def create_workflow():
workflow = Workflow(
name='transform_manual_mask')
inputs = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'refsubject_id',
'ref_funcmask',
'ref_func',
'funcs',
]), name='in')
# Find the transformation matrix func_ref -> func
# First find transform from func to manualmask's ref func
# first take the median (flirt functionality has changed and no longer automatically takes the first volume when given 4D files)
median_func = MapNode(
interface=fsl.maths.MedianImage(dimension="T"),
name='median_func',
iterfield=('in_file'),
)
findtrans = MapNode(fsl.FLIRT(),
iterfield=['in_file'],
name='findtrans'
)
# Invert the matrix transform
invert = MapNode(fsl.ConvertXFM(invert_xfm=True),
name='invert',
iterfield=['in_file'],
)
workflow.connect(findtrans, 'out_matrix_file',
invert, 'in_file')
# Transform the manualmask to be aligned with func
funcreg = MapNode(ApplyXFMRefName(),
name='funcreg',
iterfield=['in_matrix_file', 'reference'],
)
workflow.connect(inputs, 'funcs',
median_func, 'in_file')
workflow.connect(median_func, 'out_file',
findtrans, 'in_file')
workflow.connect(inputs, 'ref_func',
findtrans, 'reference')
workflow.connect(invert, 'out_file',
funcreg, 'in_matrix_file')
workflow.connect(inputs, 'ref_func',
funcreg, 'in_file')
workflow.connect(inputs, 'funcs',
funcreg, 'reference')
return workflow
def create_moco_pipeline(name='motion_correction'):
# initiate workflow
moco = Workflow(name='motion_correction')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['epi']), name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'epi_moco', 'par_moco', 'mat_moco', 'rms_moco', 'epi_mean', 'rotplot',
'transplot', 'dispplots', 'tsnr_file'
]),
name='outputnode')
# mcflirt motion correction to 1st volume
mcflirt = Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
ref_vol=1,
out_file='rest_realigned.nii.gz'),
name='mcflirt')
# plot motion parameters
rotplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation_plot.png'),
name='rotplotter')
transplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation_plot.png'),
name='transplotter')
dispplotter = MapNode(interface=fsl.PlotMotionParams(
in_source='fsl',
plot_type='displacement',
),
name='dispplotter',
iterfield=['in_file'])
dispplotter.iterables = ('plot_type', ['displacement'])
# calculate tmean
tmean = Node(fsl.maths.MeanImage(dimension='T',
out_file='rest_realigned_mean.nii.gz'),
name='tmean')
# calculate tsnr
tsnr = Node(confounds.TSNR(), name='tsnr')
# create connections
moco.connect([(inputnode, mcflirt, [('epi', 'in_file')]),
(mcflirt, tmean, [('out_file', 'in_file')]),
(mcflirt, rotplotter, [('par_file', 'in_file')]),
(mcflirt, transplotter, [('par_file', 'in_file')]),
(mcflirt, dispplotter, [('rms_files', 'in_file')]),
(tmean, outputnode, [('out_file', 'epi_mean')]),
(mcflirt, outputnode, [('out_file', 'epi_moco'),
('par_file', 'par_moco'),
('mat_file', 'mat_moco'),
('rms_files', 'rms_moco')]),
(rotplotter, outputnode, [('out_file', 'rotplot')]),
(transplotter, outputnode, [('out_file', 'transplot')]),
(dispplotter, outputnode, [('out_file', 'dispplots')]),
(mcflirt, tsnr, [('out_file', 'in_file')]),
(tsnr, outputnode, [('tsnr_file', 'tsnr_file')])])
return moco
def create_corr_ts(name='corr_ts'):
corr_ts = Workflow(name='corr_ts')
# Define nodes
inputnode = Node(util.IdentityInterface(fields=[
'ts',
'hc_mask',
]),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(
fields=['corrmap', 'corrmap_z', 'hc_ts']),
name='outputnode')
#extract mean time series of mask
mean_TS = MapNode(interface=fsl.ImageMeants(),
name="mean_TS",
iterfield='mask')
#iterate over using Eigenvalues or mean
#mean_TS.iterables = ("eig", [True, False])
#mean_TS.inputs.order = 1
#mean_TS.inputs.show_all = True
mean_TS.inputs.eig = False #use only mean of ROI
mean_TS.inputs.out_file = "TS.1D"
#calculate correlation of all voxels with seed voxel
corr_TS = MapNode(interface=afni.Fim(),
name='corr_TS',
iterfield='ideal_file')
corr_TS.inputs.out = 'Correlation'
corr_TS.inputs.out_file = "corr.nii.gz"
apply_FisherZ = MapNode(interface=afni.Calc(),
name="apply_FisherZ",
iterfield='in_file_a')
apply_FisherZ.inputs.expr = 'log((1+a)/(1-a))/2' #log = ln
apply_FisherZ.inputs.out_file = 'corr_Z.nii.gz'
apply_FisherZ.inputs.outputtype = "NIFTI"
corr_ts.connect([(inputnode, mean_TS, [('hc_mask', 'mask')]),
(inputnode, mean_TS, [('ts', 'in_file')]),
(mean_TS, outputnode, [('out_file', 'hc_ts')]),
(inputnode, corr_TS, [('ts', 'in_file')]),
(mean_TS, corr_TS, [('out_file', 'ideal_file')]),
(corr_TS, apply_FisherZ, [('out_file', 'in_file_a')]),
(corr_TS, outputnode, [('out_file', 'corrmap')]),
(apply_FisherZ, outputnode, [('out_file', 'corrmap_z')])])
return corr_ts
def create_smoothing_pipeline(name='smoothing'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI')
# initiate workflow
smoothing = Workflow(name='smoothing')
# inputnode
inputnode=Node(util.IdentityInterface(fields=['ts_transformed',
'fwhm'
]),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['ts_smoothed'
]),
name='outputnode')
#apply smoothing
smooth = MapNode(fsl.Smooth(),name = 'smooth', iterfield='in_file')
smoothing.connect([
(inputnode, smooth, [
('ts_transformed', 'in_file'),
('fwhm', 'fwhm')]
),
(smooth, outputnode, [('smoothed_file', 'ts_smoothed')]
)
])
return smoothing
def create_workflow_allin_slices(name='motion_correction', iterfield=['in_file']):
workflow = Workflow(name=name)
inputs = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'ref_func',
'ref_func_weights',
'funcs',
'funcs_masks',
'mc_method',
]), name='in')
inputs.iterables = [
('mc_method', ['afni:3dAllinSlices'])
]
mc = MapNode(
AFNIAllinSlices(),
iterfield=iterfield,
name='mc')
workflow.connect(
[(inputs, mc,
[('funcs', 'in_file'),
('ref_func_weights', 'in_weight_file'),
('ref_func', 'ref_file'),
])])
return workflow
def create_ants_registration_pipeline(name='ants_registration'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
ants_registration = Workflow(name='ants_registration')
# inputnode
inputnode = Node(util.IdentityInterface(
fields=['corr_Z', 'ants_affine', 'ants_warp', 'ref']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'ants_reg_corr_Z',
]),
name='outputnode')
#also transform to mni space
collect_transforms = Node(interface=util.Merge(2),
name='collect_transforms')
ants_reg = MapNode(ants.ApplyTransforms(input_image_type=3,
dimension=3,
interpolation='Linear'),
name='ants_reg',
iterfield='input_image')
ants_registration.connect([
(inputnode, ants_reg, [('corr_Z', 'input_image')]),
(inputnode, ants_reg, [('ref', 'reference_image')]),
(inputnode, collect_transforms, [('ants_affine', 'in1')]),
(inputnode, collect_transforms, [('ants_warp', 'in2')]),
(collect_transforms, ants_reg, [('out', 'transforms')]),
(ants_reg, outputnode, [('output_image', 'ants_reg_corr_Z')])
])
return ants_registration
def create_images_workflow():
# Correct for the sphinx position and use reorient to standard.
workflow = Workflow(name='minimal_proc')
inputs = Node(IdentityInterface(fields=['images']), name="in")
outputs = Node(IdentityInterface(fields=['images']), name="out")
sphinx = MapNode(fs.MRIConvert(sphinx=True),
iterfield=['in_file'],
name='sphinx')
workflow.connect(inputs, 'images', sphinx, 'in_file')
ro = MapNode(fsl.Reorient2Std(), iterfield=['in_file'], name='ro')
workflow.connect(sphinx, 'out_file', ro, 'in_file')
workflow.connect(ro, 'out_file', outputs, 'images')
return workflow
def create_warp_transform(name='warpmultitransform'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
warp = Workflow(name='warp')
# inputnode
inputnode = MapNode(util.IdentityInterface(fields=[
'input_image', 'atlas_aff2template', 'atlas_warp2template',
'atlas2target_composite', 'template2target_inverse', 'ref'
]),
name='inputnode',
iterfield=['input_image', 'ref'])
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'ants_reg',
]),
name='outputnode')
collect_transforms = Node(interface=util.Merge(4),
name='collect_transforms')
ants_reg = MapNode(ants.ApplyTransforms(input_image_type=3,
dimension=3,
interpolation='Linear'),
name='apply_ants_reg',
iterfield=['input_image', 'reference_image'])
ants_reg.inputs.invert_transform_flags = [False, False, False, False]
warp.connect([
(inputnode, ants_reg, [('input_image', 'input_image')]),
(inputnode, ants_reg, [('ref', 'reference_image')]),
(inputnode, collect_transforms, [('atlas_aff2template', 'in4')]),
(inputnode, collect_transforms, [('atlas_warp2template', 'in3')]),
(inputnode, collect_transforms, [('atlas2target_composite', 'in2')]),
(inputnode, collect_transforms, [('template2target_inverse', 'in1')]),
(collect_transforms, ants_reg, [
('out', 'transforms')
]), #for WarpImageMultiTransform:transformation_series
(ants_reg, outputnode, [('output_image', 'ants_reg')])
])
return warp
def _make_nodes(self, cwd=None):
"""
Cast generated nodes to be Arcana nodes
"""
for i, node in NipypeMapNode._make_nodes(self, cwd=cwd):
# "Cast" NiPype node to a Arcana Node and set Arcana Node
# parameters
node.__class__ = Node
node._arcana_init(
**{n: getattr(self, n) for n in self.arcana_params})
yield i, node
def create_workflow():
workflow = Workflow(name='transform_manual_mask')
inputs = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'manualmask',
'manualmask_func_ref',
'funcs',
]),
name='in')
# Find the transformation matrix func_ref -> func
# First find transform from func to manualmask's ref func
findtrans = MapNode(fsl.FLIRT(), iterfield=['in_file'], name='findtrans')
# Invert the matrix transform
invert = MapNode(
fsl.ConvertXFM(invert_xfm=True),
name='invert',
iterfield=['in_file'],
)
workflow.connect(findtrans, 'out_matrix_file', invert, 'in_file')
# Transform the manualmask to be aligned with func
funcreg = MapNode(
ApplyXFMRefName(),
name='funcreg',
iterfield=['in_matrix_file', 'reference'],
)
workflow.connect(inputs, 'funcs', findtrans, 'in_file')
workflow.connect(inputs, 'manualmask_func_ref', findtrans, 'reference')
workflow.connect(invert, 'out_file', funcreg, 'in_matrix_file')
workflow.connect(inputs, 'manualmask', funcreg, 'in_file')
workflow.connect(inputs, 'funcs', funcreg, 'reference')
return workflow
def _make_nodes(self, cwd=None):
"""
Cast generated nodes to be Arcana nodes
"""
for i, node in NipypeMapNode._make_nodes(self, cwd=cwd):
# "Cast" NiPype node to a Arcana Node and set Arcana Node
# parameters
node.__class__ = self.node_cls
node._environment = self._environment
node._versions = self._versions
node._wall_time = self._wall_time
node._annotations = self._annotations
yield i, node
def create_workflow(xfm_dir,
xfm_pattern,
atlas_dir,
atlas_pattern,
source_dir,
source_pattern,
work_dir,
out_dir,
name="new_data_to_atlas_space"):
wf = Workflow(name=name)
wf.base_dir = os.path.join(work_dir)
datasource_source = Node(interface=DataGrabber(sort_filelist=True),
name='datasource_source')
datasource_source.inputs.base_directory = os.path.abspath(source_dir)
datasource_source.inputs.template = source_pattern
datasource_xfm = Node(interface=DataGrabber(sort_filelist=True),
name='datasource_xfm')
datasource_xfm.inputs.base_directory = os.path.abspath(xfm_dir)
datasource_xfm.inputs.template = xfm_pattern
datasource_atlas = Node(interface=DataGrabber(sort_filelist=True),
name='datasource_atlas')
datasource_atlas.inputs.base_directory = os.path.abspath(atlas_dir)
datasource_atlas.inputs.template = atlas_pattern
