def get_signal(substitutions_a, substitutions_b,
functional_file_template="~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_trial-{scan}.nii.gz",
mask="~/ni_data/templates/DSURQEc_200micron_bin.nii.gz",
):
mask = path.abspath(path.expanduser(mask))
out_t_names = []
out_cope_names = []
out_varcb_names = []
for substitution in substitutions_a+substitutions_b:
ts_name = path.abspath(path.expanduser("{subject}_{session}.mat".format(**substitution)))
out_t_name = path.abspath(path.expanduser("{subject}_{session}_tstat.nii.gz".format(**substitution)))
out_cope_name = path.abspath(path.expanduser("{subject}_{session}_cope.nii.gz".format(**substitution)))
out_varcb_name = path.abspath(path.expanduser("{subject}_{session}_varcb.nii.gz".format(**substitution)))
out_t_names.append(out_t_name)
out_cope_names.append(out_cope_name)
out_varcb_names.append(out_varcb_name)
functional_file = path.abspath(path.expanduser(functional_file_template.format(**substitution)))
if not path.isfile(ts_name):
masker = NiftiMasker(mask_img=mask)
ts = masker.fit_transform(functional_file).T
ts = np.mean(ts, axis=0)
header = "/NumWaves 1\n/NumPoints 1490\n/PPheights 1.308540e+01 4.579890e+00\n\n/Matrix"
np.savetxt(ts_name, ts, delimiter="\n", header=header, comments="")
glm = fsl.GLM(in_file=functional_file, design=ts_name, output_type='NIFTI_GZ')
glm.inputs.contrasts = path.abspath(path.expanduser("run0.con"))
glm.inputs.out_t_name = out_t_name
glm.inputs.out_cope = out_cope_name
glm.inputs.out_varcb_name = out_varcb_name
print(glm.cmdline)
glm_run=glm.run()
copemerge = fsl.Merge(dimension='t')
varcopemerge = fsl.Merge(dimension='t')
def dr_stage1(i, **kwargs): subj, mask = i ics = os.path.join(OUTPUT, 'melodic_IC.nii.gz') desnorm = False demean=True for i in kwargs.keys(): if i == 'desnorm': if kwargs[i]: desnorm = True else: desnorm = False if i == 'ics': ics = kwargs[i] if not os.path.exists(ics): print "cannot locate melodic component maps for dual regression...must exit.." print "looked in: ", ics sys.exit(0) iFile = os.path.join(os.path.dirname(INPUT), subj, feat_pfix + subj + feat_sfix, ff_data_name) oFile = os.path.join(OUTPUT, 'stage1', 'dr_stage1_idc_' + subj + '.txt') if os.path.exists(oFile): return mask = os.path.join(OUTPUT, 'stage1', 'mask.nii.gz') fsl_glm = fsl.GLM(in_file=iFile, design=ics, terminal_output='stream', out_file=oFile, des_norm=desnorm, demean=demean, mask=mask, output_type='NIFTI_GZ') cmd_out = os.path.join(OUTPUT, 'stage1', 'stage1_fslglm_idc_' + subj + '.out') write_cmd_out(fsl_glm.cmdline, cmd_out) fsl_glm.run()
def dr_stage1(self, **kwargs):
desnorm = True
for i in kwargs.keys():
if i == 'desnorm':
if kwargs[i]:
desnorm = True
else:
desnorm = False
if desnorm:
opts_str = '--demean --des_norm'
else:
opst_str = '--demean'
for subj in self.subjects:
iFile = os.path.join(os.path.dirname(self.indir), subj,
'idc_' + subj + self.featdir_sfix,
self.ff_data_name)
oFile = os.path.join(self.outdir, 'stage1',
'dr_stage1_idc_' + subj + '.txt')
mask = os.path.join(self.outdir, 'stage1', 'mask.nii.gz')
fsl_glm = fsl.GLM(in_file=iFile,
design=self.ics,
terminal_output='stream',
out_file=oFile,
mask=mask,
options=opts_str,
output_type='NIFTI_GZ')
fsl_glm.run()
def dr_stage2(i, **kwargs): subj, mask = i regress_moco = True desnorm = True demean = True for i in kwargs.keys(): if i == 'regress_moco': if kwargs[i]: regress_moco = True else: regress_moco = False if i == 'desnorm': if kwargs[i]: desnorm = True else: desnorm = False dr_s1_txt = os.path.join(OUTPUT, 'stage1', 'dr_stage1_idc_' + subj + '.txt') moco_txt = os.path.join(os.path.dirname(INPUT), subj, feat_pfix + subj + feat_sfix, 'mc', 'prefiltered_func_data_mcf.par') dr_s1 = read_txt_file(dr_s1_txt) if regress_moco: moco_pars = read_txt_file(moco_txt) for i in range(0, len(dr_s1)): for j in range(0,6): dr_s1[i].append(moco_pars[i][j]) dr_s1_moco_txt = os.path.join(OUTPUT, 'stage1', 'dr_stage1_moco_idc_' + subj + '.txt') write_txt_file(dr_s1, dr_s1_moco_txt) designFile = dr_s1_moco_txt else: designFile = dr_s1_txt iFile = os.path.join(os.path.dirname(INPUT), subj, feat_pfix + subj + feat_sfix, ff_data_name) oFile = os.path.join(OUTPUT, 'stage2', 'dr_stage2_idc_' + subj + '.nii.gz') ozFile = os.path.join(OUTPUT, 'stage2', 'dr_stage2_Z_idc_' + subj + '.nii.gz') if os.path.exists(oFile) and os.path.exists(ozFile): return mask = os.path.join(OUTPUT, 'stage1', 'mask.nii.gz') fsl_glm = fsl.GLM(in_file=iFile, design=designFile, terminal_output='stream', out_file=oFile, out_z_name=ozFile, mask=mask, des_norm=desnorm, demean=demean, output_type='NIFTI_GZ') cmd_out = os.path.join(OUTPUT, 'stage2', 'stage2_fslglm_idc_' + subj + '.out') write_cmd_out(fsl_glm.cmdline, cmd_out) fsl_glm.run() obname = os.path.join(OUTPUT, 'stage2', 'dr_stage2_idc_' + subj + '_ic') fslsplit = fsl.Split(dimension='t', in_file=oFile, out_base_name=obname, terminal_output='stream', output_type='NIFTI_GZ') fslsplit.run() obname = os.path.join(OUTPUT, 'stage2', 'dr_stage2_idc_Z' + subj + '_ic') fslsplit = fsl.Split(dimension='t', in_file=ozFile, out_base_name=obname, terminal_output='stream', output_type='NIFTI_GZ') fslsplit.run()
