erode_mask_firstpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_firstpass')
erode_mask_firstpass.inputs.out_filename = "b0_mask_median3D_erode.nii.gz"
erode_mask_secondpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_secondpass')
erode_mask_secondpass.inputs.out_filename = "b0_mask_median3D_erode_secondpass.nii.gz"
threshold_FA = pe.Node(interface=fsl.ImageMaths(), name='threshold_FA')
threshold_FA.inputs.op_string = "-thr 0.8 -uthr 0.99"
threshold_mode = pe.Node(interface=fsl.ImageMaths(), name='threshold_mode')
threshold_mode.inputs.op_string = "-thr 0.1 -uthr 0.99"
make_termination_mask = pe.Node(interface=fsl.ImageMaths(), name='make_termination_mask')
make_termination_mask.inputs.op_string = "-bin"
get_wm_mask = pe.Node(interface=fsl.ImageMaths(), name='get_wm_mask')
get_wm_mask.inputs.op_string = "-thr 0.1"
MRmultiply = pe.Node(interface=mrtrix.MRMultiply(), name='MRmultiply')
MRmultiply.inputs.out_filename = "Eroded_FA.nii.gz"
MRmult_merge = pe.Node(interface=util.Merge(2), name='MRmultiply_merge')
median3d = pe.Node(interface=mrtrix.MedianFilter3D(), name='median3D')
fdgpet_regions = pe.Node(interface=RegionalValues(), name='fdgpet_regions')
compute_cmr_glc_interface = util.Function(input_names=["in_file", "dose", "weight", "delay",
"glycemie", "scan_time"], output_names=["out_file"], function=CMR_glucose)
compute_cmr_glc = pe.Node(interface=compute_cmr_glc_interface, name='compute_cmr_glc')
csdeconv = pe.Node(interface=mrtrix.ConstrainedSphericalDeconvolution(),
name='csdeconv')
estimateresponse = pe.Node(interface=mrtrix.EstimateResponseForSH(),
name='estimateresponse')
if tractography_type == 'probabilistic':
CSDstreamtrack = pe.Node(
interface=mrtrix.ProbabilisticSphericallyDeconvolutedStreamlineTrack(
),
name='CSDstreamtrack')
else:
CSDstreamtrack = pe.Node(
interface=mrtrix.SphericallyDeconvolutedStreamlineTrack(),
name='CSDstreamtrack')
#CSDstreamtrack.inputs.desired_number_of_tracks = 10000
CSDstreamtrack.inputs.minimum_tract_length = 50
tck2trk = pe.Node(interface=mrtrix.MRTrix2TrackVis(), name='tck2trk')
extract_PreCoTh_interface = util.Function(input_names=["in_file", "out_filename"],
output_names=["out_file"],
function=extract_PreCoTh)
thalamus2precuneus2cortex_ROIs = pe.Node(
interface=extract_PreCoTh_interface, name='thalamus2precuneus2cortex_ROIs')
wm_mask_interface = util.Function(input_names=["in_file", "out_filename"],
output_names=["out_file"],
function=wm_labels_only)
make_wm_mask = pe.Node(
interface=wm_mask_interface, name='make_wm_mask')
write_precoth_data_interface = util.Function(input_names=["dwi_network_file", "fdg_stats_file", "subject_id"],
output_names=["out_file"],
function=summarize_precoth)
write_csv_data = pe.Node(
interface=write_precoth_data_interface, name='write_csv_data')
thalamus2precuneus2cortex = pe.Node(
interface=cmtk.CreateMatrix(), name="thalamus2precuneus2cortex")
thalamus2precuneus2cortex.inputs.count_region_intersections = True
FreeSurferSource = pe.Node(
interface=nio.FreeSurferSource(), name='fssource')
mri_convert_Brain = pe.Node(
interface=fs.MRIConvert(), name='mri_convert_Brain')
mri_convert_Brain.inputs.out_type = 'niigz'
mri_convert_Brain.inputs.no_change = True
if reg_pet_T1:
reg_pet_T1 = pe.Node(interface=fsl.FLIRT(dof=6), name = 'reg_pet_T1')
reg_pet_T1.inputs.cost = ('corratio')
reslice_fdgpet = mri_convert_Brain.clone("reslice_fdgpet")
reslice_fdgpet.inputs.no_change = True
mri_convert_Ribbon = mri_convert_Brain.clone("mri_convert_Ribbon")