resample = MapNode(interface=Resample(sinc_interpolation=True),
name='resample_',
iterfield=['input_file', 'transformation'])
wf.connect(datasource_source, 'outfiles', resample, 'input_file')
wf.connect(datasource_xfm, 'outfiles', resample, 'transformation')
wf.connect(datasource_atlas, 'outfiles', resample, 'like')
bigaverage = Node(interface=BigAverage(output_float=True, robust=False),
name='bigaverage',
iterfield=['input_file'])
wf.connect(resample, 'output_file', bigaverage, 'input_files')
datasink = Node(interface=DataSink(base_directory=out_dir,
container=out_dir),
name='datasink')
wf.connect([(bigaverage, datasink, [('output_file', 'average')])])
wf.connect([(resample, datasink, [('output_file', 'atlas_space')])])
wf.connect([(datasource_xfm, datasink, [('outfiles', 'transforms')])])
return wf
name='selecttemplates')
wf.connect([(infosource, selectfiles, [('subject', 'subject'),
('ses', 'ses')])])
#wf.connect([(infosource, selecttemplates, [('ses','ses')])])
############
## Step 1 ##
############
# Bias correct the T1 and TSE
#input_image not input
T1_N4_n = MapNode(N4BiasFieldCorrection(dimension=3,
bspline_fitting_distance=300,
shrink_factor=2,
n_iterations=[50, 50, 40, 30],
rescale_intensities=True,
num_threads=20),
name='T1_N4_n',
iterfield=['input_image'])
wf.connect([(selectfiles, T1_N4_n, [('mprage', 'input_image')])])
T2_N4_n = MapNode(N4BiasFieldCorrection(dimension=3,
bspline_fitting_distance=300,
shrink_factor=2,
n_iterations=[50, 50, 40, 30],
rescale_intensities=True,
num_threads=20),
name='T2_N4_n',
iterfield=['input_image'])
wf.connect([(selectfiles, T2_N4_n, [('tse', 'input_image')])])
def create_workflow(unwarp_direction='y'):
workflow = Workflow(name='func_unwarp')
inputs = Node(
IdentityInterface(fields=[
# 'subject_id',
# 'session_id',
'funcs',
'funcmasks',
'fmap_phasediff',
'fmap_magnitude',
'fmap_mask',
]),
name='in')
outputs = Node(IdentityInterface(fields=[
'funcs',
'funcmasks',
]),
name='out')
# --- --- --- --- --- --- --- Convert to radians --- --- --- --- --- ---
# fslmaths $FUNCDIR/"$SUB"_B0_phase -div 100 -mul 3.141592653589793116
# -odt float $FUNCDIR/"$SUB"_B0_phase_rescaled
# in_file --> out_file
phase_radians = Node(fsl.ImageMaths(
op_string='-mul 3.141592653589793116 -div 100',
out_data_type='float',
suffix='_radians',
),
name='phaseRadians')
workflow.connect(inputs, 'fmap_phasediff', phase_radians, 'in_file')
# --- --- --- --- --- --- --- Unwrap Fieldmap --- --- --- --- --- ---
# --- Unwrap phase
# prelude -p $FUNCDIR/"$SUB"_B0_phase_rescaled
# -a $FUNCDIR/"$SUB"_B0_magnitude
# -o $FUNCDIR/"$SUB"_fmri_B0_phase_rescaled_unwrapped
# -m $FUNCDIR/"$SUB"_B0_magnitude_brain_mask
# magnitude_file, phase_file [, mask_file] --> unwrapped_phase_file
unwrap = MapNode(
PRELUDE(),
name='unwrap',
iterfield=['mask_file'],
)
workflow.connect([
(inputs, unwrap, [('fmap_magnitude', 'magnitude_file')]),
(inputs, unwrap, [('fmap_mask', 'mask_file')]),
(phase_radians, unwrap, [('out_file', 'phase_file')]),
])
# --- --- --- --- --- --- --- Convert to Radians / Sec --- --- --- --- ---
# fslmaths $FUNCDIR/"$SUB"_B0_phase_rescaled_unwrapped
# -mul 200 $FUNCDIR/"$SUB"_B0_phase_rescaled_unwrapped
rescale = MapNode(
fsl.ImageMaths(op_string='-mul 200'),
name='rescale',
iterfield=['in_file'],
)
workflow.connect(unwrap, 'unwrapped_phase_file', rescale, 'in_file')
# --- --- --- --- --- --- --- Unmask fieldmap --- --- --- --- ---
unmask_phase = MapNode(
FUGUE(
save_unmasked_fmap=True,
unwarp_direction=unwarp_direction,
),
name='unmask_phase',
iterfield=['mask_file', 'fmap_in_file'],
)
workflow.connect(rescale, 'out_file', unmask_phase, 'fmap_in_file')
workflow.connect(inputs, 'fmap_mask', unmask_phase, 'mask_file')
# --- --- --- --- --- --- --- Undistort functionals --- --- --- --- ---
# phasemap_in_file = phasediff
# mask_file = mask
# in_file = functional image
# dwell_time = 0.0005585 s
# unwarp_direction
undistort = MapNode(
FUGUE(
dwell_time=0.0005585,
# based on Process-NHP-MRI/Process_functional_data.md:
asym_se_time=0.020,
smooth3d=2.0,
median_2dfilter=True,
unwarp_direction=unwarp_direction,
),
name='undistort',
iterfield=['in_file', 'mask_file', 'fmap_in_file'],
)
workflow.connect(unmask_phase, 'fmap_out_file', undistort, 'fmap_in_file')
workflow.connect(inputs, 'fmap_mask', undistort, 'mask_file')
workflow.connect(inputs, 'funcs', undistort, 'in_file')
undistort_masks = undistort.clone('undistort_masks')
workflow.connect(unmask_phase, 'fmap_out_file', undistort_masks,
'fmap_in_file')
workflow.connect(inputs, 'fmap_mask', undistort_masks, 'mask_file')
workflow.connect(inputs, 'funcmasks', undistort_masks, 'in_file')
workflow.connect(undistort, 'unwarped_file', outputs, 'funcs')
workflow.connect(undistort_masks, 'unwarped_file', outputs, 'funcmasks')
return workflow
def create_moco_pipeline(working_dir, ds_dir, name='motion_correction'):
"""
Workflow for motion correction to 1st volume
based on https://github.com/NeuroanatomyAndConnectivity/pipelines/blob/master/src/lsd_lemon/func_preproc/moco.py
"""
# initiate workflow
moco_wf = Workflow(name=name)
moco_wf.base_dir = os.path.join(working_dir,'LeiCA_resting', 'rsfMRI_preprocessing')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# I/O NODES
inputnode = Node(util.IdentityInterface(fields=['epi',
'vols_to_drop']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['epi_moco',
'par_moco',
'mat_moco',
'rms_moco',
'initial_mean_epi_moco',
'rotplot',
'transplot',
'dispplots',
'tsnr_file',
'epi_mask']),
name='outputnode')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
# REMOVE FIRST VOLUMES
drop_vols = Node(util.Function(input_names=['in_file','t_min'],
output_names=['out_file'],
function=strip_rois_func),
name='remove_vol')
moco_wf.connect(inputnode, 'epi', drop_vols, 'in_file')
moco_wf.connect(inputnode, 'vols_to_drop', drop_vols, 't_min')
# MCFILRT MOCO TO 1st VOLUME
mcflirt = Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
ref_vol=0,
out_file='rest_realigned.nii.gz'
),
name='mcflirt')
moco_wf.connect(drop_vols, 'out_file', mcflirt, 'in_file')
moco_wf.connect([(mcflirt, ds, [('par_file', 'realign.par.@par'),
('mat_file', 'realign.MAT.@mat'),
('rms_files', 'realign.plots.@rms')])])
moco_wf.connect([(mcflirt, outputnode, [('out_file', 'epi_moco'),
('par_file', 'par_moco'),
('mat_file', 'mat_moco'),
('rms_files', 'rms_moco')])])
# CREATE MEAN EPI (INTENSITY NORMALIZED)
initial_mean_epi_moco = Node(fsl.maths.MeanImage(dimension='T',
out_file='initial_mean_epi_moco.nii.gz'),
name='initial_mean_epi_moco')
moco_wf.connect(mcflirt, 'out_file', initial_mean_epi_moco, 'in_file')
moco_wf.connect(initial_mean_epi_moco, 'out_file', outputnode, 'initial_mean_epi_moco')
moco_wf.connect(initial_mean_epi_moco, 'out_file', ds, 'QC.initial_mean_epi_moco')
# PLOT MOTION PARAMETERS
rotplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation_plot.png'),
name='rotplotter')
moco_wf.connect(mcflirt, 'par_file', rotplotter, 'in_file')
moco_wf.connect(rotplotter, 'out_file', ds, 'realign.plots.@rotplot')
transplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation_plot.png'),
name='transplotter')
moco_wf.connect(mcflirt, 'par_file', transplotter, 'in_file')
moco_wf.connect(transplotter, 'out_file', ds, 'realign.plots.@transplot')
dispplotter = MapNode(interface=fsl.PlotMotionParams(in_source='fsl',
plot_type='displacement'),
name='dispplotter',
iterfield=['in_file'])
dispplotter.iterables = ('plot_type', ['displacement'])
moco_wf.connect(mcflirt, 'rms_files', dispplotter, 'in_file')
moco_wf.connect(dispplotter, 'out_file', ds, 'realign.plots.@dispplots')
moco_wf.write_graph(dotfilename=moco_wf.name, graph2use='flat', format='pdf')
return moco_wf
out_fsl_file=True),
name='bbregister')
# Convert the BBRegister transformation to ANTS ITK format
convert2itk = Node(C3dAffineTool(fsl2ras=True, itk_transform=True),
name='convert2itk')
# Concatenate BBRegister's and ANTS' transforms into a list
merge = Node(Merge(2), iterfield=['in2'], name='mergexfm')
# Transform the contrast images. First to anatomical and then to the target
warpall = MapNode(ApplyTransforms(args='--float',
input_image_type=3,
interpolation='Linear',
invert_transform_flags=[False, False],
num_threads=1,
reference_image=template,
terminal_output='file'),
name='warpall',
iterfield=['input_image'])
# Transform the mean image. First to anatomical and then to the target
warpmean = Node(ApplyTransforms(args='--float',
input_image_type=3,
interpolation='Linear',
invert_transform_flags=[False, False],
num_threads=1,
reference_image=template,
terminal_output='file'),
name='warpmean')
group = Workflow(name='group')
group.base_dir=working_dir
# sink
sink = Node(nio.DataSink(base_directory=out_dir,
parameterization=False),
name='sink')
'''groupmeans and sdv
=======================
'''
# merge means
merger = MapNode(fsl.Merge(dimension='t'),
iterfield=['in_files'],
name='merger')
merger.inputs.in_files=mean_methodlist
# calculate mean of means
meaner = MapNode(fsl.maths.MeanImage(dimension='T'),
iterfield=['in_file', 'out_file'],
name='meaner')
meaner.inputs.out_file=['lin_groupmean.nii.gz','nonlin_groupmean.nii.gz','fmap_groupmean.nii.gz','topup_groupmean.nii.gz']
group.connect([(merger, meaner, [('merged_file', 'in_file')])])
# mask mean files
mean_masked = MapNode(fsl.BinaryMaths(operation='mul'),
iterfield=['in_file', 'out_file'],
name='mean_masked')
mean_masked.inputs.out_file=['lin_groupmean.nii.gz','nonlin_groupmean.nii.gz','fmap_groupmean.nii.gz','topup_groupmean.nii.gz']
corr_epi_txt = corr_fields_txt.clone(name='corr_epi_txt')
corr_epi_txt.inputs.filename='correlation_groundtruth.txt'
simulated.connect([(simulation, make_list2, [('outputnode.lin_coreg', 'file1'),
('outputnode.nonlin_coreg', 'file2'),
('outputnode.fmap_coreg', 'file3')]),
(make_list2, corr_epi, [('filelist', 'image2')]),
(groundtruth, corr_epi, [('outputnode.lin_coreg', 'image1')]),
(selectfiles, corr_epi, [('anat_brain_mask', 'mask')]),
(corr_epi, corr_epi_txt, [('linreg_stats', 'stats')])])
# similarity to anatomy
lin_sim = MapNode(interface = nutil.Similarity(),
name = 'similarity_lin',
iterfield=['metric'])
lin_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
nonlin_sim = lin_sim.clone(name='similarity_nonlin')
nonlin_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
fmap_sim = lin_sim.clone(name='similarity_fmap')
fmap_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
def write_simtext(lin_metrics, nonlin_metrics, fmap_metrics, filename):
import numpy as np
import os
lin_array = np.array(lin_metrics)
lin_array=lin_array.reshape(np.size(lin_array),1)
nonlin_array = np.array(nonlin_metrics)
nonlin_array=nonlin_array.reshape(np.size(nonlin_array),1)
fmap_array = np.array(fmap_metrics)
def build_correlation_wf(Registration=True,
use_Ankita_Function=False,
name='pearsonCorrcalc'):
corr_wf = Workflow(name=name)
if Registration:
inputnode = Node(interface=util.IdentityInterface(fields=[
'in_files', 'atlas_files', 'func2std', 'reference', 'mask_file'
]),
name='inputspec')
outputnode = Node(
interface=util.IdentityInterface(fields=['pearsonCorr_files']),
name='outputspec')
if use_Ankita_Function:
coff_matrix = MapNode(util.Function(
function=pearson_corr_Ankita,
input_names=['in_file', 'atlas_file'],
output_names=['coff_matrix_file']),
iterfield=['in_file', 'atlas_file'],
name='coff_matrix')
transform_corr = MapNode(interface=fsl.ApplyXFM(interp='spline'),
