def create_workflow(files,
target_file,
subject_id,
TR,
slice_times,
norm_threshold=1,
num_components=5,
vol_fwhm=None,
surf_fwhm=None,
lowpass_freq=-1,
highpass_freq=-1,
subjects_dir=None,
sink_directory=os.getcwd(),
target_subject=['fsaverage3', 'fsaverage4'],
name='resting'):
wf = Workflow(name=name)
# Rename files in case they are named identically
name_unique = MapNode(Rename(format_string='rest_%(run)02d'),
iterfield=['in_file', 'run'],
name='rename')
name_unique.inputs.keep_ext = True
name_unique.inputs.run = list(range(1, len(files) + 1))
name_unique.inputs.in_file = files
realign = Node(nipy.SpaceTimeRealigner(), name="spacetime_realign")
realign.inputs.slice_times = slice_times
realign.inputs.tr = TR
realign.inputs.slice_info = 2
realign.plugin_args = {'sbatch_args': '-c%d' % 4}
# Compute TSNR on realigned data regressing polynomials up to order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(realign, "out_file", tsnr, "in_file")
# Compute the median image across runs
calc_median = Node(Function(input_names=['in_files'],
output_names=['median_file'],
function=median,
imports=imports),
name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
"""Segment and Register
"""
registration = create_reg_workflow(name='registration')
wf.connect(calc_median, 'median_file', registration, 'inputspec.mean_image')
registration.inputs.inputspec.subject_id = subject_id
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = target_file
"""Quantify TSNR in each freesurfer ROI
"""
get_roi_tsnr = MapNode(fs.SegStats(default_color_table=True),
iterfield=['in_file'], name='get_aparc_tsnr')
get_roi_tsnr.inputs.avgwf_txt_file = True
wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_tsnr, 'segmentation_file')
"""Use :class:`nipype.algorithms.rapidart` to determine which of the
images in the functional series are outliers based on deviations in
intensity or movement.
"""
art = Node(interface=ArtifactDetect(), name="art")
art.inputs.use_differences = [True, True]
art.inputs.use_norm = True
art.inputs.norm_threshold = norm_threshold
art.inputs.zintensity_threshold = 9
art.inputs.mask_type = 'spm_global'
art.inputs.parameter_source = 'NiPy'
"""Here we are connecting all the nodes together. Notice that we add the merge node only if you choose
to use 4D. Also `get_vox_dims` function is passed along the input volume of normalise to set the optimal
voxel sizes.
"""
wf.connect([(name_unique, realign, [('out_file', 'in_file')]),
(realign, art, [('out_file', 'realigned_files')]),
(realign, art, [('par_file', 'realignment_parameters')]),
])
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())
mask = Node(fsl.BET(), name='getmask')
mask.inputs.mask = True
wf.connect(calc_median, 'median_file', mask, 'in_file')
# get segmentation in normalized functional space
def merge_files(in1, in2):
out_files = filename_to_list(in1)
out_files.extend(filename_to_list(in2))
return out_files
# filter some noise
# Compute motion regressors
motreg = Node(Function(input_names=['motion_params', 'order',
'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(realign, 'par_file', motreg, 'motion_params')
# Create a filter to remove motion and art confounds
createfilter1 = Node(Function(input_names=['motion_params', 'comp_norm',
'outliers', 'detrend_poly'],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 2
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
filter1 = MapNode(fsl.GLM(out_f_name='F_mcart.nii.gz',
out_pf_name='pF_mcart.nii.gz',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filtermotion')
wf.connect(realign, 'out_file', filter1, 'in_file')
wf.connect(realign, ('out_file', rename, '_filtermotart'),
filter1, 'out_res_name')
wf.connect(createfilter1, 'out_files', filter1, 'design')
createfilter2 = MapNode(ACompCor(),
iterfield=['realigned_file', 'extra_regressors'],
name='makecompcorrfilter')
createfilter2.inputs.components_file = 'noise_components.txt'
createfilter2.inputs.num_components = num_components
wf.connect(createfilter1, 'out_files', createfilter2, 'extra_regressors')
wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
wf.connect(registration, ('outputspec.segmentation_files', selectindex, [0, 2]),
createfilter2, 'mask_file')
filter2 = MapNode(fsl.GLM(out_f_name='F.nii.gz',
out_pf_name='pF.nii.gz',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filter_noise_nosmooth')
wf.connect(filter1, 'out_res', filter2, 'in_file')
wf.connect(filter1, ('out_res', rename, '_cleaned'),
filter2, 'out_res_name')
wf.connect(createfilter2, 'components_file', filter2, 'design')
wf.connect(mask, 'mask_file', filter2, 'mask')
bandpass = Node(Function(input_names=['files', 'lowpass_freq',
'highpass_freq', 'fs'],
output_names=['out_files'],
function=bandpass_filter,
imports=imports),
name='bandpass_unsmooth')
bandpass.inputs.fs = 1. / TR
bandpass.inputs.highpass_freq = highpass_freq
bandpass.inputs.lowpass_freq = lowpass_freq
wf.connect(filter2, 'out_res', bandpass, 'files')
"""Smooth the functional data using
:class:`nipype.interfaces.fsl.IsotropicSmooth`.
"""
smooth = MapNode(interface=fsl.IsotropicSmooth(), name="smooth", iterfield=["in_file"])
smooth.inputs.fwhm = vol_fwhm
wf.connect(bandpass, 'out_files', smooth, 'in_file')
collector = Node(Merge(2), name='collect_streams')
wf.connect(smooth, 'out_file', collector, 'in1')
wf.connect(bandpass, 'out_files', collector, 'in2')
"""
Transform the remaining images. First to anatomical and then to target
"""
warpall = MapNode(ants.ApplyTransforms(), iterfield=['input_image'],
name='warpall')
warpall.inputs.input_image_type = 3
warpall.inputs.interpolation = 'Linear'
warpall.inputs.invert_transform_flags = [False, False]
warpall.inputs.terminal_output = 'file'
warpall.inputs.reference_image = target_file
warpall.inputs.args = '--float'
warpall.inputs.num_threads = 2
warpall.plugin_args = {'sbatch_args': '-c%d' % 2}
# transform to target
wf.connect(collector, 'out', warpall, 'input_image')
wf.connect(registration, 'outputspec.transforms', warpall, 'transforms')
mask_target = Node(fsl.ImageMaths(op_string='-bin'), name='target_mask')
wf.connect(registration, 'outputspec.anat2target', mask_target, 'in_file')
maskts = MapNode(fsl.ApplyMask(), iterfield=['in_file'], name='ts_masker')
wf.connect(warpall, 'output_image', maskts, 'in_file')
wf.connect(mask_target, 'out_file', maskts, 'mask_file')
# map to surface
# extract aparc+aseg ROIs
# extract subcortical ROIs
# extract target space ROIs
# combine subcortical and cortical rois into a single cifti file
#######
# Convert aparc to subject functional space
# Sample the average time series in aparc ROIs
sampleaparc = MapNode(freesurfer.SegStats(default_color_table=True),
iterfield=['in_file', 'summary_file',
'avgwf_txt_file'],
name='aparc_ts')
sampleaparc.inputs.segment_id = ([8] + list(range(10, 14)) + [17, 18, 26, 47] +