mri_convert_ROIs = mri_convert_Brain.clone("mri_convert_ROIs")
mri_convert_T1 = mri_convert_Brain.clone("mri_convert_T1")
workflow = pe.Workflow(name=name)
workflow.base_output_dir = name
workflow.connect(
[(inputnode, FreeSurferSource, [("subjects_dir", "subjects_dir")])])
workflow.connect(
[(inputnode, FreeSurferSource, [("subject_id", "subject_id")])])
workflow.connect(
[(FreeSurferSource, mri_convert_T1, [('T1', 'in_file')])])
workflow.connect(
[(mri_convert_T1, reorientT1, [('out_file', 'in_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_Brain, [('brain', 'in_file')])])
workflow.connect(
[(mri_convert_Brain, reorientBrain, [('out_file', 'in_file')])])
workflow.connect(
[(reorientBrain, reorientROIs, [('out_matrix_file', 'in_matrix_file')])])
workflow.connect(
[(reorientBrain, reorientRibbon, [('out_matrix_file', 'in_matrix_file')])])
workflow.connect(
[(reorientBrain, reorientT1, [('out_matrix_file', 'in_matrix_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_ROIs, [(('aparc_aseg', select_aparc), 'in_file')])])
workflow.connect(
[(mri_convert_ROIs, reorientROIs, [('out_file', 'in_file')])])
workflow.connect(
[(reorientROIs, make_wm_mask, [('out_file', 'in_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_Ribbon, [(('ribbon', select_ribbon), 'in_file')])])
workflow.connect(
[(mri_convert_Ribbon, reorientRibbon, [('out_file', 'in_file')])])
workflow.connect(
[(reorientRibbon, make_termination_mask, [('out_file', 'in_file')])])
workflow.connect([(inputnode, fsl2mrtrix, [("bvecs", "bvec_file"),
("bvals", "bval_file")])])
workflow.connect(inputnode, 'dwi', nonlinfit_node, 'dwi')
workflow.connect(inputnode, 'subject_id', nonlinfit_node, 'base_name')
workflow.connect(inputnode, 'bvecs', nonlinfit_node, 'bvecs')
workflow.connect(inputnode, 'bvals', nonlinfit_node, 'bvals')
workflow.connect([(inputnode, compute_cmr_glc, [("dose", "dose")])])
workflow.connect([(inputnode, compute_cmr_glc, [("weight", "weight")])])
workflow.connect([(inputnode, compute_cmr_glc, [("delay", "delay")])])
workflow.connect([(inputnode, compute_cmr_glc, [("glycemie", "glycemie")])])
workflow.connect([(inputnode, compute_cmr_glc, [("scan_time", "scan_time")])])
if reg_pet_T1:
workflow.connect([(inputnode, reg_pet_T1, [("fdgpet", "in_file")])])
workflow.connect(
[(reorientBrain, reg_pet_T1, [("out_file", "reference")])])
workflow.connect(
[(reg_pet_T1, reslice_fdgpet, [("out_file", "in_file")])])
workflow.connect(
[(reorientROIs, reslice_fdgpet, [("out_file", "reslice_like")])])
workflow.connect(
[(reslice_fdgpet, compute_cmr_glc, [("out_file", "in_file")])])
else:
workflow.connect([(inputnode, reslice_fdgpet, [("fdgpet", "in_file")])])
workflow.connect(
[(reorientROIs, reslice_fdgpet, [("out_file", "reslice_like")])])
workflow.connect(
[(reslice_fdgpet, compute_cmr_glc, [("out_file", "in_file")])])
workflow.connect(
[(compute_cmr_glc, fdgpet_regions, [("out_file", "in_files")])])
workflow.connect(
[(thalamus2precuneus2cortex_ROIs, fdgpet_regions, [("out_file", "segmentation_file")])])
workflow.connect([(nonlinfit_node, coregister,[("FA","in_file")])])
workflow.connect([(make_wm_mask, coregister,[('out_file','reference')])])
workflow.connect([(nonlinfit_node, tck2trk,[("FA","image_file")])])
workflow.connect([(reorientBrain, tck2trk,[("out_file","registration_image_file")])])
workflow.connect([(coregister, tck2trk,[("out_matrix_file","matrix_file")])])
workflow.connect([(coregister, invertxfm,[("out_matrix_file","in_file")])])