iterfield=['in_file', 'in_matrix_file'],
name='transform_corr')
maskCorrFile = MapNode(interface=fsl.ImageMaths(suffix='_masked',
op_string='-mas'),
iterfield=['in_file'],
name='maskWarpFile')
make_npy_from_Corr = MapNode(util.Function(
function=make_npy_from_CorrFile,
input_names=['Corr_file', 'mask_file'],
output_names=['coff_matrix_file']),
iterfield=['Corr_file'],
name='coff_matrix_in_npy')
else:
coff_matrix = MapNode(util.Function(
function=pearsonr_with_roi_mean_w_reg,
input_names=['in_file', 'atlas_file'],
output_names=['coff_matrix_file']),
iterfield=['in_file', 'atlas_file'],
name='coff_matrix')
transform_corr = MapNode(interface=fsl.ApplyXFM(interp='spline'),
iterfield=['in_file', 'in_matrix_file'],
name='transform_corr')
maskCorrFile = MapNode(interface=fsl.ImageMaths(suffix='_masked',
op_string='-mas'),
iterfield=['in_file'],
name='maskWarpFile')
make_npy_from_Corr = MapNode(util.Function(
function=make_npy_from_CorrFile,
input_names=['Corr_file', 'mask_file'],
output_names=['coff_matrix_file']),
iterfield=['Corr_file'],
name='coff_matrix_in_npy')
datasink = Node(interface=DataSink(), name='datasink')
corr_wf.connect(inputnode, 'in_files', coff_matrix, 'in_file')
corr_wf.connect(inputnode, 'atlas_files', coff_matrix, 'atlas_file')
corr_wf.connect(coff_matrix, 'coff_matrix_file', transform_corr,
'in_file')
corr_wf.connect(inputnode, 'func2std', transform_corr,
'in_matrix_file')
corr_wf.connect(inputnode, 'reference', transform_corr, 'reference')
corr_wf.connect(transform_corr, 'out_file', maskCorrFile, 'in_file')
corr_wf.connect(inputnode, 'mask_file', maskCorrFile, 'in_file2')
corr_wf.connect(maskCorrFile, 'out_file', make_npy_from_Corr,
'Corr_file')
corr_wf.connect(inputnode, 'mask_file', make_npy_from_Corr,
'mask_file')
corr_wf.connect(make_npy_from_Corr, 'coff_matrix_file', outputnode,
'pearsonCorr_files')
corr_wf.connect(outputnode, 'pearsonCorr_files', datasink, 'out_file')
else:
inputnode = Node(interface=util.IdentityInterface(
fields=['in_files', 'atlas_file', 'mask_file']),
name='inputspec')
outputnode = Node(interface=util.IdentityInterface(
fields=['pearsonCorr_files', 'pearsonCorr_files_in_nii']),
name='outputspec')
if use_Ankita_Function:
coff_matrix = MapNode(util.Function(
function=pearson_corr_Ankita,
input_names=['in_file', 'atlas_file'],
output_names=['coff_matrix_file']),
iterfield=['in_file'],
name='coff_matrix')
maskCorrFile = MapNode(interface=fsl.ImageMaths(suffix='_masked',
op_string='-mas'),
iterfield=['in_file'],
name='maskWarpFile')
make_npy_from_Corr = MapNode(util.Function(
function=make_npy_from_CorrFile,
input_names=['Corr_file', 'mask_file'],
output_names=['coff_matrix_file']),
iterfield=['Corr_file'],
name='coff_matrix_in_npy')
datasink = Node(interface=DataSink(), name='datasink')
corr_wf.connect(inputnode, 'in_files', coff_matrix, 'in_file')
corr_wf.connect(inputnode, 'atlas_file', coff_matrix, 'atlas_file')
corr_wf.connect(coff_matrix, 'coff_matrix_file', maskCorrFile,
'in_file')
corr_wf.connect(inputnode, 'mask_file', maskCorrFile, 'in_file2')
corr_wf.connect(maskCorrFile, 'out_file', make_npy_from_Corr,
'Corr_file')
corr_wf.connect(inputnode, 'mask_file', make_npy_from_Corr,
'mask_file')
corr_wf.connect(make_npy_from_Corr, 'coff_matrix_file', outputnode,
'pearsonCorr_files')
corr_wf.connect(outputnode, 'pearsonCorr_files', datasink,
'out_file')
else:
coff_matrix = MapNode(util.Function(
function=pearsonr_with_roi_mean,
input_names=['in_file', 'atlas_file', 'mask_file'],
output_names=['coff_matrix_file', 'coff_matrix_file_in_nii']),
iterfield=['in_file'],
name='coff_matrix')
datasink = Node(interface=DataSink(), name='datasink')
# selectfile = MapNode(interface=util.Select(index=[0]), iterfield = ['inlist'],name='select')
corr_wf.connect(inputnode, 'in_files', coff_matrix, 'in_file')
corr_wf.connect(inputnode, 'atlas_file', coff_matrix, 'atlas_file')
corr_wf.connect(inputnode, 'mask_file', coff_matrix, 'mask_file')
corr_wf.connect(coff_matrix, 'coff_matrix_file', outputnode,
'pearsonCorr_files')
corr_wf.connect(coff_matrix, 'coff_matrix_file_in_nii', outputnode,
'pearsonCorr_files_in_nii')
corr_wf.connect(outputnode, 'pearsonCorr_files', datasink,
'out_file')
# coff_matrix = MapNode(util.Function(function=pearsonr_with_roi_mean_w_reg,
# input_names=['in_file','atlas_file'],
# output_names=['coff_matrix_file']),
# iterfield=['in_file'],
# name = 'coff_matrix')
# maskCorrFile = MapNode(interface=fsl.ImageMaths(suffix='_masked',
# op_string='-mas'),
# iterfield=['in_file'],
# name = 'maskWarpFile')
# make_npy_from_Corr = MapNode(util.Function(function=make_npy_from_CorrFile,
# input_names=['Corr_file','mask_file'],
# output_names=['coff_matrix_file']),
# iterfield=['Corr_file'],
# name = 'coff_matrix_in_npy')
# datasink = Node(interface=DataSink(), name='datasink')
# corr_wf.connect(inputnode, 'in_files', coff_matrix, 'in_file')
# corr_wf.connect(inputnode, 'atlas_file', coff_matrix, 'atlas_file')
# corr_wf.connect(coff_matrix,'coff_matrix_file', maskCorrFile, 'in_file')
# corr_wf.connect(inputnode, 'mask_file', maskCorrFile, 'in_file2')
# corr_wf.connect(maskCorrFile,'out_file', make_npy_from_Corr, 'Corr_file')
# corr_wf.connect(inputnode,'mask_file', make_npy_from_Corr, 'mask_file')
# corr_wf.connect(make_npy_from_Corr, 'coff_matrix_file', outputnode, 'pearsonCorr_files')
# corr_wf.connect(outputnode, 'pearsonCorr_files', datasink, 'out_file')
return corr_wf
def create_similarity_pipeline(name):
similarity=Workflow(name=name)
# inputnode
inputnode=Node(util.IdentityInterface(fields=['anat_brain',
'mask',
'lin_mean',
'nonlin_mean',
'fmap_mean',
'topup_mean',
'filename'
]),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['textfile']),
name='outputnode')
# resample all means to make sure they have the same resolution as reference anatomy
resamp_mask = Node(afni.Resample(outputtype='NIFTI_GZ'), name='resample_mask')
resamp_lin = resamp_mask.clone(name = 'resample_lin')
resamp_nonlin = resamp_mask.clone(name='resample_nonlin')
resamp_fmap = resamp_mask.clone(name='resample_fmap')
resamp_topup = resamp_mask.clone(name='resample_topup')
similarity.connect([(inputnode, resamp_mask, [('mask', 'in_file'),
('anat_brain', 'master')]),
(inputnode, resamp_lin, [('lin_mean', 'in_file'),
('anat_brain', 'master')]),
(inputnode, resamp_nonlin, [('nonlin_mean', 'in_file'),
('anat_brain', 'master')]),
(inputnode, resamp_fmap, [('fmap_mean', 'in_file'),
('anat_brain', 'master')]),
(inputnode, resamp_topup, [('topup_mean', 'in_file'),
('anat_brain', 'master')]),
])
# calculate similarity (all possible metrics) for each methods to mni
lin_sim = MapNode(interface = nutil.Similarity(),
name = 'similarity_lin',
iterfield=['metric'])
lin_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
nonlin_sim = lin_sim.clone(name='similarity_nonlin')
nonlin_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
fmap_sim = lin_sim.clone(name='similarity_fmap')
fmap_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
topup_sim = lin_sim.clone(name='similarity_topup')
topup_sim.inputs.metric = ['mi','nmi','cc','cr','crl1']
similarity.connect([(inputnode, lin_sim, [('anat_brain', 'volume1')]),
(resamp_lin, lin_sim, [('out_file', 'volume2')]),
(resamp_mask, lin_sim, [('out_file', 'mask1'),
('out_file', 'mask2')]),
(inputnode, nonlin_sim, [('anat_brain', 'volume1')]),
(resamp_nonlin, nonlin_sim, [('out_file', 'volume2')]),
(resamp_mask, nonlin_sim, [('out_file', 'mask1'),
('out_file', 'mask2')]),
(inputnode, fmap_sim, [('anat_brain', 'volume1')]),
(resamp_fmap, fmap_sim, [('out_file', 'volume2')]),
(resamp_mask, fmap_sim, [('out_file', 'mask1'),
('out_file', 'mask2')]),
(inputnode, topup_sim, [('anat_brain', 'volume1')]),
(resamp_topup, topup_sim, [('out_file', 'volume2')]),
(resamp_mask, topup_sim, [('out_file', 'mask1'),
('out_file', 'mask2')])
])
# write values to one text file per subject
def write_text(lin_metrics, nonlin_metrics, fmap_metrics, topup_metrics, filename):
import numpy as np
import os
lin_array = np.array(lin_metrics)
lin_array=lin_array.reshape(np.size(lin_array),1)
nonlin_array = np.array(nonlin_metrics)
nonlin_array=nonlin_array.reshape(np.size(nonlin_array),1)
fmap_array = np.array(fmap_metrics)
fmap_array=fmap_array.reshape(np.size(fmap_array),1)
topup_array = np.array(topup_metrics)
topup_array=topup_array.reshape(np.size(topup_array),1)
metrics=np.concatenate((lin_array, nonlin_array, fmap_array, topup_array),axis=1)
metrics_file = filename
np.savetxt(metrics_file, metrics, delimiter=' ', fmt='%f')
return os.path.abspath(filename)
write_txt = Node(interface=Function(input_names=['lin_metrics', 'nonlin_metrics', 'fmap_metrics', 'topup_metrics', 'filename'],
output_names=['txtfile'],
function=write_text),
name='write_file')
similarity.connect([(inputnode, write_txt, [('filename', 'filename')]),
(lin_sim, write_txt, [('similarity', 'lin_metrics')]),
(nonlin_sim, write_txt, [('similarity', 'nonlin_metrics')]),
(fmap_sim, write_txt, [('similarity', 'fmap_metrics')]),
(topup_sim, write_txt, [('similarity', 'topup_metrics')]),
(write_txt, outputnode, [('txtfile', 'textfile')])
])
return similarity
def create_denoise_pipeline(name='denoise'):
# workflow
denoise = Workflow(name='denoise')
# Define nodes
inputnode = Node(interface=util.IdentityInterface(fields=['brain_mask',
'epi_coreg',
'wmseg',
'csfseg',
'highpass_freq',
'tr']),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(fields=['wmcsf_mask',
'combined_motion',
'comp_regressor',
'comp_F',
'comp_pF',
'out_betas',
'ts_fullspectrum',
'ts_filtered']),
name='outputnode')
# combine tissue classes to noise mask
wmcsf_mask = Node(fsl.BinaryMaths(operation='add',
out_file='wmcsf_mask.nii'),
name='wmcsf_mask')
denoise.connect([(inputnode, wmcsf_mask, [('wmseg', 'in_file'),
('csfseg', 'operand_file')])])
#resample + binarize wm_csf mask to epi resolution.
resample_wmcsf= Node(afni.Resample(resample_mode='NN',
outputtype='NIFTI_GZ',
out_file='wmcsf_mask_lowres.nii.gz'),
name = 'resample_wmcsf')
bin_wmcsf_mask=Node(fsl.utils.ImageMaths(), name="bin_wmcsf_mask")
bin_wmcsf_mask.inputs.op_string='-nan -thr 0.99 -ero -bin'
denoise.connect([(wmcsf_mask, resample_wmcsf, [('out_file', 'in_file')]),
(inputnode, resample_wmcsf, [('brain_mask', 'master')]),
(resample_wmcsf, bin_wmcsf_mask,[('out_file', 'in_file')]),
(bin_wmcsf_mask, outputnode, [('out_file', 'wmcsf_mask')])
])
#no other denoising filters created here because AROMA performs already well.
compcor=Node(conf.ACompCor(), name="compcor")
compcor.inputs.num_components=5 #https://www.sciencedirect.com/science/article/pii/S105381191400175X?via%3Dihub
denoise.connect([
(inputnode, compcor, [('epi_coreg', 'realigned_file')]),
(bin_wmcsf_mask, compcor, [('out_file', 'mask_files')]),
])
def create_designs(compcor_regressors,epi_coreg,mask):
import numpy as np
import pandas as pd
import os
from nilearn.input_data import NiftiMasker
brain_masker = NiftiMasker(mask_img = mask,
smoothing_fwhm=None, standardize=False,
memory='nilearn_cache',
memory_level=5, verbose=2)
whole_brain = brain_masker.fit_transform(epi_coreg)
avg_signal = np.mean(whole_brain,axis=1)
all_regressors=pd.read_csv(compcor_regressors,sep='\t')
#add global signal.
all_regressors['global_signal']=avg_signal
fn=os.getcwd()+'/all_regressors.txt'
all_regressors.to_csv(fn, sep='\t', index=False)
return [fn, compcor_regressors]
#create a list of design to loop over.