list(range(49, 55)) + [58] + list(range(1001, 1036)) +
list(range(2001, 2036)))
wf.connect(registration, 'outputspec.aparc',
sampleaparc, 'segmentation_file')
wf.connect(collector, 'out', sampleaparc, 'in_file')
def get_names(files, suffix):
"""Generate appropriate names for output files
"""
from nipype.utils.filemanip import (split_filename, filename_to_list,
list_to_filename)
import os
out_names = []
for filename in files:
path, name, _ = split_filename(filename)
out_names.append(os.path.join(path, name + suffix))
return list_to_filename(out_names)
wf.connect(collector, ('out', get_names, '_avgwf.txt'),
sampleaparc, 'avgwf_txt_file')
wf.connect(collector, ('out', get_names, '_summary.stats'),
sampleaparc, 'summary_file')
# Sample the time series onto the surface of the target surface. Performs
# sampling into left and right hemisphere
target = Node(IdentityInterface(fields=['target_subject']), name='target')
target.iterables = ('target_subject', filename_to_list(target_subject))
samplerlh = MapNode(freesurfer.SampleToSurface(),
iterfield=['source_file'],
name='sampler_lh')
samplerlh.inputs.sampling_method = "average"
samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
samplerlh.inputs.sampling_units = "frac"
samplerlh.inputs.interp_method = "trilinear"
samplerlh.inputs.smooth_surf = surf_fwhm
# samplerlh.inputs.cortex_mask = True
samplerlh.inputs.out_type = 'niigz'
samplerlh.inputs.subjects_dir = subjects_dir
samplerrh = samplerlh.clone('sampler_rh')
samplerlh.inputs.hemi = 'lh'
wf.connect(collector, 'out', samplerlh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerlh, 'reg_file')
wf.connect(target, 'target_subject', samplerlh, 'target_subject')
samplerrh.set_input('hemi', 'rh')
wf.connect(collector, 'out', samplerrh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerrh, 'reg_file')
wf.connect(target, 'target_subject', samplerrh, 'target_subject')
# Combine left and right hemisphere to text file
combiner = MapNode(Function(input_names=['left', 'right'],
output_names=['out_file'],
function=combine_hemi,
imports=imports),
iterfield=['left', 'right'],
name="combiner")
wf.connect(samplerlh, 'out_file', combiner, 'left')
wf.connect(samplerrh, 'out_file', combiner, 'right')
# Sample the time series file for each subcortical roi
ts2txt = MapNode(Function(input_names=['timeseries_file', 'label_file',
'indices'],
output_names=['out_file'],
function=extract_subrois,
imports=imports),
iterfield=['timeseries_file'],
name='getsubcortts')
ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
list(range(49, 55)) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm_v2.nii.gz'))
wf.connect(maskts, 'out_file', ts2txt, 'timeseries_file')
######
substitutions = [('_target_subject_', ''),
('_filtermotart_cleaned_bp_trans_masked', ''),
('_filtermotart_cleaned_bp', ''),
]
substitutions += [("_smooth%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_ts_masker%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_getsubcortts%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_combiner%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_filtermotion%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_filter_noise_nosmooth%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_makecompcorfilter%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_get_aparc_tsnr%d/" % i, "run%d_" % (i + 1)) for i in range(11)[::-1]]
substitutions += [("T1_out_brain_pve_0_maths_warped", "compcor_csf"),
("T1_out_brain_pve_1_maths_warped", "compcor_gm"),
("T1_out_brain_pve_2_maths_warped", "compcor_wm"),
("output_warped_image_maths", "target_brain_mask"),
("median_brain_mask", "native_brain_mask"),
("corr_", "")]
regex_subs = [('_combiner.*/sar', '/smooth/'),
('_combiner.*/ar', '/unsmooth/'),
('_aparc_ts.*/sar', '/smooth/'),
('_aparc_ts.*/ar', '/unsmooth/'),
('_getsubcortts.*/sar', '/smooth/'),
('_getsubcortts.*/ar', '/unsmooth/'),
('series/sar', 'series/smooth/'),
('series/ar', 'series/unsmooth/'),
('_inverse_transform./', ''),
]
# Save the relevant data into an output directory
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
datasink.inputs.substitutions = substitutions
datasink.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(realign, 'par_file', datasink, 'resting.qa.motion')
wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
wf.connect(registration, 'outputspec.segmentation_files', datasink, 'resting.mask_files')
wf.connect(registration, 'outputspec.anat2target', datasink, 'resting.qa.ants')
wf.connect(mask, 'mask_file', datasink, 'resting.mask_files.@brainmask')
wf.connect(mask_target, 'out_file', datasink, 'resting.mask_files.target')
wf.connect(filter1, 'out_f', datasink, 'resting.qa.compmaps.@mc_F')
wf.connect(filter1, 'out_pf', datasink, 'resting.qa.compmaps.@mc_pF')
wf.connect(filter2, 'out_f', datasink, 'resting.qa.compmaps')
wf.connect(filter2, 'out_pf', datasink, 'resting.qa.compmaps.@p')
wf.connect(registration, 'outputspec.min_cost_file', datasink, 'resting.qa.mincost')
wf.connect(tsnr, 'tsnr_file', datasink, 'resting.qa.tsnr.@map')
wf.connect([(get_roi_tsnr, datasink, [('avgwf_txt_file', 'resting.qa.tsnr'),
('summary_file', 'resting.qa.tsnr.@summary')])])
wf.connect(bandpass, 'out_files', datasink, 'resting.timeseries.@bandpassed')
wf.connect(smooth, 'out_file', datasink, 'resting.timeseries.@smoothed')
wf.connect(createfilter1, 'out_files',
datasink, 'resting.regress.@regressors')
wf.connect(createfilter2, 'components_file',
datasink, 'resting.regress.@compcorr')
wf.connect(maskts, 'out_file', datasink, 'resting.timeseries.target')
wf.connect(sampleaparc, 'summary_file',
datasink, 'resting.parcellations.aparc')
wf.connect(sampleaparc, 'avgwf_txt_file',
datasink, 'resting.parcellations.aparc.@avgwf')
wf.connect(ts2txt, 'out_file',
datasink, 'resting.parcellations.grayo.@subcortical')
datasink2 = Node(interface=DataSink(), name="datasink2")
datasink2.inputs.base_directory = sink_directory
datasink2.inputs.container = subject_id
datasink2.inputs.substitutions = substitutions
datasink2.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(combiner, 'out_file',
datasink2, 'resting.parcellations.grayo.@surface')
return wf
def create_workflow(files,
subject_id,
n_vol=0,
despike=True,
TR=None,
slice_times=None,
slice_thickness=None,
fieldmap_images=[],
norm_threshold=1,
num_components=6,
vol_fwhm=None,
surf_fwhm=None,
lowpass_freq=-1,
highpass_freq=-1,
sink_directory=os.getcwd(),
FM_TEdiff=2.46,
FM_sigma=2,
FM_echo_spacing=.7,
target_subject=['fsaverage3', 'fsaverage4'],
name='resting'):
wf = Workflow(name=name)
# Skip starting volumes
remove_vol = MapNode(fsl.ExtractROI(t_min=n_vol, t_size=-1),
iterfield=['in_file'],
name="remove_volumes")
remove_vol.inputs.in_file = files
# Run AFNI's despike. This is always run, however, whether this is fed to
# realign depends on the input configuration
despiker = MapNode(afni.Despike(outputtype='NIFTI_GZ'),