workflow.connect([(invertxfm, WM_to_FA,[("out_file","in_matrix_file")])])
workflow.connect([(make_wm_mask, WM_to_FA,[("out_file","in_file")])])
workflow.connect([(nonlinfit_node, WM_to_FA,[("FA","reference")])])
workflow.connect([(invertxfm, TermMask_to_FA,[("out_file","in_matrix_file")])])
workflow.connect([(make_termination_mask, TermMask_to_FA,[("out_file","in_file")])])
workflow.connect([(nonlinfit_node, TermMask_to_FA,[("FA","reference")])])
workflow.connect([(nonlinfit_node, median3d, [("binary_mask", "in_file")])])
workflow.connect(
[(median3d, erode_mask_firstpass, [("out_file", "in_file")])])
workflow.connect(
[(erode_mask_firstpass, erode_mask_secondpass, [("out_file", "in_file")])])
workflow.connect([(nonlinfit_node, MRmult_merge, [("FA", "in1")])])
workflow.connect(
[(erode_mask_secondpass, MRmult_merge, [("out_file", "in2")])])
workflow.connect([(MRmult_merge, MRmultiply, [("out", "in_files")])])
workflow.connect([(MRmultiply, threshold_FA, [("out_file", "in_file")])])
workflow.connect(
[(threshold_FA, estimateresponse, [("out_file", "mask_image")])])
workflow.connect([(inputnode, estimateresponse, [("dwi", "in_file")])])
workflow.connect(
[(fsl2mrtrix, estimateresponse, [("encoding_file", "encoding_file")])])
workflow.connect([(inputnode, csdeconv, [("dwi", "in_file")])])
#workflow.connect(
# [(TermMask_to_FA, csdeconv, [("out_file", "mask_image")])])
workflow.connect(
[(estimateresponse, csdeconv, [("response", "response_file")])])
workflow.connect(
[(fsl2mrtrix, csdeconv, [("encoding_file", "encoding_file")])])
workflow.connect(
[(WM_to_FA, CSDstreamtrack, [("out_file", "seed_file")])])
workflow.connect(
[(TermMask_to_FA, CSDstreamtrack, [("out_file", "mask_file")])])
workflow.connect(
[(csdeconv, CSDstreamtrack, [("spherical_harmonics_image", "in_file")])])
workflow.connect([(CSDstreamtrack, tck2trk, [("tracked", "in_file")])])
workflow.connect(
[(tck2trk, thalamus2precuneus2cortex, [("out_file", "tract_file")])])
workflow.connect(
[(inputnode, thalamus2precuneus2cortex, [("subject_id", "out_matrix_file")])])
workflow.connect(
[(inputnode, thalamus2precuneus2cortex, [("subject_id", "out_matrix_mat_file")])])
workflow.connect(
[(reorientROIs, thalamus2precuneus2cortex_ROIs, [("out_file", "in_file")])])
workflow.connect(
[(thalamus2precuneus2cortex_ROIs, thalamus2precuneus2cortex, [("out_file", "roi_file")])])
workflow.connect(
[(thalamus2precuneus2cortex, fdgpet_regions, [("matrix_file", "resolution_network_file")])])
workflow.connect(
[(inputnode, write_csv_data, [("subject_id", "subject_id")])])
workflow.connect(
[(fdgpet_regions, write_csv_data, [("stats_file", "fdg_stats_file")])])
workflow.connect(
[(thalamus2precuneus2cortex, write_csv_data, [("intersection_matrix_file", "dwi_network_file")])])
output_fields = ["fa", "rgb_fa", "md", "csdeconv", "tracts_tck", "rois", "t1",
"t1_brain", "wmmask_dtispace", "fa_t1space", "summary", "filtered_tractographies",
"matrix_file", "connectome", "CMR_nodes", "fiber_labels_noorphans", "fiber_length_file",
"fiber_label_file", "intersection_matrix_mat_file"]
outputnode = pe.Node(
interface=util.IdentityInterface(fields=output_fields),
name="outputnode")
workflow.connect(
[(CSDstreamtrack, outputnode, [("tracked", "tracts_tck")]),
(csdeconv, outputnode,
[("spherical_harmonics_image", "csdeconv")]),
(nonlinfit_node, outputnode, [("FA", "fa")]),
(coregister, outputnode, [("out_file", "fa_t1space")]),
(reorientBrain, outputnode, [("out_file", "t1_brain")]),