create_design = Node(util.Function(input_names=['compcor_regressors','epi_coreg','mask'], output_names=['reg_list'], function=create_designs),
name='create_design')
denoise.connect([
(compcor, create_design, [('components_file', 'compcor_regressors')]),
(inputnode, create_design, [('epi_coreg', 'epi_coreg')]),
(inputnode, create_design, [('brain_mask', 'mask')])
])
# regress compcor and other noise components
filter2 = MapNode(fsl.GLM(out_f_name='F_noise.nii.gz',
out_pf_name='pF_noise.nii.gz',
out_res_name='rest2anat_denoised.nii.gz',
output_type='NIFTI_GZ',
demean=True),
iterfield=['design'],
name='filternoise')
filter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, filter2, [('epi_coreg', 'in_file')]),
#(createfilter2, filter2, [('out_files', 'design')]),
#(compcor, filter2, [('components_file', 'design')]),
(create_design, filter2, [('reg_list', 'design')]),
(inputnode, filter2, [('brain_mask', 'mask')]),
(filter2, outputnode, [('out_f', 'comp_F'),
('out_pf', 'comp_pF'),
('out_file', 'out_betas'),
('out_res', 'ts_fullspectrum'),
])
])
def calc_sigma(TR,highpass):
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1205&L=FSL&P=R57592&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4
sigma=1. / (2 * TR * highpass)
return sigma
calc_s=Node(util.Function(input_names=['TR', 'highpass'], output_names=['sigma'], function=calc_sigma),
name='calc_s')
denoise.connect(inputnode, 'tr', calc_s, 'TR')
denoise.connect(inputnode, 'highpass_freq', calc_s, 'highpass')
#use only highpass filter (because high-frequency content is already somewhat filtered in AROMA))
highpass_filter = MapNode(fsl.TemporalFilter(out_file='rest_denoised_highpassed.nii'),
name='highpass_filter', iterfield=['in_file'])
highpass_filter.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(calc_s, highpass_filter, [('sigma', 'highpass_sigma')]),
(filter2, highpass_filter, [('out_res', 'in_file')]),
(highpass_filter, outputnode, [('out_file', 'ts_filtered')])
])
return denoise
def create_denoise_pipeline(name='denoise'):
# workflow
denoise = Workflow(name='denoise')
# Define nodes
inputnode = Node(interface=util.IdentityInterface(fields=[
'anat_brain', 'brain_mask', 'epi2anat_dat', 'unwarped_mean',
'epi_coreg', 'moco_par', 'highpass_sigma', 'lowpass_sigma', 'tr'
]),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(fields=[
'wmcsf_mask', 'brain_mask_resamp', 'brain_mask2epi', 'combined_motion',
'outlier_files', 'intensity_files', 'outlier_stats', 'outlier_plots',
'mc_regressor', 'mc_F', 'mc_pF', 'comp_regressor', 'comp_F', 'comp_pF',
'normalized_file'
]),
name='outputnode')
# run fast to get tissue probability classes
fast = Node(fsl.FAST(), name='fast')
denoise.connect([(inputnode, fast, [('anat_brain', 'in_files')])])
# functions to select tissue classes
def selectindex(files, idx):
import numpy as np
from nipype.utils.filemanip import filename_to_list, list_to_filename
return list_to_filename(
np.array(filename_to_list(files))[idx].tolist())
def selectsingle(files, idx):
return files[idx]
# resample tissue classes
resample_tissue = MapNode(afni.Resample(resample_mode='NN',
outputtype='NIFTI_GZ'),
iterfield=['in_file'],
name='resample_tissue')
denoise.connect([
(inputnode, resample_tissue, [('epi_coreg', 'master')]),
(fast, resample_tissue, [(('partial_volume_files', selectindex,
[0, 2]), 'in_file')]),
])
# binarize tissue classes
binarize_tissue = MapNode(
fsl.ImageMaths(op_string='-nan -thr 0.99 -ero -bin'),
iterfield=['in_file'],
name='binarize_tissue')
denoise.connect([
(resample_tissue, binarize_tissue, [('out_file', 'in_file')]),
])
# combine tissue classes to noise mask
wmcsf_mask = Node(fsl.BinaryMaths(operation='add',
out_file='wmcsf_mask_lowres.nii.gz'),
name='wmcsf_mask')
denoise.connect([(binarize_tissue, wmcsf_mask,
[(('out_file', selectsingle, 0), 'in_file'),
(('out_file', selectsingle, 1), 'operand_file')]),
(wmcsf_mask, outputnode, [('out_file', 'wmcsf_mask')])])
# resample brain mask
resample_brain = Node(afni.Resample(
resample_mode='NN',
outputtype='NIFTI_GZ',
out_file='T1_brain_mask_lowres.nii.gz'),
name='resample_brain')
denoise.connect([(inputnode, resample_brain, [('brain_mask', 'in_file'),
('epi_coreg', 'master')]),
(resample_brain, outputnode, [('out_file',
'brain_mask_resamp')])])
# project brain mask into original epi space fpr quality assessment
brainmask2epi = Node(fs.ApplyVolTransform(
interp='nearest',
inverse=True,
transformed_file='T1_brain_mask2epi.nii.gz',
),
name='brainmask2epi')
denoise.connect([
(inputnode, brainmask2epi, [('brain_mask', 'target_file'),
('epi2anat_dat', 'reg_file'),
('unwarped_mean', 'source_file')]),
(brainmask2epi, outputnode, [('transformed_file', 'brain_mask2epi')])
])
# perform artefact detection
artefact = Node(ra.ArtifactDetect(save_plot=True,
use_norm=True,
parameter_source='FSL',
mask_type='file',
norm_threshold=1,
zintensity_threshold=3,
use_differences=[True, False]),
name='artefact')
artefact.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([
(inputnode, artefact, [('epi_coreg', 'realigned_files'),
('moco_par', 'realignment_parameters')]),
(resample_brain, artefact, [('out_file', 'mask_file')]),
(artefact, outputnode, [('norm_files', 'combined_motion'),
('outlier_files', 'outlier_files'),
('intensity_files', 'intensity_files'),
('statistic_files', 'outlier_stats'),
('plot_files', 'outlier_plots')])
])
# Compute motion regressors
motreg = Node(util.Function(
input_names=['motion_params', 'order', 'derivatives'],
output_names=['out_files'],
function=motion_regressors),
name='getmotionregress')
motreg.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, motreg, [('moco_par', 'motion_params')])])
# Create a filter to remove motion and art confounds
createfilter1 = Node(util.Function(
input_names=['motion_params', 'comp_norm', 'outliers', 'detrend_poly'],
output_names=['out_files'],
function=build_filter1),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 2
createfilter1.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([
(motreg, createfilter1, [('out_files', 'motion_params')]),
(
artefact,
createfilter1,
[ #('norm_files', 'comp_norm'),
('outlier_files', 'outliers')
]),
(createfilter1, outputnode, [('out_files', 'mc_regressor')])
])
# regress out motion and art confounds
filter1 = Node(fsl.GLM(out_f_name='F_mcart.nii.gz',
out_pf_name='pF_mcart.nii.gz',
out_res_name='rest_mc_denoised.nii.gz',
demean=True),
name='filtermotion')
filter1.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, filter1, [('epi_coreg', 'in_file')]),
(createfilter1, filter1,
[(('out_files', list_to_filename), 'design')]),
(filter1, outputnode, [('out_f', 'mc_F'),
('out_pf', 'mc_pF')])])
# create filter with compcor components
createfilter2 = Node(util.Function(input_names=[
'realigned_file', 'mask_file', 'num_components', 'extra_regressors'
],
output_names=['out_files'],
function=extract_noise_components),
name='makecompcorfilter')
createfilter2.inputs.num_components = 6
createfilter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([
(createfilter1, createfilter2, [(('out_files', list_to_filename),
'extra_regressors')]),
(filter1, createfilter2, [('out_res', 'realigned_file')]),
(wmcsf_mask, createfilter2, [('out_file', 'mask_file')]),
(createfilter2, outputnode, [('out_files', 'comp_regressor')]),
])
# regress compcor and other noise components
filter2 = Node(fsl.GLM(out_f_name='F_noise.nii.gz',
out_pf_name='pF_noise.nii.gz',
out_res_name='rest2anat_denoised.nii.gz',
demean=True),
name='filternoise')
filter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(filter1, filter2, [('out_res', 'in_file')]),
(createfilter2, filter2, [('out_files', 'design')]),
(resample_brain, filter2, [('out_file', 'mask')]),
(filter2, outputnode, [('out_f', 'comp_F'),
('out_pf', 'comp_pF')])])
# bandpass filter denoised file
bandpass_filter = Node(
fsl.TemporalFilter(out_file='rest_denoised_bandpassed.nii.gz'),
name='bandpass_filter')
bandpass_filter.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, bandpass_filter,
[('highpass_sigma', 'highpass_sigma'),
('lowpass_sigma', 'lowpass_sigma')]),
(filter2, bandpass_filter, [('out_res', 'in_file')])])
# time-normalize scans
normalize_time = Node(util.Function(input_names=['in_file', 'tr'],
output_names=['out_file'],
function=time_normalizer),
name='normalize_time')
normalize_time.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([
(inputnode, normalize_time, [('tr', 'tr')]),
(bandpass_filter, normalize_time, [('out_file', 'in_file')]),
(normalize_time, outputnode, [('out_file', 'normalized_file')])
])
return denoise
def calc_local_metrics(cfg):
import os
from nipype import config
from nipype.pipeline.engine import Node, Workflow, MapNode
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
import nipype.interfaces.freesurfer as freesurfer
import CPAC.alff.alff as cpac_alff
import CPAC.reho.reho as cpac_reho
import CPAC.utils.utils as cpac_utils
import CPAC.vmhc.vmhc as cpac_vmhc
import CPAC.registration.registration as cpac_registration
import CPAC.network_centrality.z_score as cpac_centrality_z_score
import utils as calc_metrics_utils
# INPUT PARAMETERS
dicom_dir = cfg['dicom_dir']
preprocessed_data_dir = cfg['preprocessed_data_dir']
working_dir = cfg['working_dir']
freesurfer_dir = cfg['freesurfer_dir']
template_dir = cfg['template_dir']
script_dir = cfg['script_dir']
ds_dir = cfg['ds_dir']
subject_id = cfg['subject_id']
TR_list = cfg['TR_list']
vols_to_drop = cfg['vols_to_drop']
rois_list = cfg['rois_list']
lp_cutoff_freq = cfg['lp_cutoff_freq']
hp_cutoff_freq = cfg['hp_cutoff_freq']
use_fs_brainmask = cfg['use_fs_brainmask']
use_n_procs = cfg['use_n_procs']
plugin_name = cfg['plugin_name']
#####################################
# GENERAL SETTINGS
#####################################
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
freesurfer.FSCommand.set_default_subjects_dir(freesurfer_dir)
wf = Workflow(name='LeiCA_metrics')
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(logging=dict(workflow_level='DEBUG'), execution={'stop_on_first_crash': True,
'remove_unnecessary_outputs': True,
'job_finished_timeout': 120})
config.update_config(nipype_cfg)
wf.config['execution']['crashdump_dir'] = os.path.join(working_dir, 'crash')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
ds.inputs.regexp_substitutions = [('_variabilty_MNIspace_3mm[0-9]*/', ''), ('_z_score[0-9]*/', '')]
#####################################
# SET ITERATORS
#####################################
# GET SCAN TR_ID ITERATOR
scan_infosource = Node(util.IdentityInterface(fields=['TR_id']), name='scan_infosource')
scan_infosource.iterables = ('TR_id', TR_list)
# get atlas data
templates_atlases = { # 'GM_mask_MNI_2mm': 'SPM_GM/SPM_GM_mask_2mm.nii.gz',
# 'GM_mask_MNI_3mm': 'SPM_GM/SPM_GM_mask_3mm.nii.gz',
'FSL_MNI_3mm_template': 'MNI152_T1_3mm_brain.nii.gz',
'vmhc_symm_brain': 'cpac_image_resources/symmetric/MNI152_T1_2mm_brain_symmetric.nii.gz',
'vmhc_symm_brain_3mm': 'cpac_image_resources/symmetric/MNI152_T1_3mm_brain_symmetric.nii.gz',
'vmhc_symm_skull': 'cpac_image_resources/symmetric/MNI152_T1_2mm_symmetric.nii.gz',
'vmhc_symm_brain_mask_dil': 'cpac_image_resources/symmetric/MNI152_T1_2mm_brain_mask_symmetric_dil.nii.gz',
'vmhc_config_file_2mm': 'cpac_image_resources/symmetric/T1_2_MNI152_2mm_symmetric.cnf'
}
selectfiles_anat_templates = Node(nio.SelectFiles(templates_atlases,
base_directory=template_dir),
name="selectfiles_anat_templates")
# GET SUBJECT SPECIFIC FUNCTIONAL AND STRUCTURAL DATA
selectfiles_templates = {
'epi_2_MNI_warp': '{subject_id}/rsfMRI_preprocessing/registration/epi_2_MNI_warp/TR_{TR_id}/*.nii.gz',
'epi_mask': '{subject_id}/rsfMRI_preprocessing/masks/brain_mask_epiSpace/TR_{TR_id}/*.nii.gz',
'preproc_epi_full_spectrum': '{subject_id}/rsfMRI_preprocessing/epis/01_denoised/TR_{TR_id}/*.nii.gz',
'preproc_epi_bp': '{subject_id}/rsfMRI_preprocessing/epis/02_denoised_BP/TR_{TR_id}/*.nii.gz',
'preproc_epi_bp_tNorm': '{subject_id}/rsfMRI_preprocessing/epis/03_denoised_BP_tNorm/TR_{TR_id}/*.nii.gz',
'epi_2_struct_mat': '{subject_id}/rsfMRI_preprocessing/registration/epi_2_struct_mat/TR_{TR_id}/*.mat',
't1w': '{subject_id}/raw_niftis/sMRI/t1w_reoriented.nii.gz',
't1w_brain': '{subject_id}/rsfMRI_preprocessing/struct_prep/t1w_brain/t1w_reoriented_maths.nii.gz',
}
selectfiles = Node(nio.SelectFiles(selectfiles_templates,
base_directory=preprocessed_data_dir),
name="selectfiles")
wf.connect(scan_infosource, 'TR_id', selectfiles, 'TR_id')
selectfiles.inputs.subject_id = subject_id
# CREATE TRANSFORMATIONS
# creat MNI 2 epi warp
MNI_2_epi_warp = Node(fsl.InvWarp(), name='MNI_2_epi_warp')
MNI_2_epi_warp.inputs.reference = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
wf.connect(selectfiles, 'epi_mask', MNI_2_epi_warp, 'reference')
wf.connect(selectfiles, 'epi_2_MNI_warp', MNI_2_epi_warp, 'warp')
# # CREATE GM MASK IN EPI SPACE
# GM_mask_epiSpace = Node(fsl.ApplyWarp(), name='GM_mask_epiSpace')
# GM_mask_epiSpace.inputs.out_file = 'GM_mask_epiSpace.nii.gz'
#
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_2mm', GM_mask_epiSpace, 'in_file')