iterfield=['in_file'],
name='despike')
#despiker.plugin_args = {'qsub_args': '-l nodes=1:ppn='}
wf.connect(remove_vol, 'roi_file', despiker, 'in_file')
# Run Nipy joint slice timing and realignment algorithm
realign = Node(nipy.SpaceTimeRealigner(), name='realign')
realign.inputs.tr = TR
realign.inputs.slice_times = slice_times
realign.inputs.slice_info = 2
if despike:
wf.connect(despiker, 'out_file', realign, 'in_file')
else:
wf.connect(remove_vol, 'roi_file', realign, 'in_file')
# Comute TSNR on realigned data regressing polynomials upto order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(realign, 'out_file', tsnr, 'in_file')
# Compute the median image across runs
calc_median = Node(Function(input_names=['in_files'],
output_names=['median_file'],
function=median,
imports=imports),
name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
# Coregister the median to the surface
register = Node(freesurfer.BBRegister(), name='bbregister')
register.inputs.subject_id = subject_id
register.inputs.init = 'fsl'
register.inputs.contrast_type = 't2'
register.inputs.out_fsl_file = True
register.inputs.epi_mask = True
# Compute fieldmaps and unwarp using them
if fieldmap_images:
fieldmap = Node(interface=EPIDeWarp(), name='fieldmap_unwarp')
fieldmap.inputs.tediff = FM_TEdiff
fieldmap.inputs.esp = FM_echo_spacing
fieldmap.inputs.sigma = FM_sigma
fieldmap.inputs.mag_file = fieldmap_images[0]
fieldmap.inputs.dph_file = fieldmap_images[1]
wf.connect(calc_median, 'median_file', fieldmap, 'exf_file')
dewarper = MapNode(interface=fsl.FUGUE(),
iterfield=['in_file'],
name='dewarper')
wf.connect(tsnr, 'detrended_file', dewarper, 'in_file')
wf.connect(fieldmap, 'exf_mask', dewarper, 'mask_file')
wf.connect(fieldmap, 'vsm_file', dewarper, 'shift_in_file')
wf.connect(fieldmap, 'exfdw', register, 'source_file')
else:
wf.connect(calc_median, 'median_file', register, 'source_file')
# Get the subject's freesurfer source directory
fssource = Node(FreeSurferSource(), name='fssource')
fssource.inputs.subject_id = subject_id
fssource.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
# Extract wm+csf, brain masks by eroding freesurfer labels and then
# transform the masks into the space of the median
wmcsf = Node(freesurfer.Binarize(), name='wmcsfmask')
mask = wmcsf.clone('anatmask')
wmcsftransform = Node(freesurfer.ApplyVolTransform(inverse=True,
interp='nearest'),
name='wmcsftransform')
wmcsftransform.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
wmcsf.inputs.wm_ven_csf = True
wmcsf.inputs.match = [4, 5, 14, 15, 24, 31, 43, 44, 63]
wmcsf.inputs.binary_file = 'wmcsf.nii.gz'
wmcsf.inputs.erode = int(np.ceil(slice_thickness))
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), wmcsf, 'in_file')
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', wmcsftransform, 'source_file')
else:
wf.connect(calc_median, 'median_file', wmcsftransform, 'source_file')
wf.connect(register, 'out_reg_file', wmcsftransform, 'reg_file')
wf.connect(wmcsf, 'binary_file', wmcsftransform, 'target_file')
mask.inputs.binary_file = 'mask.nii.gz'
mask.inputs.dilate = int(np.ceil(slice_thickness)) + 1
mask.inputs.erode = int(np.ceil(slice_thickness))
mask.inputs.min = 0.5
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), mask, 'in_file')
masktransform = wmcsftransform.clone("masktransform")
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', masktransform, 'source_file')
else:
wf.connect(calc_median, 'median_file', masktransform, 'source_file')
wf.connect(register, 'out_reg_file', masktransform, 'reg_file')
wf.connect(mask, 'binary_file', masktransform, 'target_file')
# Compute Art outliers
art = Node(interface=ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=norm_threshold,
zintensity_threshold=3,
parameter_source='NiPy',
bound_by_brainmask=True,
save_plot=False,
mask_type='file'),
name="art")
if fieldmap_images:
wf.connect(dewarper, 'unwarped_file', art, 'realigned_files')
else:
wf.connect(tsnr, 'detrended_file', art, 'realigned_files')
wf.connect(realign, 'par_file', art, 'realignment_parameters')
wf.connect(masktransform, 'transformed_file', art, 'mask_file')
# Compute motion regressors
motreg = Node(Function(
input_names=['motion_params', 'order', 'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(realign, 'par_file', motreg, 'motion_params')
# Create a filter to remove motion and art confounds
createfilter1 = Node(Function(
input_names=['motion_params', 'comp_norm', 'outliers'],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
# Filter the motion and art confounds
filter1 = MapNode(fsl.GLM(out_res_name='timeseries.nii.gz', demean=True),
iterfield=['in_file', 'design'],
name='filtermotion')
if fieldmap_images:
wf.connect(dewarper, 'unwarped_file', filter1, 'in_file')
else:
wf.connect(tsnr, 'detrended_file', filter1, 'in_file')
wf.connect(createfilter1, 'out_files', filter1, 'design')
wf.connect(masktransform, 'transformed_file', filter1, 'mask')
# Create a filter to remove noise components based on white matter and CSF
createfilter2 = MapNode(Function(
input_names=['realigned_file', 'mask_file', 'num_components'],
output_names=['out_files'],
function=extract_noise_components,
imports=imports),
iterfield=['realigned_file'],
name='makecompcorrfilter')
createfilter2.inputs.num_components = num_components
wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
wf.connect(masktransform, 'transformed_file', createfilter2, 'mask_file')
# Filter noise components
filter2 = MapNode(fsl.GLM(out_res_name='timeseries_cleaned.nii.gz',
demean=True),
iterfield=['in_file', 'design'],
name='filtercompcorr')
wf.connect(filter1, 'out_res', filter2, 'in_file')
wf.connect(createfilter2, 'out_files', filter2, 'design')
wf.connect(masktransform, 'transformed_file', filter2, 'mask')
# Smoothing using surface and volume smoothing
smooth = MapNode(freesurfer.Smooth(), iterfield=['in_file'], name='smooth')
smooth.inputs.proj_frac_avg = (0.1, 0.9, 0.1)
if surf_fwhm is None:
surf_fwhm = 5 * slice_thickness
smooth.inputs.surface_fwhm = surf_fwhm
if vol_fwhm is None:
vol_fwhm = 2 * slice_thickness
smooth.inputs.vol_fwhm = vol_fwhm
wf.connect(filter2, 'out_res', smooth, 'in_file')
wf.connect(register, 'out_reg_file', smooth, 'reg_file')
# Bandpass filter the data
bandpass = MapNode(fsl.TemporalFilter(),
iterfield=['in_file'],
name='bandpassfilter')
if highpass_freq < 0:
bandpass.inputs.highpass_sigma = -1
else:
bandpass.inputs.highpass_sigma = 1. / (2 * TR * highpass_freq)
if lowpass_freq < 0:
bandpass.inputs.lowpass_sigma = -1
else:
bandpass.inputs.lowpass_sigma = 1. / (2 * TR * lowpass_freq)
wf.connect(smooth, 'smoothed_file', bandpass, 'in_file')
# Convert aparc to subject functional space
aparctransform = wmcsftransform.clone("aparctransform")