(reorientT1, outputnode, [("out_file", "t1")]),
(thalamus2precuneus2cortex_ROIs, outputnode, [("out_file", "rois")]),
(thalamus2precuneus2cortex, outputnode, [("filtered_tractographies", "filtered_tractographies")]),
(thalamus2precuneus2cortex, outputnode, [("matrix_file", "connectome")]),
(thalamus2precuneus2cortex, outputnode, [("fiber_labels_noorphans", "fiber_labels_noorphans")]),
(thalamus2precuneus2cortex, outputnode, [("fiber_length_file", "fiber_length_file")]),
(thalamus2precuneus2cortex, outputnode, [("fiber_label_file", "fiber_label_file")]),
(thalamus2precuneus2cortex, outputnode, [("intersection_matrix_mat_file", "intersection_matrix_mat_file")]),
(fdgpet_regions, outputnode, [("networks", "CMR_nodes")]),
(nonlinfit_node, outputnode, [("rgb_fa", "rgb_fa")]),
(nonlinfit_node, outputnode, [("MD", "md")]),
(write_csv_data, outputnode, [("out_file", "summary")]),
])
return workflow
def damaged_brain_dti_processing(name="dwi_preproc", use_FAST_masks=True):
'''
Uses both Freesurfer and FAST to mask the white matter
because neither works sufficiently well in patients
'''
'''
Define inputs and outputs of the workflow
'''
inputnode = pe.Node(
interface=util.IdentityInterface(fields=["subjects_dir",
"subject_id",
"dwi",
"bvecs",
"bvals"]),
name="inputnode")
outputnode = pe.Node(
interface=util.IdentityInterface(fields=["single_fiber_mask",
"fa",
"rgb_fa",
"md",
"mode",
"t1",
"t1_brain",
"wm_mask",
"term_mask",
"aparc_aseg",
"tissue_class_files",
"gm_prob",
"wm_prob",
"csf_prob"]),
name="outputnode")
'''
Define the nodes
'''
nonlinfit_interface = util.Function(
input_names=["dwi", "bvecs", "bvals", "base_name"],
output_names=["tensor", "FA", "MD", "evecs", "evals",
"rgb_fa", "norm", "mode", "binary_mask", "b0_masked"],
function=nonlinfit_fn)
nonlinfit_node = pe.Node(
interface=nonlinfit_interface, name="nonlinfit_node")
erode_mask_firstpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_firstpass')
erode_mask_firstpass.inputs.out_filename = "b0_mask_median3D_erode.nii.gz"
erode_mask_secondpass = pe.Node(interface=mrtrix.Erode(),
name='erode_mask_secondpass')
erode_mask_secondpass.inputs.out_filename = "b0_mask_median3D_erode_secondpass.nii.gz"
threshold_FA = pe.Node(interface=fsl.ImageMaths(), name='threshold_FA')
threshold_FA.inputs.op_string = "-thr 0.8 -uthr 0.99"
threshold_mode = pe.Node(interface=fsl.ImageMaths(), name='threshold_mode')
threshold_mode.inputs.op_string = "-thr 0.9 -fmedian -fmedian"
fast_seg_T1 = pe.Node(interface=fsl.FAST(), name='fast_seg_T1')
fast_seg_T1.inputs.segments = True
fast_seg_T1.inputs.probability_maps = True
if not use_FAST_masks:
fix_wm_mask = pe.Node(interface=fsl.MultiImageMaths(), name='fix_wm_mask')
fix_wm_mask.inputs.op_string = "-mul %s"
if use_FAST_masks:
make_termination_mask = pe.Node(
interface=fsl.MultiImageMaths(), name='make_termination_mask')
make_termination_mask.inputs.op_string = "-add %s -bin"
else:
make_termination_mask = pe.Node(
interface=fsl.ImageMaths(), name='make_termination_mask')
make_termination_mask.inputs.op_string = "-bin"
fix_termination_mask = pe.Node(
interface=fsl.MultiImageMaths(), name='fix_termination_mask')
fix_termination_mask.inputs.op_string = "-binv -mul %s"
wm_mask_interface = util.Function(input_names=["in_file", "out_filename"],
output_names=["out_file"],
function=wm_labels_only)
make_wm_mask = pe.Node(interface=wm_mask_interface, name='make_wm_mask')
MRmultiply = pe.Node(interface=mrtrix.MRMultiply(), name='MRmultiply')