# wf.connect(selectfiles, 'epi_mask', GM_mask_epiSpace, 'ref_file')
# wf.connect(MNI_2_epi_warp, 'inverse_warp', GM_mask_epiSpace, 'field_file')
# wf.connect(GM_mask_epiSpace, 'out_file', ds, 'GM_mask_epiSpace')
# fixme
# # CREATE TS IN MNI SPACE
# # is it ok to apply the 2mm warpfield to the 3mm template?
# # seems ok: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=FSL&P=R14011&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
# epi_bp_MNIspace_3mm = Node(fsl.ApplyWarp(), name='epi_bp_MNIspace_3mm')
# epi_bp_MNIspace_3mm.inputs.interp = 'spline'
# epi_bp_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
# wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', epi_bp_MNIspace_3mm, 'ref_file')
# wf.connect(selectfiles, 'preproc_epi_bp', epi_bp_MNIspace_3mm, 'in_file')
# wf.connect(selectfiles, 'epi_2_MNI_warp', epi_bp_MNIspace_3mm, 'field_file')
# CREATE EPI MASK IN MNI SPACE
epi_mask_MNIspace_3mm = Node(fsl.ApplyWarp(), name='epi_mask_MNIspace_3mm')
epi_mask_MNIspace_3mm.inputs.interp = 'nn'
epi_mask_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', epi_mask_MNIspace_3mm, 'ref_file')
wf.connect(selectfiles, 'epi_mask', epi_mask_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', epi_mask_MNIspace_3mm, 'field_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', ds, 'epi_mask_MNIspace_3mm')
#####################
# CALCULATE METRICS
#####################
# f/ALFF
alff = cpac_alff.create_alff('alff')
alff.inputs.hp_input.hp = 0.01
alff.inputs.lp_input.lp = 0.1
wf.connect(selectfiles, 'preproc_epi_full_spectrum', alff, 'inputspec.rest_res')
# wf.connect(GM_mask_epiSpace, 'out_file', alff, 'inputspec.rest_mask')
wf.connect(selectfiles, 'epi_mask', alff, 'inputspec.rest_mask')
wf.connect(alff, 'outputspec.alff_img', ds, 'alff.alff')
wf.connect(alff, 'outputspec.falff_img', ds, 'alff.falff')
# f/ALFF 2 MNI
# fixme spline or default?
alff_MNIspace_3mm = Node(fsl.ApplyWarp(), name='alff_MNIspace_3mm')
alff_MNIspace_3mm.inputs.interp = 'spline'
alff_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', alff_MNIspace_3mm, 'ref_file')
wf.connect(alff, 'outputspec.alff_img', alff_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', alff_MNIspace_3mm, 'field_file')
wf.connect(alff_MNIspace_3mm, 'out_file', ds, 'alff.alff_MNI_3mm')
falff_MNIspace_3mm = Node(fsl.ApplyWarp(), name='falff_MNIspace_3mm')
falff_MNIspace_3mm.inputs.interp = 'spline'
falff_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', falff_MNIspace_3mm, 'ref_file')
wf.connect(alff, 'outputspec.falff_img', falff_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', falff_MNIspace_3mm, 'field_file')
wf.connect(falff_MNIspace_3mm, 'out_file', ds, 'alff.falff_MNI_3mm')
# f/ALFF_MNI Z-SCORE
alff_MNIspace_3mm_Z = cpac_utils.get_zscore(input_name='alff_MNIspace_3mm', wf_name='alff_MNIspace_3mm_Z')
wf.connect(alff_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', alff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(alff_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'alff.alff_MNI_3mm_Z')
falff_MNIspace_3mm_Z = cpac_utils.get_zscore(input_name='falff_MNIspace_3mm', wf_name='falff_MNIspace_3mm_Z')
wf.connect(falff_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', falff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(falff_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'alff.falff_MNI_3mm_Z')
# f/ALFF_MNI STANDARDIZE BY MEAN
alff_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='alff_MNIspace_3mm_standardized_mean')
wf.connect(alff_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(alff_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds, 'alff.alff_MNI_3mm_standardized_mean')
falff_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='falff_MNIspace_3mm_standardized_mean')
wf.connect(falff_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(falff_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds, 'alff.falff_MNI_3mm_standardized_mean')
# REHO
reho = cpac_reho.create_reho()
reho.inputs.inputspec.cluster_size = 27
wf.connect(selectfiles, 'preproc_epi_bp', reho, 'inputspec.rest_res_filt')
# wf.connect(GM_mask_epiSpace, 'out_file', reho, 'inputspec.rest_mask')
wf.connect(selectfiles, 'epi_mask', reho, 'inputspec.rest_mask')
wf.connect(reho, 'outputspec.raw_reho_map', ds, 'reho.reho')
# REHO 2 MNI
# fixme spline or default?
reho_MNIspace_3mm = Node(fsl.ApplyWarp(), name='reho_MNIspace_3mm')
reho_MNIspace_3mm.inputs.interp = 'spline'
reho_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', reho_MNIspace_3mm, 'ref_file')
wf.connect(reho, 'outputspec.raw_reho_map', reho_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', reho_MNIspace_3mm, 'field_file')
wf.connect(reho_MNIspace_3mm, 'out_file', ds, 'reho.reho_MNI_3mm')
# REHO_MNI Z-SCORE
reho_MNIspace_3mm_Z = cpac_utils.get_zscore(input_name='reho_MNIspace_3mm', wf_name='reho_MNIspace_3mm_Z')
wf.connect(alff_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', reho_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(reho_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'reho.reho_MNI_3mm_Z')
# REHO_MNI STANDARDIZE BY MEAN
reho_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='reho_MNIspace_3mm_standardized_mean')
wf.connect(reho_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(reho_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds, 'reho.reho_MNI_3mm_standardized_mean')
# VMHC
# create registration to symmetrical MNI template
struct_2_MNI_symm = cpac_registration.create_nonlinear_register(name='struct_2_MNI_symm')
wf.connect(selectfiles_anat_templates, 'vmhc_config_file_2mm', struct_2_MNI_symm, 'inputspec.fnirt_config')
wf.connect(selectfiles_anat_templates, 'vmhc_symm_brain', struct_2_MNI_symm, 'inputspec.reference_brain')
wf.connect(selectfiles_anat_templates, 'vmhc_symm_skull', struct_2_MNI_symm, 'inputspec.reference_skull')
wf.connect(selectfiles_anat_templates, 'vmhc_symm_brain_mask_dil', struct_2_MNI_symm, 'inputspec.ref_mask')
wf.connect(selectfiles, 't1w', struct_2_MNI_symm, 'inputspec.input_skull')
wf.connect(selectfiles, 't1w_brain', struct_2_MNI_symm, 'inputspec.input_brain')
wf.connect(struct_2_MNI_symm, 'outputspec.output_brain', ds, 'vmhc.symm_reg.@output_brain')
wf.connect(struct_2_MNI_symm, 'outputspec.linear_xfm', ds, 'vmhc.symm_reg.@linear_xfm')
wf.connect(struct_2_MNI_symm, 'outputspec.invlinear_xfm', ds, 'vmhc.symm_reg.@invlinear_xfm')
wf.connect(struct_2_MNI_symm, 'outputspec.nonlinear_xfm', ds, 'vmhc.symm_reg.@nonlinear_xfm')
# fixme
vmhc = cpac_vmhc.create_vmhc(use_ants=False, name='vmhc')
vmhc.inputs.fwhm_input.fwhm = 4
wf.connect(selectfiles_anat_templates, 'vmhc_symm_brain_3mm', vmhc, 'inputspec.standard_for_func')
wf.connect(selectfiles, 'preproc_epi_bp_tNorm', vmhc, 'inputspec.rest_res')
wf.connect(selectfiles, 'epi_2_struct_mat', vmhc, 'inputspec.example_func2highres_mat')
wf.connect(struct_2_MNI_symm, 'outputspec.nonlinear_xfm', vmhc, 'inputspec.fnirt_nonlinear_warp')
# wf.connect(GM_mask_epiSpace, 'out_file', vmhc, 'inputspec.rest_mask')
wf.connect(selectfiles, 'epi_mask', vmhc, 'inputspec.rest_mask')
wf.connect(vmhc, 'outputspec.rest_res_2symmstandard', ds, 'vmhc.rest_res_2symmstandard')
wf.connect(vmhc, 'outputspec.VMHC_FWHM_img', ds, 'vmhc.VMHC_FWHM_img')
wf.connect(vmhc, 'outputspec.VMHC_Z_FWHM_img', ds, 'vmhc.VMHC_Z_FWHM_img')
wf.connect(vmhc, 'outputspec.VMHC_Z_stat_FWHM_img', ds, 'vmhc.VMHC_Z_stat_FWHM_img')
# VARIABILITY SCORES
variability = Node(util.Function(input_names=['in_file'],
output_names=['out_file_list'],
function=calc_metrics_utils.calc_variability),
name='variability')
wf.connect(selectfiles, 'preproc_epi_bp', variability, 'in_file')
wf.connect(variability, 'out_file_list', ds, 'variability.subjectSpace.@out_files')
# #fixme spline?
variabilty_MNIspace_3mm = MapNode(fsl.ApplyWarp(), iterfield=['in_file'], name='variabilty_MNIspace_3mm')
variabilty_MNIspace_3mm.inputs.interp = 'spline'
variabilty_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', variabilty_MNIspace_3mm, 'ref_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', variabilty_MNIspace_3mm, 'field_file')
wf.connect(variability, 'out_file_list', variabilty_MNIspace_3mm, 'in_file')
wf.connect(variabilty_MNIspace_3mm, 'out_file', ds, 'variability.MNI_3mm.@out_file')
# CALC Z SCORE
variabilty_MNIspace_3mm_Z = cpac_centrality_z_score.get_cent_zscore(wf_name='variabilty_MNIspace_3mm_Z')
wf.connect(variabilty_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', variabilty_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(variabilty_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'variability.MNI_3mm_Z.@out_file')
# STANDARDIZE BY MEAN
variabilty_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='variabilty_MNIspace_3mm_standardized_mean')
wf.connect(variabilty_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(variabilty_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds,
'variability.MNI_3mm_standardized_mean.@out_file')
wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == 'CondorDAGMan':
wf.run(plugin=plugin_name)
if plugin_name == 'MultiProc':
wf.run(plugin=plugin_name, plugin_args={'n_procs': use_n_procs})
def create_struct_preproc_pipeline(working_dir,
freesurfer_dir,
ds_dir,
use_fs_brainmask,
name='struct_preproc'):
"""
"""
# initiate workflow
struct_preproc_wf = Workflow(name=name)
struct_preproc_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting',
'rsfMRI_preprocessing')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['t1w', 'subject_id']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
't1w_brain', 'struct_brain_mask', 'fast_partial_volume_files',
'wm_mask', 'csf_mask', 'wm_mask_4_bbr', 'gm_mask'
]),
name='outputnode')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
# CREATE BRAIN MASK
if use_fs_brainmask:
# brainmask with fs
fs_source = Node(interface=nio.FreeSurferSource(), name='fs_source')
fs_source.inputs.subjects_dir = freesurfer_dir
struct_preproc_wf.connect(inputnode, 'subject_id', fs_source,
'subject_id')
# get aparc+aseg from list
def get_aparc_aseg(files):
for name in files:
if 'aparc+aseg' in name:
return name
aseg = Node(fs.MRIConvert(out_type='niigz', out_file='aseg.nii.gz'),
name='aseg')
struct_preproc_wf.connect(fs_source, ('aparc_aseg', get_aparc_aseg),
aseg, 'in_file')
fs_brainmask = Node(
fs.Binarize(
min=0.5, #dilate=1,
out_type='nii.gz'),
name='fs_brainmask')
struct_preproc_wf.connect(aseg, 'out_file', fs_brainmask, 'in_file')
# fill holes in mask, smooth, rebinarize
fillholes = Node(fsl.maths.MathsCommand(
args='-fillh -s 3 -thr 0.1 -bin', out_file='T1_brain_mask.nii.gz'),
name='fillholes')
struct_preproc_wf.connect(fs_brainmask, 'binary_file', fillholes,
'in_file')
fs_2_struct_mat = Node(util.Function(
input_names=['moving_image', 'target_image'],
output_names=['fsl_file'],
function=tkregister2_fct),
name='fs_2_struct_mat')
struct_preproc_wf.connect([(fs_source, fs_2_struct_mat,
[('T1', 'moving_image'),
('rawavg', 'target_image')])])
struct_brain_mask = Node(fsl.ApplyXfm(interp='nearestneighbour'),
name='struct_brain_mask_fs')
struct_preproc_wf.connect(fillholes, 'out_file', struct_brain_mask,
'in_file')
struct_preproc_wf.connect(inputnode, 't1w', struct_brain_mask,
'reference')
struct_preproc_wf.connect(fs_2_struct_mat, 'fsl_file',
struct_brain_mask, 'in_matrix_file')
struct_preproc_wf.connect(struct_brain_mask, 'out_file', outputnode,
'struct_brain_mask')
struct_preproc_wf.connect(struct_brain_mask, 'out_file', ds,
'struct_prep.struct_brain_mask')
# multiply t1w with fs brain mask
t1w_brain = Node(fsl.maths.BinaryMaths(operation='mul'),
name='t1w_brain')
struct_preproc_wf.connect(inputnode, 't1w', t1w_brain, 'in_file')
struct_preproc_wf.connect(struct_brain_mask, 'out_file', t1w_brain,
'operand_file')
struct_preproc_wf.connect(t1w_brain, 'out_file', outputnode,
't1w_brain')
struct_preproc_wf.connect(t1w_brain, 'out_file', ds,
'struct_prep.t1w_brain')
else: # use bet
t1w_brain = Node(fsl.BET(mask=True, outline=True, surfaces=True),
name='t1w_brain')
struct_preproc_wf.connect(inputnode, 't1w', t1w_brain, 'in_file')
struct_preproc_wf.connect(t1w_brain, 'out_file', outputnode,
't1w_brain')
def struct_brain_mask_bet_fct(in_file):
return in_file
struct_brain_mask = Node(util.Function(
input_names=['in_file'],
output_names=['out_file'],
function=struct_brain_mask_bet_fct),
name='struct_brain_mask')
struct_preproc_wf.connect(t1w_brain, 'mask_file', struct_brain_mask,
'in_file')
struct_preproc_wf.connect(struct_brain_mask, 'out_file', outputnode,
'struct_brain_mask')
struct_preproc_wf.connect(struct_brain_mask, 'out_file', ds,
'struct_prep.struct_brain_mask')
# SEGMENTATION WITH FAST
fast = Node(fsl.FAST(), name='fast')
struct_preproc_wf.connect(t1w_brain, 'out_file', fast, 'in_files')
struct_preproc_wf.connect(fast, 'partial_volume_files', outputnode,
'fast_partial_volume_files')
struct_preproc_wf.connect(fast, 'partial_volume_files', ds,
'struct_prep.fast')
# functions to select tissue classes
def selectindex(files, idx):
import numpy as np
from nipype.utils.filemanip import filename_to_list, list_to_filename
return list_to_filename(
np.array(filename_to_list(files))[idx].tolist())
def selectsingle(files, idx):
return files[idx]
# pve0: CSF
# pve1: GM
# pve2: WM
# binarize tissue classes
binarize_tissue = MapNode(
fsl.ImageMaths(op_string='-nan -thr 0.99 -ero -bin'),
iterfield=['in_file'],
name='binarize_tissue')
struct_preproc_wf.connect(fast,
('partial_volume_files', selectindex, [0, 2]),
binarize_tissue, 'in_file')
# OUTPUT WM AND CSF MASKS FOR CPAC DENOISING
struct_preproc_wf.connect([(binarize_tissue, outputnode,
[(('out_file', selectsingle, 0), 'csf_mask'),
(('out_file', selectsingle, 1), 'wm_mask')])])
# WRITE WM MASK WITH P > .5 FOR FSL BBR
# use threshold of .5 like FSL's epi_reg script
wm_mask_4_bbr = Node(fsl.ImageMaths(op_string='-thr 0.5 -bin'),
name='wm_mask_4_bbr')
struct_preproc_wf.connect(fast, ('partial_volume_files', selectindex, [2]),
wm_mask_4_bbr, 'in_file')
struct_preproc_wf.connect(wm_mask_4_bbr, 'out_file', outputnode,
'wm_mask_4_bbr')
struct_preproc_wf.write_graph(dotfilename=struct_preproc_wf.name,
graph2use='flat',
format='pdf')
return struct_preproc_wf
base_directory='/',
template='%s/%s',
template_args=info,
sort_filelist=True),
name='selectfiles')
# For merging seed and nuisance mask paths and then distributing them downstream
seed_plus_nuisance = Node(utilMerge(2), name='seed_plus_nuisance')
seed_plus_nuisance.inputs.in2 = nuisance_masks
# 1. Obtain timeseries for seed and nuisance variables
# 1a. Merge all 3D functional images into a single 4D image
merge = Node(Merge(dimension='t', output_type='NIFTI', tr=TR), name='merge')
# 1b. Take mean of all voxels in each roi at each timepoint
ts = MapNode(ImageMeants(), name='ts', iterfield=['mask'])