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', aparctransform, 'source_file')
else:
wf.connect(calc_median, 'median_file', aparctransform, 'source_file')
wf.connect(register, 'out_reg_file', aparctransform, 'reg_file')
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), aparctransform,
'target_file')
# Sample the average time series in aparc ROIs
sampleaparc = MapNode(freesurfer.SegStats(avgwf_txt_file=True,
default_color_table=True),
iterfield=['in_file'],
name='aparc_ts')
sampleaparc.inputs.segment_id = ([8] + range(10, 14) + [17, 18, 26, 47] +
range(49, 55) + [58] + range(1001, 1036) +
range(2001, 2036))
wf.connect(aparctransform, 'transformed_file', sampleaparc,
'segmentation_file')
wf.connect(bandpass, 'out_file', sampleaparc, 'in_file')
# Sample the time series onto the surface of the target surface. Performs
# sampling into left and right hemisphere
target = Node(IdentityInterface(fields=['target_subject']), name='target')
target.iterables = ('target_subject', filename_to_list(target_subject))
samplerlh = MapNode(freesurfer.SampleToSurface(),
iterfield=['source_file'],
name='sampler_lh')
samplerlh.inputs.sampling_method = "average"
samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
samplerlh.inputs.sampling_units = "frac"
samplerlh.inputs.interp_method = "trilinear"
#samplerlh.inputs.cortex_mask = True
samplerlh.inputs.out_type = 'niigz'
samplerlh.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
samplerrh = samplerlh.clone('sampler_rh')
samplerlh.inputs.hemi = 'lh'
wf.connect(bandpass, 'out_file', samplerlh, 'source_file')
wf.connect(register, 'out_reg_file', samplerlh, 'reg_file')
wf.connect(target, 'target_subject', samplerlh, 'target_subject')
samplerrh.set_input('hemi', 'rh')
wf.connect(bandpass, 'out_file', samplerrh, 'source_file')
wf.connect(register, 'out_reg_file', samplerrh, 'reg_file')
wf.connect(target, 'target_subject', samplerrh, 'target_subject')
# Combine left and right hemisphere to text file
combiner = MapNode(Function(input_names=['left', 'right'],
output_names=['out_file'],
function=combine_hemi,
imports=imports),
iterfield=['left', 'right'],
name="combiner")
wf.connect(samplerlh, 'out_file', combiner, 'left')
wf.connect(samplerrh, 'out_file', combiner, 'right')
# Compute registration between the subject's structural and MNI template
# This is currently set to perform a very quick registration. However, the
# registration can be made significantly more accurate for cortical
# structures by increasing the number of iterations
# All parameters are set using the example from:
# https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh
reg = Node(ants.Registration(), name='antsRegister')
reg.inputs.output_transform_prefix = "output_"
reg.inputs.transforms = ['Translation', 'Rigid', 'Affine', 'SyN']
reg.inputs.transform_parameters = [(0.1, ), (0.1, ), (0.1, ),
(0.2, 3.0, 0.0)]
# reg.inputs.number_of_iterations = ([[10000, 111110, 11110]]*3 +
# [[100, 50, 30]])
reg.inputs.number_of_iterations = [[100, 100, 100]] * 3 + [[100, 20, 10]]
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = False
reg.inputs.metric = ['Mattes'] * 3 + [['Mattes', 'CC']]
reg.inputs.metric_weight = [1] * 3 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 3 + [[32, 4]]
reg.inputs.sampling_strategy = ['Regular'] * 3 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 3 + [[None, None]]
reg.inputs.convergence_threshold = [1.e-8] * 3 + [-0.01]
reg.inputs.convergence_window_size = [20] * 3 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 3 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ['vox'] * 4
reg.inputs.shrink_factors = [[6, 4, 2]] + [[3, 2, 1]] * 2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 4
reg.inputs.use_histogram_matching = [False] * 3 + [True]
reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
reg.inputs.fixed_image = \
os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz')
reg.inputs.num_threads = 4
reg.plugin_args = {'qsub_args': '-l nodes=1:ppn=4'}
# Convert T1.mgz to nifti for using with ANTS
convert = Node(freesurfer.MRIConvert(out_type='niigz'), name='convert2nii')
wf.connect(fssource, 'T1', convert, 'in_file')
# Mask the T1.mgz file with the brain mask computed earlier
maskT1 = Node(fsl.BinaryMaths(operation='mul'), name='maskT1')
wf.connect(mask, 'binary_file', maskT1, 'operand_file')
wf.connect(convert, 'out_file', maskT1, 'in_file')
wf.connect(maskT1, 'out_file', reg, 'moving_image')
# Convert the BBRegister transformation to ANTS ITK format
convert2itk = MapNode(C3dAffineTool(),
iterfield=['transform_file', 'source_file'],
name='convert2itk')
convert2itk.inputs.fsl2ras = True
convert2itk.inputs.itk_transform = True
wf.connect(register, 'out_fsl_file', convert2itk, 'transform_file')
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', convert2itk, 'source_file')
else:
wf.connect(calc_median, 'median_file', convert2itk, 'source_file')
wf.connect(convert, 'out_file', convert2itk, 'reference_file')
# Concatenate the affine and ants transforms into a list
pickfirst = lambda x: x[0]
merge = MapNode(Merge(2), iterfield=['in2'], name='mergexfm')
wf.connect(convert2itk, 'itk_transform', merge, 'in2')
wf.connect(reg, ('composite_transform', pickfirst), merge, 'in1')
# Apply the combined transform to the time series file
sample2mni = MapNode(ants.ApplyTransforms(),
iterfield=['input_image', 'transforms'],
name='sample2mni')
sample2mni.inputs.input_image_type = 3
sample2mni.inputs.interpolation = 'BSpline'
sample2mni.inputs.invert_transform_flags = [False, False]
sample2mni.inputs.reference_image = \
os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz')
sample2mni.inputs.terminal_output = 'file'
wf.connect(bandpass, 'out_file', sample2mni, 'input_image')
wf.connect(merge, 'out', sample2mni, 'transforms')
# Sample the time series file for each subcortical roi
ts2txt = MapNode(Function(
input_names=['timeseries_file', 'label_file', 'indices'],
output_names=['out_file'],
function=extract_subrois,
imports=imports),
iterfield=['timeseries_file'],
name='getsubcortts')
ts2txt.inputs.indices = [8] + range(10, 14) + [17, 18, 26, 47] +\
range(49, 55) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm.nii.gz'))
wf.connect(sample2mni, 'output_image', ts2txt, 'timeseries_file')
# Save the relevant data into an output directory
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
datasink.inputs.substitutions = [('_target_subject_', '')]
datasink.inputs.regexp_substitutions = (r'(/_.*(\d+/))', r'/run\2')
wf.connect(despiker, 'out_file', datasink, 'resting.qa.despike')
wf.connect(realign, 'par_file', datasink, 'resting.qa.motion')
wf.connect(tsnr, 'tsnr_file', datasink, 'resting.qa.tsnr')
wf.connect(tsnr, 'mean_file', datasink, 'resting.qa.tsnr.@mean')
wf.connect(tsnr, 'stddev_file', datasink, 'resting.qa.@tsnr_stddev')