MRmultiply.inputs.out_filename = "Eroded_FA.nii.gz"
MultFAbyMode = pe.Node(interface=mrtrix.MRMultiply(), name='MultFAbyMode')
MRmult_merge = pe.Node(interface=util.Merge(2), name='MRmultiply_merge')
MultFAbyMode_merge = pe.Node(
interface=util.Merge(2), name='MultFAbyMode_merge')
median3d = pe.Node(interface=mrtrix.MedianFilter3D(), name='median3D')
FreeSurferSource = pe.Node(
interface=nio.FreeSurferSource(), name='fssource')
mri_convert_Brain = pe.Node(
interface=fs.MRIConvert(), name='mri_convert_Brain')
mri_convert_Brain.inputs.out_type = 'nii'
mri_convert_Brain.inputs.no_change = True
mri_convert_Ribbon = mri_convert_Brain.clone("mri_convert_Ribbon")
mri_convert_ROIs = mri_convert_Brain.clone("mri_convert_ROIs")
mri_convert_T1 = mri_convert_Brain.clone("mri_convert_T1")
'''
Connect the workflow
'''
workflow = pe.Workflow(name=name)
workflow.base_dir = name
'''
Structural processing to create seed and termination masks
'''
workflow.connect(
[(inputnode, FreeSurferSource, [("subjects_dir", "subjects_dir")])])
workflow.connect(
[(inputnode, FreeSurferSource, [("subject_id", "subject_id")])])
workflow.connect(
[(FreeSurferSource, mri_convert_T1, [('T1', 'in_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_Brain, [('brain', 'in_file')])])
workflow.connect(
[(inputnode, mri_convert_T1, [(('subject_id', add_subj_name_to_T1), 'out_file')])])
workflow.connect(
[(inputnode, mri_convert_Brain, [(('subject_id', add_subj_name_to_T1brain), 'out_file')])])
workflow.connect(
[(mri_convert_Brain, fast_seg_T1, [('out_file', 'in_files')])])
workflow.connect(
[(inputnode, fast_seg_T1, [("subject_id", "out_basename")])])
workflow.connect(
[(FreeSurferSource, mri_convert_ROIs, [(('aparc_aseg', select_aparc), 'in_file')])])
workflow.connect(
[(inputnode, mri_convert_ROIs, [(('subject_id', add_subj_name_to_aparc), 'out_file')])])
if use_FAST_masks:
workflow.connect(
[(fast_seg_T1, outputnode, [(('tissue_class_files', select_WM), 'wm_mask')])])
workflow.connect(
[(fast_seg_T1, make_termination_mask, [(('tissue_class_files', select_GM), 'in_file')])])
workflow.connect(
[(fast_seg_T1, make_termination_mask, [(('tissue_class_files', select_WM), 'operand_files')])])
workflow.connect(
[(inputnode, make_termination_mask, [(('subject_id', add_subj_name_to_termmask), 'out_file')])])
workflow.connect(
[(make_termination_mask, outputnode, [("out_file", "term_mask")])])
else:
workflow.connect(
[(mri_convert_ROIs, make_wm_mask, [('out_file', 'in_file')])])
workflow.connect(
[(make_wm_mask, fix_wm_mask, [('out_file', 'operand_files')])])
workflow.connect(
[(fast_seg_T1, fix_wm_mask, [(('tissue_class_files', select_WM), 'in_file')])])
workflow.connect(
[(FreeSurferSource, mri_convert_Ribbon, [(('ribbon', select_ribbon), 'in_file')])])
workflow.connect(
[(mri_convert_Ribbon, make_termination_mask, [('out_file', 'in_file')])])
workflow.connect(
[(make_termination_mask, fix_termination_mask, [('out_file', 'operand_files')])])
workflow.connect(
[(fast_seg_T1, fix_termination_mask, [(('tissue_class_files', select_CSF), 'in_file')])])
'''
Diffusion processing
'''
workflow.connect(inputnode, 'subject_id', nonlinfit_node, 'base_name')
workflow.connect(inputnode, 'dwi', nonlinfit_node, 'dwi')
workflow.connect(inputnode, 'bvecs', nonlinfit_node, 'bvecs')
workflow.connect(inputnode, 'bvals', nonlinfit_node, 'bvals')
workflow.connect(
[(nonlinfit_node, median3d, [("binary_mask", "in_file")])])
workflow.connect(
[(median3d, erode_mask_firstpass, [("out_file", "in_file")])])