# 1c. - Merge nuisance ts with motion parameters to create nuisance_regressors.txt.
# - Take temporal derivatives of nuisance_regressors.txt and append to nuisance_regressors.txt
# to create nuisance_regressors_tempderiv.txt
# - Square nuisance_regressors_tempderiv.txt and append to nuisance_regressors_tempderiv.txt,
# then append seed timeseries in front to create seed_nuisance_regressors.txt
def make_regressors_files(regressors_ts_list, mot_params, func):
import numpy as np
import os
num_timepoints = len(func)
num_nuisance = len(regressors_ts_list) - 1
# make nuisance_regressors.txt
nr = np.zeros((num_timepoints, num_nuisance))
def create_moco_pipeline(name='motion_correction'):
# initiate workflow
moco = Workflow(name='motion_correction')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['epi']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=['epi_moco',
'par_moco',
'mat_moco',
'rms_moco',
'epi_mean',
'rotplot',
'transplot',
'dispplots',
'tsnr_file']),
name='outputnode')
# mcflirt motion correction to 1st volume
mcflirt = Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
#ref_vol=1,
mean_vol = True,
out_file='rest_realigned.nii.gz'
),
name='mcflirt')
# plot motion parameters
rotplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation_plot.png'),
name='rotplotter')
transplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation_plot.png'),
name='transplotter')
dispplotter = MapNode(interface=fsl.PlotMotionParams(in_source='fsl',
plot_type='displacement',
),
name='dispplotter',
iterfield=['in_file'])
dispplotter.iterables = ('plot_type', ['displacement'])
# calculate tmean
tmean = Node(fsl.maths.MeanImage(dimension='T',
out_file='rest_realigned_mean.nii.gz'),
name='tmean')
# calculate tsnr
tsnr = Node(misc.TSNR(),
name='tsnr')
# create connections
moco.connect([(inputnode, mcflirt, [('epi', 'in_file')]),
(mcflirt, tmean, [('out_file', 'in_file')]),
(mcflirt, rotplotter, [('par_file', 'in_file')]),
(mcflirt, transplotter, [('par_file', 'in_file')]),
(mcflirt, dispplotter, [('rms_files', 'in_file')]),
(tmean, outputnode, [('out_file', 'epi_mean')]),
(mcflirt, outputnode, [('out_file', 'epi_moco'),
('par_file', 'par_moco'),
('mat_file', 'mat_moco'),
('rms_files', 'rms_moco')]),
(rotplotter, outputnode, [('out_file', 'rotplot')]),
(transplotter, outputnode, [('out_file', 'transplot')]),
(dispplotter, outputnode, [('out_file', 'dispplots')]),
(mcflirt, tsnr, [('out_file', 'in_file')]),
(tsnr, outputnode, [('tsnr_file', 'tsnr_file')])
])
return moco
susan.get_node('meanfunc2').interface.num_threads = 1
susan.get_node('meanfunc2').interface.mem_gb = 3
susan.get_node('merge').interface.num_threads = 1
susan.get_node('merge').interface.mem_gb = 3
susan.get_node('multi_inputs').interface.num_threads = 1
susan.get_node('multi_inputs').interface.mem_gb = 3
susan.get_node('smooth').interface.num_threads = 1
susan.get_node('smooth').interface.mem_gb = 3
susan.get_node('outputnode').interface.num_threads = 1
susan.get_node('outputnode').interface.mem_gb = 0.1
# ======================================================================
# DEFINE NODE: FUNCTION TO GET THE SUBJECT-SPECIFIC INFORMATION
# ======================================================================
subject_info = MapNode(Function(input_names=['events', 'confounds'],
output_names=['subject_info', 'event_names'],
function=get_subject_info),
name='subject_info',
iterfield=['events', 'confounds'])
# set expected thread and memory usage for the node:
subject_info.interface.num_threads = 1
subject_info.interface.mem_gb = 0.1
# subject_info.inputs.events = selectfiles_results.outputs.events
# subject_info.inputs.confounds = selectfiles_results.outputs.confounds
# subject_info_results = subject_info.run()
# subject_info_results.outputs.subject_info
# ======================================================================
# DEFINE NODE: REMOVE DUMMY VARIABLES (USING FSL ROI)
# ======================================================================
# function: extract region of interest (ROI) from an image
trim = MapNode(ExtractROI(), name='trim', iterfield=['in_file'])
# define index of the first selected volume (i.e., minimum index):
data[global_mask] = filter_data.T
else:
filter_data = np.real(
np.fft.ifftn(np.fft.fftn(filter_data) * F[:, np.newaxis]))
data[global_mask] = filter_data.T
img_out = nb.Nifti1Image(data, img.get_affine(), img.get_header())
out_file = os.path.join(os.getcwd(), 'bp_' + in_file.split('/')[-1])
img_out.to_filename(out_file)
return (out_file)
bpfilter = MapNode(Function(function=bandpass_filter,
input_names=['in_file', 'brainmask'],
output_names=['out_file']),
iterfield='in_file',
name='bpfilter')
def get_ants_files(ants_output):
"""
Gets output from ANTs to pass to normalising all the things.
"""
trans = [ants_output[0], ants_output[1]]
return (trans)
ants_list = Node(Function(function=get_ants_files,
input_names=['ants_output'],
output_names=['trans']),
def test_mapnode(config, moving_image, fixed_image):
import nipype.interfaces.fsl as fsl
from nipype.pipeline.engine import Node, Workflow, MapNode
from nipype.interfaces.io import DataSink, DataGrabber
from nipype.interfaces.utility import IdentityInterface, Function
import os
moving_mse = get_mseid(moving_image[0])
fixed_mse = get_mseid(fixed_image[0])
print(moving_mse, fixed_mse)
seriesNum_moving = get_seriesnum(moving_image)
seriesNum_fixed = get_seriesnum(fixed_image)
print("seriesNum for moving and fixed are {}, {} respectively".format(seriesNum_moving, seriesNum_fixed))
register = Workflow(name="test_mapnode")
register.base_dir = config["working_directory"]
inputnode = Node(IdentityInterface(fields=["moving_image", "fixed_image"]),
name="inputspec")
inputnode.inputs.moving_image = moving_image
inputnode.inputs.fixed_image = fixed_image
check_len = Node(Function(input_names=["moving_image", "fixed_image"],
output_names=["new_moving_image", "new_fixed_image"], function=check_length),
name="check_len")
register.connect(inputnode, 'moving_image', check_len, 'moving_image')
register.connect(inputnode, 'fixed_image', check_len, 'fixed_image')
flt_rigid = MapNode(fsl.FLIRT(), iterfield=['in_file', 'reference'], name="FLIRT_RIGID")
flt_rigid.inputs.dof = 6
flt_rigid.output_type = 'NIFTI_GZ'
register.connect(check_len, 'new_moving_image', flt_rigid, 'in_file')
register.connect(check_len, 'new_fixed_image', flt_rigid, 'reference')
sinker = Node(DataSink(), name="DataSink")
sinker.inputs.base_directory = '/data/henry7/james'
sinker.inputs.container = 'test_mapnode'
"""
def getsubs(moving_image, fixed_image, moving_mse, fixed_mse, seriesNum_moving, seriesNum_fixed):
N = len(moving_image) * len(fixed_image)
subs = []
print("N is :" ,N)
for i in range(N):
for j in seriesNum_moving:
seri_moving = ''
if j != '':
seri_moving = '_' + j
for k in seriesNum_fixed:
seri_fixed = ''
if k != '':
seri_fixed = '_' + k
subs += [('_FLIRT_RIGID%d'%i, moving_mse + seri_moving + '__' + fixed_mse + seri_fixed)]
print("subs are: ", subs)
return subs
"""
def getsubs(moving_image, fixed_image, moving_mse, fixed_mse):
N = len(moving_image) * len(fixed_image)
subs = [('_flirt', '_trans')]
if N == 1:
subs += [('_FLIRT_RIGID%d'%0, moving_mse + '__' + fixed_mse)]
else:
for i in range(N):
subs += [('_FLIRT_RIGID%d'%i, moving_mse + '__' + fixed_mse + '_' + str(i+1))]
return subs
get_subs = Node(Function(input_names=["moving_image", "fixed_image", "moving_mse", "fixed_mse"],
output_names=["subs"], function=getsubs),
name="get_subs")
get_subs.inputs.moving_mse = moving_mse
get_subs.inputs.fixed_mse = fixed_mse
# get_subs.inputs.seriesNum_moving = seriesNum_moving
# get_subs.inputs.seriesNum_fixed = seriesNum_fixed
register.connect(inputnode, 'moving_image', get_subs, 'moving_image')
register.connect(inputnode, 'fixed_image', get_subs, "fixed_image")
register.connect(get_subs, 'subs', sinker, 'substitutions')
register.connect(flt_rigid, 'out_file', sinker, '@mapnode_out')
register.write_graph(graph2use='orig')
register.config["Execution"] = {"keep_inputs": True, "remove_unnecessary_outputs": False}
return register
'7tt2w': 'derivatives/preprocessing/{subject_id}/{subject_id}_ses-01_7T_T2w_NlinMoCo_res-iso.3_N4corrected_denoised_brain_preproc.nii.gz',
}
selectfiles = Node(SelectFiles(templates, base_directory=experiment_dir), name='selectfiles')
#PLAN:: antsBE+ n4, mult mask to flair and space > n4 flair+ space, > min mask with fsl > WM mask? > scale to MNI > fslmaths (div)
#PLAN 7T: min mask with fsl? > wm mask > scale to CC > fslmaths (div)
#should scale to the CC for tse as well?