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', datasink, 'resting.reference')
else:
wf.connect(calc_median, 'median_file', datasink, 'resting.reference')
wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
wf.connect(mask, 'binary_file', datasink, 'resting.mask')
wf.connect(masktransform, 'transformed_file', datasink,
'resting.mask.@transformed_file')
wf.connect(register, 'out_reg_file', datasink,
'resting.registration.bbreg')
wf.connect(reg, ('composite_transform', pickfirst), datasink,
'resting.registration.ants')
wf.connect(register, 'min_cost_file', datasink,
'resting.qa.bbreg.@mincost')
wf.connect(smooth, 'smoothed_file', datasink,
'resting.timeseries.fullpass')
wf.connect(bandpass, 'out_file', datasink, 'resting.timeseries.bandpassed')
wf.connect(sample2mni, 'output_image', datasink, 'resting.timeseries.mni')
wf.connect(createfilter1, 'out_files', datasink,
'resting.regress.@regressors')
wf.connect(createfilter2, 'out_files', datasink,
'resting.regress.@compcorr')
wf.connect(sampleaparc, 'summary_file', datasink,
'resting.parcellations.aparc')
wf.connect(sampleaparc, 'avgwf_txt_file', datasink,
'resting.parcellations.aparc.@avgwf')
wf.connect(ts2txt, 'out_file', datasink,
'resting.parcellations.grayo.@subcortical')
datasink2 = Node(interface=DataSink(), name="datasink2")
datasink2.inputs.base_directory = sink_directory
datasink2.inputs.container = subject_id
datasink2.inputs.substitutions = [('_target_subject_', '')]
datasink2.inputs.regexp_substitutions = (r'(/_.*(\d+/))', r'/run\2')
wf.connect(combiner, 'out_file', datasink2,
'resting.parcellations.grayo.@surface')
return wf
def create_workflow(files,
target_file,
subject_id,
TR,
slice_times,
norm_threshold=1,
num_components=5,
vol_fwhm=None,
surf_fwhm=None,
lowpass_freq=-1,
highpass_freq=-1,
subjects_dir=None,
sink_directory=os.getcwd(),
target_subject=['fsaverage3', 'fsaverage4'],
name='resting'):
wf = Workflow(name=name)
# Rename files in case they are named identically
name_unique = MapNode(Rename(format_string='rest_%(run)02d'),
iterfield=['in_file', 'run'],
name='rename')
name_unique.inputs.keep_ext = True
name_unique.inputs.run = list(range(1, len(files) + 1))
name_unique.inputs.in_file = files
realign = Node(interface=spm.Realign(), name="realign")
realign.inputs.jobtype = 'estwrite'
num_slices = len(slice_times)
slice_timing = Node(interface=spm.SliceTiming(), name="slice_timing")
slice_timing.inputs.num_slices = num_slices
slice_timing.inputs.time_repetition = TR
slice_timing.inputs.time_acquisition = TR - TR / float(num_slices)
slice_timing.inputs.slice_order = (np.argsort(slice_times) + 1).tolist()
slice_timing.inputs.ref_slice = int(num_slices / 2)
# Comute TSNR on realigned data regressing polynomials upto order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(slice_timing, 'timecorrected_files', tsnr, 'in_file')
# Compute the median image across runs
calc_median = Node(Function(input_names=['in_files'],
output_names=['median_file'],
function=median,
imports=imports),
name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
"""Segment and Register
"""
registration = create_reg_workflow(name='registration')
wf.connect(calc_median, 'median_file', registration,
'inputspec.mean_image')
registration.inputs.inputspec.subject_id = subject_id
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = target_file
"""Use :class:`nipype.algorithms.rapidart` to determine which of the
images in the functional series are outliers based on deviations in
intensity or movement.
"""
art = Node(interface=ArtifactDetect(), name="art")
art.inputs.use_differences = [True, True]
art.inputs.use_norm = True
art.inputs.norm_threshold = norm_threshold
art.inputs.zintensity_threshold = 9
art.inputs.mask_type = 'spm_global'
art.inputs.parameter_source = 'SPM'
"""Here we are connecting all the nodes together. Notice that we add the merge node only if you choose
to use 4D. Also `get_vox_dims` function is passed along the input volume of normalise to set the optimal
voxel sizes.
"""
wf.connect([
(name_unique, realign, [('out_file', 'in_files')]),
(realign, slice_timing, [('realigned_files', 'in_files')]),
(slice_timing, art, [('timecorrected_files', 'realigned_files')]),
(realign, art, [('realignment_parameters', 'realignment_parameters')]),
])
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())
mask = Node(fsl.BET(), name='getmask')
mask.inputs.mask = True
wf.connect(calc_median, 'median_file', mask, 'in_file')
# get segmentation in normalized functional space
def merge_files(in1, in2):
out_files = filename_to_list(in1)
out_files.extend(filename_to_list(in2))
return out_files
# filter some noise
# Compute motion regressors
motreg = Node(Function(
input_names=['motion_params', 'order', 'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(realign, 'realignment_parameters', motreg, 'motion_params')
# Create a filter to remove motion and art confounds
createfilter1 = Node(Function(
input_names=['motion_params', 'comp_norm', 'outliers', 'detrend_poly'],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 2
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
filter1 = MapNode(fsl.GLM(out_f_name='F_mcart.nii',
out_pf_name='pF_mcart.nii',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filtermotion')
wf.connect(slice_timing, 'timecorrected_files', filter1, 'in_file')
wf.connect(slice_timing, ('timecorrected_files', rename, '_filtermotart'),
filter1, 'out_res_name')
wf.connect(createfilter1, 'out_files', filter1, 'design')
createfilter2 = MapNode(Function(input_names=[
'realigned_file', 'mask_file', 'num_components', 'extra_regressors'
],
output_names=['out_files'],
function=extract_noise_components,
imports=imports),
iterfield=['realigned_file', 'extra_regressors'],
name='makecompcorrfilter')
createfilter2.inputs.num_components = num_components
wf.connect(createfilter1, 'out_files', createfilter2, 'extra_regressors')
wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
wf.connect(registration,
('outputspec.segmentation_files', selectindex, [0, 2]),
createfilter2, 'mask_file')
filter2 = MapNode(fsl.GLM(out_f_name='F.nii',
out_pf_name='pF.nii',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filter_noise_nosmooth')
wf.connect(filter1, 'out_res', filter2, 'in_file')
wf.connect(filter1, ('out_res', rename, '_cleaned'), filter2,
'out_res_name')
wf.connect(createfilter2, 'out_files', filter2, 'design')
wf.connect(mask, 'mask_file', filter2, 'mask')
bandpass = Node(Function(
input_names=['files', 'lowpass_freq', 'highpass_freq', 'fs'],
output_names=['out_files'],
function=bandpass_filter,
imports=imports),
name='bandpass_unsmooth')
bandpass.inputs.fs = 1. / TR
bandpass.inputs.highpass_freq = highpass_freq
bandpass.inputs.lowpass_freq = lowpass_freq
wf.connect(filter2, 'out_res', bandpass, 'files')
"""Smooth the functional data using
:class:`nipype.interfaces.spm.Smooth`.