workflow.connect(
[(erode_mask_firstpass, erode_mask_secondpass, [("out_file", "in_file")])])
workflow.connect([(nonlinfit_node, MRmult_merge, [("FA", "in1")])])
workflow.connect(
[(erode_mask_secondpass, MRmult_merge, [("out_file", "in2")])])
workflow.connect([(MRmult_merge, MRmultiply, [("out", "in_files")])])
workflow.connect([(MRmultiply, threshold_FA, [("out_file", "in_file")])])
'''
Create a single fiber mask
'''
workflow.connect([(nonlinfit_node, threshold_mode, [("mode", "in_file")])])
workflow.connect(
[(threshold_mode, MultFAbyMode_merge, [("out_file", "in1")])])
workflow.connect(
[(threshold_FA, MultFAbyMode_merge, [("out_file", "in2")])])
workflow.connect(
[(MultFAbyMode_merge, MultFAbyMode, [("out", "in_files")])])
'''
Fix output names with subject ID
'''
workflow.connect(
[(inputnode, MultFAbyMode, [(('subject_id', add_subj_name_to_sfmask), 'out_filename')])])
if not use_FAST_masks:
workflow.connect(
[(inputnode, make_wm_mask, [(('subject_id', add_subj_name_to_wmmask), 'out_filename')])])
workflow.connect(
[(inputnode, fix_wm_mask, [(('subject_id', add_subj_name_to_wmmask), 'out_file')])])
workflow.connect(
[(inputnode, fix_termination_mask, [(('subject_id', add_subj_name_to_termmask), 'out_file')])])
'''
Connect outputnode
'''
workflow.connect(
[(fast_seg_T1, outputnode, [("tissue_class_files", "tissue_class_files")])])
workflow.connect(
[(fast_seg_T1, outputnode, [(('probability_maps', select_GM), 'gm_prob')])])
workflow.connect(
[(fast_seg_T1, outputnode, [(('probability_maps', select_WM), 'wm_prob')])])
workflow.connect(
[(fast_seg_T1, outputnode, [(('probability_maps', select_CSF), 'csf_prob')])])
workflow.connect([
(mri_convert_ROIs, outputnode, [("out_file", "aparc_aseg")]),
(nonlinfit_node, outputnode, [("FA", "fa")]),
(nonlinfit_node, outputnode, [("rgb_fa", "rgb_fa")]),
(nonlinfit_node, outputnode, [("MD", "md")]),
(nonlinfit_node, outputnode, [("mode", "mode")]),
(MultFAbyMode, outputnode, [("out_file", "single_fiber_mask")]),
(mri_convert_Brain, outputnode, [("out_file", "t1_brain")]),
(mri_convert_T1, outputnode, [("out_file", "t1")]),
])
if not use_FAST_masks:
workflow.connect(
[(fix_wm_mask, outputnode, [("out_file", "wm_mask")])])
workflow.connect(
[(fix_termination_mask, outputnode, [("out_file", "term_mask")])])
return workflow
#Wraps the executable command ``AverageImages``.
ants_AverageImages = pe.Node(interface=ants.AverageImages(),
name='ants_AverageImages')
#Wraps the executable command ``modelfit``.
camino_ModelFit = pe.Node(interface=camino.ModelFit(), name='camino_ModelFit')
#Wraps the executable command ``vtkstreamlines``.
camino_VtkStreamlines = pe.Node(interface=camino.VtkStreamlines(),
name='camino_VtkStreamlines')
#Wraps the executable command ``dt2nii``.
camino_DT2NIfTI = pe.Node(interface=camino.DT2NIfTI(), name='camino_DT2NIfTI')
#Wraps the executable command ``erode``.
mrtrix_Erode = pe.Node(interface=mrtrix.Erode(), name='mrtrix_Erode')
#Converts separate b-values and b-vectors from text files (FSL style) into a
mrtrix_FSL2MRTrix = pe.Node(interface=mrtrix.FSL2MRTrix(),
name='mrtrix_FSL2MRTrix')
#Wraps the executable command ``mrconvert``.
mrtrix_MRConvert = pe.Node(interface=mrtrix.MRConvert(),
name='mrtrix_MRConvert')
#Use spm to perform slice timing correction.
spm_SliceTiming = pe.Node(interface=spm.SliceTiming(), name='spm_SliceTiming')
#uses spm_reslice to resample in_file into space of space_defining
spm_Reslice = pe.Node(interface=spm.Reslice(), name='spm_Reslice')