wf.connect([(infosource, selectfiles, [('subject_id', 'subject_id')])])
wf.connect([(infosource, selectfiles, [('session_id', 'session_id')])])
###########
## flirt ##
###########
#3t
flirt_n_space = MapNode(fsl.FLIRT(cost_func='mutualinfo', uses_qform=True),
name='flirt_node_space', iterfield=['in_file'])
wf.connect([(selectfiles, flirt_n_space, [('t1w', 'reference')])])
wf.connect([(selectfiles, flirt_n_space, [('space', 'in_file')])])
flirt_n_flair = MapNode(fsl.FLIRT(cost_func='mutualinfo', uses_qform=True),
name='flirt_node_flair', iterfield=['in_file'])
wf.connect([(selectfiles, flirt_n_flair, [('t1w', 'reference')])])
wf.connect([(selectfiles, flirt_n_flair, [('flair', 'in_file')])])
####################
## ants_brain_ext ##
####################
ants_be_n = MapNode(BrainExtraction(dimension=3, brain_template='/data/fasttemp/uqtshaw/tomcat/data/derivatives/myelin_mapping/T_template.nii.gz', brain_probability_mask='/data/fasttemp/uqtshaw/tomcat/data/derivatives/myelin_mapping/T_template_BrainCerebellumProbabilityMask.nii.gz'),
name='ants_be_node', iterfield=['anatomical_image'])
wf.connect([(selectfiles, ants_be_n, [('t1w', 'anatomical_image')])])
############
## antsCT ##
############
def firstlevel_wf(subject_id, sink_directory, name='wmaze_frstlvl_wf'):
frstlvl_wf = Workflow(name='frstlvl_wf')
info = dict(
task_mri_files=[['subject_id',
'wmaze']], #dictionary used in datasource
motion_noise_files=[['subject_id']])
#function node to call subjectinfo function with name, onset, duration, and amplitude info
subject_info = Node(Function(input_names=['subject_id'],
output_names=['output'],
function=subjectinfo),
name='subject_info')
subject_info.inputs.ignore_exception = False
subject_info.inputs.subject_id = subject_id
#function node to define contrasts
getcontrasts = Node(Function(input_names=['subject_id', 'info'],
output_names=['contrasts'],
function=get_contrasts),
name='getcontrasts')
getcontrasts.inputs.ignore_exception = False
getcontrasts.inputs.subject_id = subject_id
frstlvl_wf.connect(subject_info, 'output', getcontrasts, 'info')
#function node to substitute names of folders and files created during pipeline
getsubs = Node(
Function(
input_names=['cons'],
output_names=['subs'],
# Calls the function 'get_subs'
function=get_subs),
name='getsubs')
getsubs.inputs.ignore_exception = False
getsubs.inputs.subject_id = subject_id
frstlvl_wf.connect(subject_info, 'output', getsubs, 'info')
frstlvl_wf.connect(getcontrasts, 'contrasts', getsubs, 'cons')
#datasource node to get task_mri and motion-noise files
datasource = Node(DataGrabber(infields=['subject_id'],
outfields=info.keys()),
name='datasource')
datasource.inputs.template = '*'
datasource.inputs.subject_id = subject_id
datasource.inputs.base_directory = os.path.abspath(
'/home/data/madlab/data/mri/wmaze/preproc/')
datasource.inputs.field_template = dict(
task_mri_files=
'%s/func/smoothed_fullspectrum/_maskfunc2*/*%s*.nii.gz', #functional files
motion_noise_files='%s/noise/filter_regressor??.txt'
) #filter regressor noise files
datasource.inputs.template_args = info
datasource.inputs.sort_filelist = True
datasource.inputs.ignore_exception = False
datasource.inputs.raise_on_empty = True
#function node to remove last three volumes from functional data
fslroi_epi = MapNode(
ExtractROI(t_min=0,
t_size=197), #start from first volume and end on -3
iterfield=['in_file'],
name='fslroi_epi')
fslroi_epi.output_type = 'NIFTI_GZ'
fslroi_epi.terminal_output = 'stream'
frstlvl_wf.connect(datasource, 'task_mri_files', fslroi_epi, 'in_file')
#function node to modify the motion and noise files to be single regressors
motionnoise = Node(Function(input_names=['subjinfo', 'files'],
output_names=['subjinfo'],
function=motion_noise),
name='motionnoise')
motionnoise.inputs.ignore_exception = False
frstlvl_wf.connect(subject_info, 'output', motionnoise, 'subjinfo')
frstlvl_wf.connect(datasource, 'motion_noise_files', motionnoise, 'files')
#node to create model specifications compatible with spm/fsl designers (requires subjectinfo to be received in the form of a Bunch)
specify_model = Node(SpecifyModel(), name='specify_model')
specify_model.inputs.high_pass_filter_cutoff = -1.0 #high-pass filter cutoff in seconds
specify_model.inputs.ignore_exception = False
specify_model.inputs.input_units = 'secs' #input units in either 'secs' or 'scans'
specify_model.inputs.time_repetition = 2.0 #TR
frstlvl_wf.connect(
fslroi_epi, 'roi_file', specify_model,
'functional_runs') #editted data files for model -- list of 4D files
#list of event description files in 3 column format corresponding to onsets, durations, and amplitudes
frstlvl_wf.connect(motionnoise, 'subjinfo', specify_model, 'subject_info')
#node for basic interface class generating identity mappings
modelfit_inputspec = Node(IdentityInterface(fields=[
'session_info', 'interscan_interval', 'contrasts', 'film_threshold',
'functional_data', 'bases', 'model_serial_correlations'
],
mandatory_inputs=True),
name='modelfit_inputspec')
modelfit_inputspec.inputs.bases = {'dgamma': {'derivs': False}}
modelfit_inputspec.inputs.film_threshold = 0.0
modelfit_inputspec.inputs.interscan_interval = 2.0
modelfit_inputspec.inputs.model_serial_correlations = True
frstlvl_wf.connect(fslroi_epi, 'roi_file', modelfit_inputspec,
'functional_data')
frstlvl_wf.connect(getcontrasts, 'contrasts', modelfit_inputspec,
'contrasts')
frstlvl_wf.connect(specify_model, 'session_info', modelfit_inputspec,
'session_info')
#node for first level SPM design matrix to demonstrate contrasts and motion/noise regressors
level1_design = MapNode(Level1Design(),
iterfield=['contrasts', 'session_info'],
name='level1_design')
level1_design.inputs.ignore_exception = False
frstlvl_wf.connect(modelfit_inputspec, 'interscan_interval', level1_design,
'interscan_interval')
frstlvl_wf.connect(modelfit_inputspec, 'session_info', level1_design,
'session_info')
frstlvl_wf.connect(modelfit_inputspec, 'contrasts', level1_design,
'contrasts')
frstlvl_wf.connect(modelfit_inputspec, 'bases', level1_design, 'bases')
frstlvl_wf.connect(modelfit_inputspec, 'model_serial_correlations',
level1_design, 'model_serial_correlations')
#MapNode to generate a design.mat file for each run
generate_model = MapNode(FEATModel(),
iterfield=['fsf_file', 'ev_files'],
name='generate_model')
generate_model.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
generate_model.inputs.ignore_exception = False
generate_model.inputs.output_type = 'NIFTI_GZ'
generate_model.inputs.terminal_output = 'stream'
frstlvl_wf.connect(level1_design, 'fsf_files', generate_model, 'fsf_file')
frstlvl_wf.connect(level1_design, 'ev_files', generate_model, 'ev_files')
#MapNode to estimate the model using FILMGLS -- fits the design matrix to the voxel timeseries
estimate_model = MapNode(FILMGLS(),
iterfield=['design_file', 'in_file', 'tcon_file'],
name='estimate_model')
estimate_model.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
estimate_model.inputs.ignore_exception = False
estimate_model.inputs.mask_size = 5 #Susan-smooth mask size
estimate_model.inputs.output_type = 'NIFTI_GZ'
estimate_model.inputs.results_dir = 'results'
estimate_model.inputs.smooth_autocorr = True #smooth auto-correlation estimates
estimate_model.inputs.terminal_output = 'stream'
frstlvl_wf.connect(modelfit_inputspec, 'film_threshold', estimate_model,
'threshold')
frstlvl_wf.connect(modelfit_inputspec, 'functional_data', estimate_model,
'in_file')
frstlvl_wf.connect(
generate_model, 'design_file', estimate_model,
'design_file') #mat file containing ascii matrix for design
frstlvl_wf.connect(generate_model, 'con_file', estimate_model,
'tcon_file') #contrast file containing contrast vectors
#merge node to merge the contrasts - necessary for fsl 5.0.7 and greater
merge_contrasts = MapNode(Merge(2),
iterfield=['in1'],
name='merge_contrasts')
frstlvl_wf.connect(estimate_model, 'zstats', merge_contrasts, 'in1')
#MapNode to transform the z2pval
z2pval = MapNode(ImageMaths(), iterfield=['in_file'], name='z2pval')
z2pval.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
z2pval.inputs.ignore_exception = False
z2pval.inputs.op_string = '-ztop' #defines the operation used
z2pval.inputs.output_type = 'NIFTI_GZ'
z2pval.inputs.suffix = '_pval'
z2pval.inputs.terminal_output = 'stream'
frstlvl_wf.connect(merge_contrasts, ('out', pop_lambda), z2pval, 'in_file')
#outputspec node using IdentityInterface() to receive information from estimate_model, merge_contrasts, z2pval, generate_model, and estimate_model
modelfit_outputspec = Node(IdentityInterface(fields=[
'copes', 'varcopes', 'dof_file', 'pfiles', 'parameter_estimates',
'zstats', 'design_image', 'design_file', 'design_cov', 'sigmasquareds'
],
mandatory_inputs=True),
name='modelfit_outputspec')
frstlvl_wf.connect(estimate_model, 'copes', modelfit_outputspec,
'copes') #lvl1 cope files
frstlvl_wf.connect(estimate_model, 'varcopes', modelfit_outputspec,
'varcopes') #lvl1 varcope files
frstlvl_wf.connect(merge_contrasts, 'out', modelfit_outputspec,
'zstats') #zstats across runs
frstlvl_wf.connect(z2pval, 'out_file', modelfit_outputspec, 'pfiles')
frstlvl_wf.connect(
generate_model, 'design_image', modelfit_outputspec,
'design_image') #graphical representation of design matrix
frstlvl_wf.connect(
generate_model, 'design_file', modelfit_outputspec,
'design_file') #mat file containing ascii matrix for design
frstlvl_wf.connect(
generate_model, 'design_cov', modelfit_outputspec,
'design_cov') #graphical representation of design covariance
frstlvl_wf.connect(estimate_model, 'param_estimates', modelfit_outputspec,
'parameter_estimates'
) #parameter estimates for columns of design matrix
frstlvl_wf.connect(estimate_model, 'dof_file', modelfit_outputspec,
'dof_file') #degrees of freedom
frstlvl_wf.connect(estimate_model, 'sigmasquareds', modelfit_outputspec,
'sigmasquareds') #summary of residuals
#datasink node to save output from multiple points in the pipeline
sinkd = MapNode(DataSink(),
iterfield=[
'substitutions', 'modelfit.contrasts.@copes',
'modelfit.contrasts.@varcopes', 'modelfit.estimates',
'modelfit.contrasts.@zstats'
],
name='sinkd')
sinkd.inputs.base_directory = sink_directory
sinkd.inputs.container = subject_id
frstlvl_wf.connect(getsubs, 'subs', sinkd, 'substitutions')
frstlvl_wf.connect(modelfit_outputspec, 'parameter_estimates', sinkd,
'modelfit.estimates')
frstlvl_wf.connect(modelfit_outputspec, 'sigmasquareds', sinkd,
'modelfit.estimates.@sigsq')
frstlvl_wf.connect(modelfit_outputspec, 'dof_file', sinkd, 'modelfit.dofs')
frstlvl_wf.connect(modelfit_outputspec, 'copes', sinkd,
'modelfit.contrasts.@copes')
frstlvl_wf.connect(modelfit_outputspec, 'varcopes', sinkd,
'modelfit.contrasts.@varcopes')
frstlvl_wf.connect(modelfit_outputspec, 'zstats', sinkd,
'modelfit.contrasts.@zstats')
frstlvl_wf.connect(modelfit_outputspec, 'design_image', sinkd,
'modelfit.design')
frstlvl_wf.connect(modelfit_outputspec, 'design_cov', sinkd,
'modelfit.design.@cov')
frstlvl_wf.connect(modelfit_outputspec, 'design_file', sinkd,
'modelfit.design.@matrix')
frstlvl_wf.connect(modelfit_outputspec, 'pfiles', sinkd,
'modelfit.contrasts.@pstats')
return frstlvl_wf
'fsaverage'
] # name of the surface subject/space the to be transformed ROIs are in
subject_list = ['sub-01'] # create the subject_list variable
output_dir = 'output_inverse_transform_ROIs_ALPACA' # name of norm output folder
working_dir = 'workingdir_inverse_transform_ROIs_ALPACA' # name of norm working directory
##### Create & specify nodes to be used and connected during the normalization pipeline #####
# Concatenate BBRegister's and ANTS' transforms into a list
merge = Node(Merge(2), iterfield=['in2'], name='mergexfm')
# Binarize node - binarizes mask again after transformation
binarize_post2ant = MapNode(Binarize(min=0.1),
iterfield=['in_file'],
name='binarize_post2ant')
binarize_pt2pp = binarize_post2ant.clone('binarize_pt2pp')
# FreeSurferSource - Data grabber specific for FreeSurfer data
fssource_lh = Node(FreeSurferSource(subjects_dir=fs_dir, hemi='lh'),
run_without_submitting=True,
name='fssource_lh')
fssource_rh = Node(FreeSurferSource(subjects_dir=fs_dir, hemi='rh'),
run_without_submitting=True,
name='fssource_rh')
# Transform the volumetric ROIs to the target space
inverse_transform_mni_volume_post2ant = MapNode(
def create_transform_pipeline(name='transfrom_timeseries'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
transform_ts = Workflow(name='transform_timeseries')
# inputnode
inputnode=Node(util.IdentityInterface(fields=['orig_ts',
'anat_head',
'mat_moco',
'fullwarp',
'resolution',
'brain_mask'
]),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['trans_ts',
'trans_ts_mean',
'trans_ts_masked',
'resamp_brain',
'brain_mask_resamp',
'out_dvars'
]),
name='outputnode')
#resample anatomy
resample = Node(fsl.FLIRT(datatype='float',
out_file='T1_resampled.nii.gz'),
name = 'resample_anat')
transform_ts.connect([(inputnode, resample, [('anat_head', 'in_file'),
('anat_head', 'reference'),
('resolution', 'apply_isoxfm')
]),
(resample, outputnode, [('out_file', 'resamp_brain')])
])
# split timeseries in single volumes
split=Node(fsl.Split(dimension='t',
out_base_name='timeseries'),
name='split')
transform_ts.connect([(inputnode, split, [('orig_ts','in_file')])])
# applymoco premat and fullwarpfield
applywarp = MapNode(fsl.ApplyWarp(interp='spline',
relwarp=True,
out_file='rest2anat.nii.gz',
datatype='float'),
iterfield=['in_file', 'premat'],
name='applywarp')
transform_ts.connect([(split, applywarp, [('out_files', 'in_file')]),
(inputnode, applywarp,
[('mat_moco', 'premat'),
('fullwarp','field_file')]),
(resample, applywarp, [('out_file', 'ref_file')])
])
# re-concatenate volumes
merge=Node(fsl.Merge(dimension='t',
merged_file='rest2anat.nii.gz'),
name='merge')
transform_ts.connect([(applywarp,merge,[('out_file','in_files')]),
(merge, outputnode, [('merged_file', 'trans_ts')])])
# calculate new mean
tmean = Node(fsl.maths.MeanImage(dimension='T',
out_file='rest_mean2anat_lowres.nii.gz'),
name='tmean')
transform_ts.connect([(merge, tmean, [('merged_file', 'in_file')]),
(tmean, outputnode, [('out_file', 'trans_ts_mean')])
])
# resample brain mask
resample_brain = Node(afni.Resample(resample_mode='NN',
outputtype='NIFTI_GZ',
out_file='T1_brain_mask_lowres.nii.gz'),
name = 'resample_brain')
transform_ts.connect([(inputnode, resample_brain, [('brain_mask', 'in_file')]),
(tmean, resample_brain, [('out_file', 'master')]),
(resample_brain, outputnode, [('out_file', 'brain_mask_resamp')])
])
#mask the transformed file
mask = Node(fsl.ApplyMask(), name="mask")
transform_ts.connect([(resample_brain,mask, [('out_file', 'mask_file')]),
(merge, mask, [('merged_file', 'in_file')]),
(mask, outputnode, [('out_file', 'trans_ts_masked')])
])
#calculate DVARS
dvars = Node(confounds.ComputeDVARS(save_all=True, save_plot=True), name="dvars")
transform_ts.connect([(resample_brain, dvars, [('out_file', 'in_mask')]),
(merge, dvars, [('merged_file', 'in_file')]),
(dvars, outputnode, [('out_all', 'out_dvars')])
])
return transform_ts
outfields=['struct']),
name='datasource')
datasource.inputs.base_directory = dataDir
datasource.inputs.template = '*'