"""
smooth = Node(interface=spm.Smooth(), name="smooth")
smooth.inputs.fwhm = vol_fwhm
wf.connect(bandpass, 'out_files', smooth, 'in_files')
collector = Node(Merge(2), name='collect_streams')
wf.connect(smooth, 'smoothed_files', collector, 'in1')
wf.connect(bandpass, 'out_files', collector, 'in2')
"""
Transform the remaining images. First to anatomical and then to target
"""
warpall = MapNode(ants.ApplyTransforms(),
iterfield=['input_image'],
name='warpall')
warpall.inputs.input_image_type = 3
warpall.inputs.interpolation = 'Linear'
warpall.inputs.invert_transform_flags = [False, False]
warpall.inputs.terminal_output = 'file'
warpall.inputs.reference_image = target_file
warpall.inputs.args = '--float'
warpall.inputs.num_threads = 1
# transform to target
wf.connect(collector, 'out', warpall, 'input_image')
wf.connect(registration, 'outputspec.transforms', warpall, 'transforms')
mask_target = Node(fsl.ImageMaths(op_string='-bin'), name='target_mask')
wf.connect(registration, 'outputspec.anat2target', mask_target, 'in_file')
maskts = MapNode(fsl.ApplyMask(), iterfield=['in_file'], name='ts_masker')
wf.connect(warpall, 'output_image', maskts, 'in_file')
wf.connect(mask_target, 'out_file', maskts, 'mask_file')
# map to surface
# extract aparc+aseg ROIs
# extract subcortical ROIs
# extract target space ROIs
# combine subcortical and cortical rois into a single cifti file
#######
# Convert aparc to subject functional space
# Sample the average time series in aparc ROIs
sampleaparc = MapNode(
freesurfer.SegStats(default_color_table=True),
iterfield=['in_file', 'summary_file', 'avgwf_txt_file'],
name='aparc_ts')
sampleaparc.inputs.segment_id = ([8] + list(range(10, 14)) +
[17, 18, 26, 47] + list(range(49, 55)) +
[58] + list(range(1001, 1036)) +
list(range(2001, 2036)))
wf.connect(registration, 'outputspec.aparc', sampleaparc,
'segmentation_file')
wf.connect(collector, 'out', sampleaparc, 'in_file')
def get_names(files, suffix):
"""Generate appropriate names for output files
"""
from nipype.utils.filemanip import (split_filename, filename_to_list,
list_to_filename)
out_names = []
for filename in files:
_, name, _ = split_filename(filename)
out_names.append(name + suffix)
return list_to_filename(out_names)
wf.connect(collector, ('out', get_names, '_avgwf.txt'), sampleaparc,
'avgwf_txt_file')
wf.connect(collector, ('out', get_names, '_summary.stats'), sampleaparc,
'summary_file')
# Sample the time series onto the surface of the target surface. Performs
# sampling into left and right hemisphere
target = Node(IdentityInterface(fields=['target_subject']), name='target')
target.iterables = ('target_subject', filename_to_list(target_subject))
samplerlh = MapNode(freesurfer.SampleToSurface(),
iterfield=['source_file'],
name='sampler_lh')
samplerlh.inputs.sampling_method = "average"
samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
samplerlh.inputs.sampling_units = "frac"
samplerlh.inputs.interp_method = "trilinear"
samplerlh.inputs.smooth_surf = surf_fwhm
# samplerlh.inputs.cortex_mask = True
samplerlh.inputs.out_type = 'niigz'
samplerlh.inputs.subjects_dir = subjects_dir
samplerrh = samplerlh.clone('sampler_rh')
samplerlh.inputs.hemi = 'lh'
wf.connect(collector, 'out', samplerlh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerlh, 'reg_file')
wf.connect(target, 'target_subject', samplerlh, 'target_subject')
samplerrh.set_input('hemi', 'rh')
wf.connect(collector, 'out', samplerrh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerrh, 'reg_file')
wf.connect(target, 'target_subject', samplerrh, 'target_subject')
# Combine left and right hemisphere to text file
combiner = MapNode(Function(input_names=['left', 'right'],
output_names=['out_file'],
function=combine_hemi,
imports=imports),
iterfield=['left', 'right'],
name="combiner")
wf.connect(samplerlh, 'out_file', combiner, 'left')
wf.connect(samplerrh, 'out_file', combiner, 'right')
# Sample the time series file for each subcortical roi
ts2txt = MapNode(Function(
input_names=['timeseries_file', 'label_file', 'indices'],
output_names=['out_file'],
function=extract_subrois,
imports=imports),
iterfield=['timeseries_file'],
name='getsubcortts')
ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
list(range(49, 55)) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm_v2.nii.gz'))
wf.connect(maskts, 'out_file', ts2txt, 'timeseries_file')
######
substitutions = [('_target_subject_', ''),
('_filtermotart_cleaned_bp_trans_masked', ''),
('_filtermotart_cleaned_bp', '')]
regex_subs = [
('_ts_masker.*/sar', '/smooth/'),
('_ts_masker.*/ar', '/unsmooth/'),
('_combiner.*/sar', '/smooth/'),
('_combiner.*/ar', '/unsmooth/'),
('_aparc_ts.*/sar', '/smooth/'),
('_aparc_ts.*/ar', '/unsmooth/'),
('_getsubcortts.*/sar', '/smooth/'),
('_getsubcortts.*/ar', '/unsmooth/'),
('series/sar', 'series/smooth/'),
('series/ar', 'series/unsmooth/'),
('_inverse_transform./', ''),
]
# Save the relevant data into an output directory
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
datasink.inputs.substitutions = substitutions
datasink.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(realign, 'realignment_parameters', datasink,
'resting.qa.motion')
wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
wf.connect(registration, 'outputspec.segmentation_files', datasink,
'resting.mask_files')
wf.connect(registration, 'outputspec.anat2target', datasink,
'resting.qa.ants')
wf.connect(mask, 'mask_file', datasink, 'resting.mask_files.@brainmask')
wf.connect(mask_target, 'out_file', datasink, 'resting.mask_files.target')
wf.connect(filter1, 'out_f', datasink, 'resting.qa.compmaps.@mc_F')
wf.connect(filter1, 'out_pf', datasink, 'resting.qa.compmaps.@mc_pF')
wf.connect(filter2, 'out_f', datasink, 'resting.qa.compmaps')
wf.connect(filter2, 'out_pf', datasink, 'resting.qa.compmaps.@p')
wf.connect(bandpass, 'out_files', datasink,
'resting.timeseries.@bandpassed')
wf.connect(smooth, 'smoothed_files', datasink,
'resting.timeseries.@smoothed')
wf.connect(createfilter1, 'out_files', datasink,
'resting.regress.@regressors')
wf.connect(createfilter2, 'out_files', datasink,
'resting.regress.@compcorr')
wf.connect(maskts, 'out_file', datasink, 'resting.timeseries.target')
wf.connect(sampleaparc, 'summary_file', datasink,
'resting.parcellations.aparc')
wf.connect(sampleaparc, 'avgwf_txt_file', datasink,
'resting.parcellations.aparc.@avgwf')
wf.connect(ts2txt, 'out_file', datasink,
'resting.parcellations.grayo.@subcortical')
datasink2 = Node(interface=DataSink(), name="datasink2")
datasink2.inputs.base_directory = sink_directory
datasink2.inputs.container = subject_id
datasink2.inputs.substitutions = substitutions
datasink2.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(combiner, 'out_file', datasink2,
'resting.parcellations.grayo.@surface')
return wf
def create_workflow(files,
subject_id,
n_vol=0,
despike=True,
TR=None,
slice_times=None,
slice_thickness=None,
fieldmap_images=[],
norm_threshold=1,
num_components=6,
vol_fwhm=None,
surf_fwhm=None,
lowpass_freq=-1,
highpass_freq=-1,
sink_directory=os.getcwd(),
FM_TEdiff=2.46,
FM_sigma=2,
FM_echo_spacing=.7,
target_subject=['fsaverage3', 'fsaverage4'],
name='resting'):
wf = Workflow(name=name)
# Skip starting volumes
remove_vol = MapNode(fsl.ExtractROI(t_min=n_vol, t_size=-1),
iterfield=['in_file'],
name="remove_volumes")
remove_vol.inputs.in_file = files
# Run AFNI's despike. This is always run, however, whether this is fed to
# realign depends on the input configuration
despiker = MapNode(afni.Despike(outputtype='NIFTI_GZ'),
iterfield=['in_file'],
name='despike')