datasource.inputs.field_template = field_template
datasource.inputs.template_args = template_args
datasource.inputs.subject_id = subs
datasource.inputs.sort_filelist = False
# Specify workflow name.
strucProc = Workflow(name='strucProc', base_dir=outDir + '/tmp')
strucProc.connect([(infosource, datasource, [('subject_id', 'subject_id')])])
# New Segment
segment = MapNode(interface=NewSegment(),
iterfield=['channel_files'],
name="segment")
segment.inputs.channel_info = (0.0001, 60, (True, True))
segment.inputs.write_deformation_fields = [
False, False
] # inverse and forward defomration fields
tpmPath = '/afs/cbs.mpg.de/software/spm/12.6685/9.0/precise/tpm/'
# The "True" statement tells NewSegment to create DARTEL output for:
tissue1 = (
(tpmPath + 'TPM.nii', 1), 2, (False, True), (False, False)) # grey matter
tissue2 = (
(tpmPath + 'TPM.nii', 2), 2, (False, True), (False, False)) # white matter
tissue3 = ((tpmPath + 'TPM.nii', 3), 2, (False, False), (False, False))
tissue4 = ((tpmPath + 'TPM.nii', 4), 2, (False, False), (False, False))
tissue5 = ((tpmPath + 'TPM.nii', 5), 2, (False, False), (False, False))
tissue6 = ((tpmPath + 'TPM.nii', 6), 2, (False, False), (False, False))
def run_workflow(session=None, csv_file=None):
from nipype import config
#config.enable_debug_mode()
method = 'fs' # freesurfer's mri_convert is faster
if method == 'fs':
import nipype.interfaces.freesurfer as fs # freesurfer
else:
assert method == 'fsl'
import nipype.interfaces.fsl as fsl # fsl
# ------------------ Specify variables
ds_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
data_dir = ds_root
output_dir = 'derivatives/resampled-isotropic-06mm'
working_dir = 'workingdirs'
# ------------------ Input Files
infosource = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'datatype',
]),
name="infosource")
if csv_file is not None:
# Read csv and use pandas to set-up image and ev-processing
df = pd.read_csv(csv_file)
# init lists
sub_img = []
ses_img = []
dt_img = []
# fill lists to iterate mapnodes
for index, row in df.iterrows():
for dt in row.datatype.strip("[]").split(" "):
if dt in ['anat']: # only for anatomicals
sub_img.append(row.subject)
ses_img.append(row.session)
dt_img.append(dt)
# check if the file definitions are ok
if len(dt_img) > 0:
print('There are images to process. Will continue.')
else:
print('No images specified. Check your csv-file.')
infosource.iterables = [('session_id', ses_img),
('subject_id', sub_img), ('datatype', dt_img)]
infosource.synchronize = True
else:
print('No csv-file specified. Cannot continue.')
# SelectFiles
templates = {
'image':
'sub-{subject_id}/ses-{session_id}/{datatype}/'
'sub-{subject_id}_ses-{session_id}_*.nii.gz',
}
inputfiles = Node(nio.SelectFiles(templates, base_directory=data_dir),
name="input_files")
# ------------------ Output Files
# Datasink
outputfiles = Node(nio.DataSink(base_directory=ds_root,
container=output_dir,
parameterization=True),
name="output_files")
# Use the following DataSink output substitutions
outputfiles.inputs.substitutions = [
('subject_id_', 'sub-'),
('session_id_', 'ses-'),
# BIDS Extension Proposal: BEP003
('_resample.nii.gz', '_res-06x06x06_preproc.nii.gz'),
# remove subdirectories:
('resampled-isotropic-06mm/isoxfm-06mm', 'resampled-isotropic-06mm'),
('resampled-isotropic-06mm/mriconv-06mm', 'resampled-isotropic-06mm'),
]
# Put result into a BIDS-like format
outputfiles.inputs.regexp_substitutions = [
# this works only if datatype is specified in input
(r'_datatype_([a-z]*)_ses-([a-zA-Z0-9]*)_sub-([a-zA-Z0-9]*)',
r'sub-\3/ses-\2/\1'),
(r'_fs_iso06mm[0-9]*/', r''),
(r'/_ses-([a-zA-Z0-9]*)_sub-([a-zA-Z0-9]*)', r'/sub-\2/ses-\1/'),
# stupid hacks for when datatype is not specified
(r'//(sub-[^/]*_bold_res-.*)', r'/func/\1'),
(r'//(sub-[^/]*_phasediff_res-.*.nii.gz)', r'/fmap/\1'),
(r'//(sub-[^/]*_magnitude1_res-.*.nii.gz)', r'/fmap/\1'),
(r'//(sub-[^/]*_epi_res-.*.nii.gz)', r'/fmap/\1'),
(r'//(sub-[^/]*_T1w_res-.*.nii.gz)', r'/anat/\1'),
(r'//(sub-[^/]*_T2w_res-.*.nii.gz)', r'/anat/\1'),
(r'//(sub-[^/]*_dwi_res-.*.nii.gz)', r'/dwi/\1'),
]
# -------------------------------------------- Create Pipeline
isotropic_flow = Workflow(name='resample_isotropic06mm',
base_dir=os.path.join(ds_root, working_dir))
isotropic_flow.connect([(infosource, inputfiles, [
('subject_id', 'subject_id'),
('session_id', 'session_id'),
('datatype', 'datatype'),
])])
# --- Convert to 1m isotropic voxels
if method == 'fs':
fs_iso06mm = MapNode(
fs.Resample(
voxel_size=(0.6, 0.6, 0.6),
# suffix is not accepted by fs.Resample
# suffix='_res-1x1x1_preproc',
# BIDS Extension Proposal: BEP003
),
name='fs_iso06mm',
iterfield=['in_file'],
)
isotropic_flow.connect(inputfiles, 'image', fs_iso06mm, 'in_file')
isotropic_flow.connect(fs_iso06mm, 'resampled_file', outputfiles,
'mriconv-06mm')
elif method == 'fsl':
# in_file --> out_file
isoxfm = Node(fsl.FLIRT(apply_isoxfm=0.6, ), name='isoxfm')
isotropic_flow.connect(inputfiles, 'image', isoxfm, 'in_file')
isotropic_flow.connect(inputfiles, 'image', isoxfm, 'reference')
isotropic_flow.connect(isoxfm, 'out_file', outputfiles, 'isoxfm-06mm')
isotropic_flow.stop_on_first_crash = False # True
isotropic_flow.keep_inputs = True
isotropic_flow.remove_unnecessary_outputs = False
isotropic_flow.write_graph()
outgraph = isotropic_flow.run()
def secondlevel_wf(subject_id, sink_directory, name='GLM1_scndlvl_wf'):
scndlvl_wf = Workflow(name='scndlvl_wf')
base_dir = os.path.abspath('/home/data/madlab/data/mri/wmaze/')
contrasts = [
'all_before_B_corr', 'all_before_B_incorr', 'all_remaining',
'all_corr_minus_all_incorr', 'all_incorr_minus_all_corr'
]
cnt_file_list = []
for curr_contrast in contrasts:
cnt_file_list.append(
glob(
os.path.join(
base_dir,
'frstlvl/model_GLM1/{0}/modelfit/contrasts/_estimate_model*/cope??_{1}.nii.gz'
.format(subject_id, curr_contrast))))
dof_runs = [[], [], [], [], []]
for i, curr_file_list in enumerate(cnt_file_list):
if not isinstance(curr_file_list, list):
curr_file_list = [curr_file_list]
for curr_file in curr_file_list:
dof_runs[i].append(
curr_file.split('/')[-2][-1]) #grabs the estimate_model #
info = dict(copes=[['subject_id', contrasts]],
varcopes=[['subject_id', contrasts]],
mask_file=[['subject_id', 'aparc+aseg_thresh']],
dof_files=[['subject_id', dof_runs, 'dof']])
#datasource node to get task_mri and motion-noise files
datasource = Node(DataGrabber(infields=['subject_id'],
outfields=info.keys()),
name='datasource')
datasource.inputs.template = '*'
datasource.inputs.subject_id = subject_id
datasource.inputs.base_directory = os.path.abspath(
'/home/data/madlab/data/mri/wmaze/')
datasource.inputs.field_template = dict(
copes=
'frstlvl/model_GLM1/%s/modelfit/contrasts/_estimate_model*/cope*_%s.nii.gz',
varcopes=
'frstlvl/model_GLM1/%s/modelfit/contrasts/_estimate_model*/varcope*_%s.nii.gz',
mask_file='preproc/%s/ref/_fs_threshold20/%s*_thresh.nii',
dof_files='frstlvl/model_GLM1/%s/modelfit/dofs/_estimate_model%s/%s')
datasource.inputs.template_args = info
datasource.inputs.sort_filelist = True
datasource.inputs.ignore_exception = False
datasource.inputs.raise_on_empty = True
#inputspec to deal with copes and varcopes doublelist issues
fixedfx_inputspec = Node(IdentityInterface(
fields=['copes', 'varcopes', 'dof_files'], mandatory_inputs=True),
name='fixedfx_inputspec')
scndlvl_wf.connect(datasource, ('copes', doublelist), fixedfx_inputspec,
'copes')
scndlvl_wf.connect(datasource, ('varcopes', doublelist), fixedfx_inputspec,
'varcopes')
scndlvl_wf.connect(datasource, ('dof_files', doublelist),
fixedfx_inputspec, 'dof_files')
#merge all of copes into a single matrix across subject runs
copemerge = MapNode(Merge(), iterfield=['in_files'], name='copemerge')
copemerge.inputs.dimension = 't'
copemerge.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
copemerge.inputs.ignore_exception = False
copemerge.inputs.output_type = 'NIFTI_GZ'
copemerge.inputs.terminal_output = 'stream'
scndlvl_wf.connect(fixedfx_inputspec, 'copes', copemerge, 'in_files')
#generate DOF volume for second level
gendofvolume = Node(Function(input_names=['dof_files', 'cope_files'],
output_names=['dof_volumes'],
function=get_dofvolumes),
name='gendofvolume')
gendofvolume.inputs.ignore_exception = False
scndlvl_wf.connect(fixedfx_inputspec, 'dof_files', gendofvolume,
'dof_files')
scndlvl_wf.connect(copemerge, 'merged_file', gendofvolume, 'cope_files')
#merge all of the varcopes into a single matrix across subject runs per voxel
varcopemerge = MapNode(Merge(),
iterfield=['in_files'],
name='varcopemerge')
varcopemerge.inputs.dimension = 't'
varcopemerge.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
varcopemerge.inputs.ignore_exception = False
varcopemerge.inputs.output_type = 'NIFTI_GZ'
varcopemerge.inputs.terminal_output = 'stream'
scndlvl_wf.connect(fixedfx_inputspec, 'varcopes', varcopemerge, 'in_files')
#define contrasts from the names of the copes
getcontrasts = Node(Function(input_names=['data_inputs'],
output_names=['contrasts'],
function=get_contrasts),
name='getcontrasts')
getcontrasts.inputs.ignore_exception = False
scndlvl_wf.connect(datasource, ('copes', doublelist), getcontrasts,
'data_inputs')
#rename output files to be more descriptive
getsubs = Node(Function(input_names=['subject_id', 'cons'],
output_names=['subs'],
function=get_subs),
name='getsubs')
getsubs.inputs.ignore_exception = False
getsubs.inputs.subject_id = subject_id
scndlvl_wf.connect(getcontrasts, 'contrasts', getsubs, 'cons')
#l2model node for fixed effects analysis (aka within subj across runs)
l2model = MapNode(L2Model(), iterfield=['num_copes'], name='l2model')
l2model.inputs.ignore_exception = False
scndlvl_wf.connect(datasource, ('copes', num_copes), l2model, 'num_copes')
#FLAMEO Node to run the fixed effects analysis
flameo_fe = MapNode(FLAMEO(),
iterfield=[
'cope_file', 'var_cope_file', 'dof_var_cope_file',
'design_file', 't_con_file', 'cov_split_file'
],
name='flameo_fe')
flameo_fe.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
flameo_fe.inputs.ignore_exception = False
flameo_fe.inputs.log_dir = 'stats'
flameo_fe.inputs.output_type = 'NIFTI_GZ'
flameo_fe.inputs.run_mode = 'fe'
flameo_fe.inputs.terminal_output = 'stream'
scndlvl_wf.connect(varcopemerge, 'merged_file', flameo_fe, 'var_cope_file')
scndlvl_wf.connect(l2model, 'design_mat', flameo_fe, 'design_file')
scndlvl_wf.connect(l2model, 'design_con', flameo_fe, 't_con_file')
scndlvl_wf.connect(l2model, 'design_grp', flameo_fe, 'cov_split_file')
scndlvl_wf.connect(gendofvolume, 'dof_volumes', flameo_fe,
'dof_var_cope_file')
scndlvl_wf.connect(datasource, 'mask_file', flameo_fe, 'mask_file')
scndlvl_wf.connect(copemerge, 'merged_file', flameo_fe, 'cope_file')
#outputspec node
scndlvl_outputspec = Node(IdentityInterface(
fields=['res4d', 'copes', 'varcopes', 'zstats', 'tstats'],
mandatory_inputs=True),
name='scndlvl_outputspec')
scndlvl_wf.connect(flameo_fe, 'res4d', scndlvl_outputspec, 'res4d')
scndlvl_wf.connect(flameo_fe, 'copes', scndlvl_outputspec, 'copes')
scndlvl_wf.connect(flameo_fe, 'var_copes', scndlvl_outputspec, 'varcopes')
scndlvl_wf.connect(flameo_fe, 'zstats', scndlvl_outputspec, 'zstats')
scndlvl_wf.connect(flameo_fe, 'tstats', scndlvl_outputspec, 'tstats')
#datasink node
sinkd = Node(DataSink(), name='sinkd')
sinkd.inputs.base_directory = sink_directory
sinkd.inputs.container = subject_id
scndlvl_wf.connect(scndlvl_outputspec, 'copes', sinkd, 'fixedfx.@copes')
scndlvl_wf.connect(scndlvl_outputspec, 'varcopes', sinkd,
'fixedfx.@varcopes')
scndlvl_wf.connect(scndlvl_outputspec, 'tstats', sinkd, 'fixedfx.@tstats')
scndlvl_wf.connect(scndlvl_outputspec, 'zstats', sinkd, 'fixedfx.@zstats')
scndlvl_wf.connect(scndlvl_outputspec, 'res4d', sinkd, 'fixedfx.@pvals')
scndlvl_wf.connect(getsubs, 'subs', sinkd, 'substitutions')
return scndlvl_wf