#despiker.plugin_args = {'qsub_args': '-l nodes=1:ppn='}
wf.connect(remove_vol, 'roi_file', despiker, 'in_file')
# Run Nipy joint slice timing and realignment algorithm
realign = Node(nipy.SpaceTimeRealigner(), name='realign')
realign.inputs.tr = TR
realign.inputs.slice_times = slice_times
realign.inputs.slice_info = 2
if despike:
wf.connect(despiker, 'out_file', realign, 'in_file')
else:
wf.connect(remove_vol, 'roi_file', realign, 'in_file')
# Comute TSNR on realigned data regressing polynomials upto order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(realign, 'out_file', tsnr, 'in_file')
# Compute the median image across runs
calc_median = Node(Function(input_names=['in_files'],
output_names=['median_file'],
function=median,
imports=imports),
name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
# Coregister the median to the surface
register = Node(freesurfer.BBRegister(),
name='bbregister')
register.inputs.subject_id = subject_id
register.inputs.init = 'fsl'
register.inputs.contrast_type = 't2'
register.inputs.out_fsl_file = True
register.inputs.epi_mask = True
# Compute fieldmaps and unwarp using them
if fieldmap_images:
fieldmap = Node(interface=EPIDeWarp(), name='fieldmap_unwarp')
fieldmap.inputs.tediff = FM_TEdiff
fieldmap.inputs.esp = FM_echo_spacing
fieldmap.inputs.sigma = FM_sigma
fieldmap.inputs.mag_file = fieldmap_images[0]
fieldmap.inputs.dph_file = fieldmap_images[1]
wf.connect(calc_median, 'median_file', fieldmap, 'exf_file')
dewarper = MapNode(interface=fsl.FUGUE(), iterfield=['in_file'],
name='dewarper')
wf.connect(tsnr, 'detrended_file', dewarper, 'in_file')
wf.connect(fieldmap, 'exf_mask', dewarper, 'mask_file')
wf.connect(fieldmap, 'vsm_file', dewarper, 'shift_in_file')
wf.connect(fieldmap, 'exfdw', register, 'source_file')
else:
wf.connect(calc_median, 'median_file', register, 'source_file')
# Get the subject's freesurfer source directory
fssource = Node(FreeSurferSource(),
name='fssource')
fssource.inputs.subject_id = subject_id
fssource.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
# Extract wm+csf, brain masks by eroding freesurfer lables and then
# transform the masks into the space of the median
wmcsf = Node(freesurfer.Binarize(), name='wmcsfmask')
mask = wmcsf.clone('anatmask')
wmcsftransform = Node(freesurfer.ApplyVolTransform(inverse=True,
interp='nearest'),
name='wmcsftransform')
wmcsftransform.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
wmcsf.inputs.wm_ven_csf = True
wmcsf.inputs.match = [4, 5, 14, 15, 24, 31, 43, 44, 63]
wmcsf.inputs.binary_file = 'wmcsf.nii.gz'
wmcsf.inputs.erode = int(np.ceil(slice_thickness))
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), wmcsf, 'in_file')
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', wmcsftransform, 'source_file')
else:
wf.connect(calc_median, 'median_file', wmcsftransform, 'source_file')
wf.connect(register, 'out_reg_file', wmcsftransform, 'reg_file')
wf.connect(wmcsf, 'binary_file', wmcsftransform, 'target_file')
mask.inputs.binary_file = 'mask.nii.gz'
mask.inputs.dilate = int(np.ceil(slice_thickness)) + 1
mask.inputs.erode = int(np.ceil(slice_thickness))
mask.inputs.min = 0.5
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), mask, 'in_file')
masktransform = wmcsftransform.clone("masktransform")
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', masktransform, 'source_file')
else:
wf.connect(calc_median, 'median_file', masktransform, 'source_file')
wf.connect(register, 'out_reg_file', masktransform, 'reg_file')
wf.connect(mask, 'binary_file', masktransform, 'target_file')
# Compute Art outliers
art = Node(interface=ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=norm_threshold,
zintensity_threshold=3,
parameter_source='NiPy',
bound_by_brainmask=True,
save_plot=False,
mask_type='file'),
name="art")
if fieldmap_images:
wf.connect(dewarper, 'unwarped_file', art, 'realigned_files')
else:
wf.connect(tsnr, 'detrended_file', art, 'realigned_files')
wf.connect(realign, 'par_file',
art, 'realignment_parameters')
wf.connect(masktransform, 'transformed_file', art, 'mask_file')
# Compute motion regressors
motreg = Node(Function(input_names=['motion_params', 'order',
'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(realign, 'par_file', motreg, 'motion_params')
# Create a filter to remove motion and art confounds
createfilter1 = Node(Function(input_names=['motion_params', 'comp_norm',
'outliers'],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
# Filter the motion and art confounds
filter1 = MapNode(fsl.GLM(out_res_name='timeseries.nii.gz',
demean=True),
iterfield=['in_file', 'design'],
name='filtermotion')
if fieldmap_images:
wf.connect(dewarper, 'unwarped_file', filter1, 'in_file')
else:
wf.connect(tsnr, 'detrended_file', filter1, 'in_file')
wf.connect(createfilter1, 'out_files', filter1, 'design')
wf.connect(masktransform, 'transformed_file', filter1, 'mask')
# Create a filter to remove noise components based on white matter and CSF
createfilter2 = MapNode(Function(input_names=['realigned_file', 'mask_file',
'num_components'],
output_names=['out_files'],
function=extract_noise_components,
imports=imports),
iterfield=['realigned_file'],
name='makecompcorrfilter')
createfilter2.inputs.num_components = num_components
wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
wf.connect(masktransform, 'transformed_file', createfilter2, 'mask_file')
# Filter noise components
filter2 = MapNode(fsl.GLM(out_res_name='timeseries_cleaned.nii.gz',
demean=True),
iterfield=['in_file', 'design'],
name='filtercompcorr')
wf.connect(filter1, 'out_res', filter2, 'in_file')
wf.connect(createfilter2, 'out_files', filter2, 'design')
wf.connect(masktransform, 'transformed_file', filter2, 'mask')
# Smoothing using surface and volume smoothing
smooth = MapNode(freesurfer.Smooth(),
iterfield=['in_file'],
name='smooth')
smooth.inputs.proj_frac_avg = (0.1, 0.9, 0.1)
if surf_fwhm is None:
surf_fwhm = 5 * slice_thickness
smooth.inputs.surface_fwhm = surf_fwhm
if vol_fwhm is None:
vol_fwhm = 2 * slice_thickness
smooth.inputs.vol_fwhm = vol_fwhm
wf.connect(filter2, 'out_res', smooth, 'in_file')
wf.connect(register, 'out_reg_file', smooth, 'reg_file')
# Bandpass filter the data
bandpass = MapNode(fsl.TemporalFilter(),
iterfield=['in_file'],
name='bandpassfilter')
if highpass_freq < 0:
bandpass.inputs.highpass_sigma = -1
else:
bandpass.inputs.highpass_sigma = 1. / (2 * TR * highpass_freq)
if lowpass_freq < 0:
bandpass.inputs.lowpass_sigma = -1
else:
bandpass.inputs.lowpass_sigma = 1. / (2 * TR * lowpass_freq)
wf.connect(smooth, 'smoothed_file', bandpass, 'in_file')
# Convert aparc to subject functional space
aparctransform = wmcsftransform.clone("aparctransform")
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', aparctransform, 'source_file')
else:
wf.connect(calc_median, 'median_file', aparctransform, 'source_file')
wf.connect(register, 'out_reg_file', aparctransform, 'reg_file')
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg),
aparctransform, 'target_file')
# Sample the average time series in aparc ROIs
sampleaparc = MapNode(freesurfer.SegStats(avgwf_txt_file=True,
default_color_table=True),
iterfield=['in_file'],
name='aparc_ts')
sampleaparc.inputs.segment_id = ([8] + range(10, 14) + [17, 18, 26, 47] +
range(49, 55) + [58] + range(1001, 1036) +
range(2001, 2036))
wf.connect(aparctransform, 'transformed_file',
sampleaparc, 'segmentation_file')
wf.connect(bandpass, 'out_file', sampleaparc, 'in_file')
# Sample the time series onto the surface of the target surface. Performs
# sampling into left and right hemisphere
target = Node(IdentityInterface(fields=['target_subject']), name='target')
target.iterables = ('target_subject', filename_to_list(target_subject))
samplerlh = MapNode(freesurfer.SampleToSurface(),
iterfield=['source_file'],
name='sampler_lh')
samplerlh.inputs.sampling_method = "average"
samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
samplerlh.inputs.sampling_units = "frac"
samplerlh.inputs.interp_method = "trilinear"
#samplerlh.inputs.cortex_mask = True
samplerlh.inputs.out_type = 'niigz'
samplerlh.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
samplerrh = samplerlh.clone('sampler_rh')
samplerlh.inputs.hemi = 'lh'
wf.connect(bandpass, 'out_file', samplerlh, 'source_file')
wf.connect(register, 'out_reg_file', samplerlh, 'reg_file')
wf.connect(target, 'target_subject', samplerlh, 'target_subject')
samplerrh.set_input('hemi', 'rh')
wf.connect(bandpass, 'out_file', samplerrh, 'source_file')
wf.connect(register, 'out_reg_file', samplerrh, 'reg_file')
wf.connect(target, 'target_subject', samplerrh, 'target_subject')
# Combine left and right hemisphere to text file
combiner = MapNode(Function(input_names=['left', 'right'],
output_names=['out_file'],
function=combine_hemi,
imports=imports),
iterfield=['left', 'right'],
name="combiner")
wf.connect(samplerlh, 'out_file', combiner, 'left')
wf.connect(samplerrh, 'out_file', combiner, 'right')
# Compute registration between the subject's structural and MNI template
# This is currently set to perform a very quick registration. However, the
# registration can be made significantly more accurate for cortical
# structures by increasing the number of iterations
# All parameters are set using the example from:
# https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh
reg = Node(ants.Registration(), name='antsRegister')
reg.inputs.output_transform_prefix = "output_"
reg.inputs.transforms = ['Translation', 'Rigid', 'Affine', 'SyN']
reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.1,), (0.2, 3.0, 0.0)]
# reg.inputs.number_of_iterations = ([[10000, 111110, 11110]]*3 +
# [[100, 50, 30]])
reg.inputs.number_of_iterations = [[100, 100, 100]] * 3 + [[100, 20, 10]]
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = False
reg.inputs.metric = ['Mattes'] * 3 + [['Mattes', 'CC']]
reg.inputs.metric_weight = [1] * 3 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 3 + [[32, 4]]
reg.inputs.sampling_strategy = ['Regular'] * 3 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 3 + [[None, None]]
reg.inputs.convergence_threshold = [1.e-8] * 3 + [-0.01]
reg.inputs.convergence_window_size = [20] * 3 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 3 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ['vox'] * 4
reg.inputs.shrink_factors = [[6, 4, 2]] + [[3, 2, 1]]*2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 4
reg.inputs.use_histogram_matching = [False] * 3 + [True]
reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
reg.inputs.fixed_image = \
os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz')
reg.inputs.num_threads = 4
reg.plugin_args = {'qsub_args': '-l nodes=1:ppn=4'}
# Convert T1.mgz to nifti for using with ANTS
convert = Node(freesurfer.MRIConvert(out_type='niigz'), name='convert2nii')
wf.connect(fssource, 'T1', convert, 'in_file')
# Mask the T1.mgz file with the brain mask computed earlier
maskT1 = Node(fsl.BinaryMaths(operation='mul'), name='maskT1')
wf.connect(mask, 'binary_file', maskT1, 'operand_file')
wf.connect(convert, 'out_file', maskT1, 'in_file')
wf.connect(maskT1, 'out_file', reg, 'moving_image')
# Convert the BBRegister transformation to ANTS ITK format
convert2itk = MapNode(C3dAffineTool(),
iterfield=['transform_file', 'source_file'],
name='convert2itk')
convert2itk.inputs.fsl2ras = True
convert2itk.inputs.itk_transform = True
wf.connect(register, 'out_fsl_file', convert2itk, 'transform_file')
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', convert2itk, 'source_file')
else:
wf.connect(calc_median, 'median_file', convert2itk, 'source_file')
wf.connect(convert, 'out_file', convert2itk, 'reference_file')
# Concatenate the affine and ants transforms into a list
pickfirst = lambda x: x[0]
merge = MapNode(Merge(2), iterfield=['in2'], name='mergexfm')
wf.connect(convert2itk, 'itk_transform', merge, 'in2')
wf.connect(reg, ('composite_transform', pickfirst), merge, 'in1')
# Apply the combined transform to the time series file
sample2mni = MapNode(ants.ApplyTransforms(),
iterfield=['input_image', 'transforms'],
name='sample2mni')
sample2mni.inputs.input_image_type = 3
sample2mni.inputs.interpolation = 'BSpline'
sample2mni.inputs.invert_transform_flags = [False, False]
sample2mni.inputs.reference_image = \
os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz')
sample2mni.inputs.terminal_output = 'file'
wf.connect(bandpass, 'out_file', sample2mni, 'input_image')
wf.connect(merge, 'out', sample2mni, 'transforms')
# Sample the time series file for each subcortical roi
ts2txt = MapNode(Function(input_names=['timeseries_file', 'label_file',
'indices'],
output_names=['out_file'],
function=extract_subrois,
imports=imports),
iterfield=['timeseries_file'],
name='getsubcortts')
ts2txt.inputs.indices = [8] + range(10, 14) + [17, 18, 26, 47] +\
range(49, 55) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm.nii.gz'))
wf.connect(sample2mni, 'output_image', ts2txt, 'timeseries_file')
# Save the relevant data into an output directory
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
datasink.inputs.substitutions = [('_target_subject_', '')]
datasink.inputs.regexp_substitutions = (r'(/_.*(\d+/))', r'/run\2')
wf.connect(despiker, 'out_file', datasink, 'resting.qa.despike')
wf.connect(realign, 'par_file', datasink, 'resting.qa.motion')
wf.connect(tsnr, 'tsnr_file', datasink, 'resting.qa.tsnr')
wf.connect(tsnr, 'mean_file', datasink, 'resting.qa.tsnr.@mean')
wf.connect(tsnr, 'stddev_file', datasink, 'resting.qa.@tsnr_stddev')
if fieldmap_images:
wf.connect(fieldmap, 'exf_mask', datasink, 'resting.reference')
else:
wf.connect(calc_median, 'median_file', datasink, 'resting.reference')
wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
wf.connect(mask, 'binary_file', datasink, 'resting.mask')
wf.connect(masktransform, 'transformed_file',
datasink, 'resting.mask.@transformed_file')
wf.connect(register, 'out_reg_file', datasink, 'resting.registration.bbreg')
wf.connect(reg, ('composite_transform', pickfirst),
datasink, 'resting.registration.ants')
wf.connect(register, 'min_cost_file',
datasink, 'resting.qa.bbreg.@mincost')
wf.connect(smooth, 'smoothed_file', datasink, 'resting.timeseries.fullpass')
wf.connect(bandpass, 'out_file', datasink, 'resting.timeseries.bandpassed')
wf.connect(sample2mni, 'output_image', datasink, 'resting.timeseries.mni')
wf.connect(createfilter1, 'out_files',
datasink, 'resting.regress.@regressors')
wf.connect(createfilter2, 'out_files',
datasink, 'resting.regress.@compcorr')
wf.connect(sampleaparc, 'summary_file',
datasink, 'resting.parcellations.aparc')
wf.connect(sampleaparc, 'avgwf_txt_file',
datasink, 'resting.parcellations.aparc.@avgwf')
wf.connect(ts2txt, 'out_file',
datasink, 'resting.parcellations.grayo.@subcortical')
datasink2 = Node(interface=DataSink(), name="datasink2")
datasink2.inputs.base_directory = sink_directory
datasink2.inputs.container = subject_id
datasink2.inputs.substitutions = [('_target_subject_', '')]
datasink2.inputs.regexp_substitutions = (r'(/_.*(\d+/))', r'/run\2')
wf.connect(combiner, 'out_file',
datasink2, 'resting.parcellations.grayo.@surface')
return wf