def init_seedconnectivity_wf(seeds, use_mov_pars, name="firstlevel"):
"""
create workflow to calculate seed connectivity maps
for resting state functional scans
:param seeds: dictionary of filenames by user-defined names
of binary masks that define the seed regions
:param use_mov_pars: if true, regress out movement parameters when
calculating seed connectivity
:param name: workflow name (Default value = "firstlevel")
"""
workflow = pe.Workflow(name=name)
# inputs are the bold file, the mask file and the confounds file
# that contains the movement parameters
inputnode = pe.Node(niu.IdentityInterface(
fields=["bold_file", "mask_file", "confounds_file"]),
name="inputnode")
# make two (ordered) lists from (unordered) dictionary of seeds
seednames = list(seeds.keys()) # contains the keys (seed names)
seed_paths = [seeds[k]
for k in seednames] # contains the values (filenames)
# calculate the mean time series of the region defined by each mask
meants = pe.MapNode(interface=fsl.ImageMeants(),
name="meants",
iterfield=["mask"])
meants.inputs.mask = seed_paths
# calculate the regression of the mean time series onto the functional image
# the result is the seed connectivity map
glm = pe.MapNode(interface=fsl.GLM(out_file="beta.nii.gz",
out_cope="cope.nii.gz",
out_varcb_name="varcope.nii.gz",
out_z_name="zstat.nii.gz",
demean=True),
name="glm",
iterfield=["design"])
# generate dof text file
gendoffile = pe.Node(interface=Dof(num_regressors=1), name="gendoffile")
# split regression outputs by name
splitimgs = pe.Node(
interface=niu.Split(splits=[1 for seedname in seednames]),
name="splitimgs")
splitvarcopes = pe.Node(
interface=niu.Split(splits=[1 for seedname in seednames]),
name="splitvarcopes")
splitzstats = pe.Node(
interface=niu.Split(splits=[1 for seedname in seednames]),
name="splitzstats")
# outputs are cope, varcope and zstat for each seed region and a dof_file
outputnode = pe.Node(niu.IdentityInterface(fields=sum(
[["%s_img" % seedname,
"%s_varcope" % seedname,
"%s_zstat" % seedname]
for seedname in seednames], []) + ["dof_file"]),
name="outputnode")
workflow.connect([
(inputnode, meants, [("bold_file", "in_file")]),
(inputnode, glm, [("bold_file", "in_file"), ("mask_file", "mask")]),
(meants, glm, [("out_file", "design")]),
(glm, splitimgs, [
("out_cope", "inlist"),
]),
(glm, splitvarcopes, [
("out_varcb", "inlist"),
]),
(glm, splitzstats, [
("out_z", "inlist"),
]),
(inputnode, gendoffile, [
("bold_file", "in_file"),
]),
(gendoffile, outputnode, [
("out_file", "dof_file"),
]),
])
# connect outputs named for the seeds
for i, seedname in enumerate(seednames):
workflow.connect(splitimgs, "out%i" % (i + 1), outputnode,
"%s_img" % seedname)
workflow.connect(splitvarcopes, "out%i" % (i + 1), outputnode,
"%s_varcope" % seedname)
workflow.connect(splitzstats, "out%i" % (i + 1), outputnode,
"%s_zstat" % seedname)
return workflow, seednames
def init_dualregression_wf(componentsfile, use_mov_pars, name="firstlevel"):
"""
create a workflow to calculate dual regression for ICA seeds
:param componentsfile: 4d image file with ica components
:param use_mov_pars: if true, regress out movement parameters when
calculating dual regression
:param name: workflow name (Default value = "firstlevel")
"""
workflow = pe.Workflow(name=name)
# inputs are the bold file, the mask file and the confounds file
# that contains the movement parameters
inputnode = pe.Node(niu.IdentityInterface(
fields=["bold_file", "mask_file", "confounds_file"]),
name="inputnode")
# extract number of ICA components from 4d image and name them
ncomponents = nib.load(componentsfile).shape[3]
fname, _ = _splitext(os.path.basename(componentsfile))
componentnames = ["%s_%d" % (fname, i) for i in range(ncomponents)]
# first step, calculate spatial regression of ICA components on to the
# bold file
glm0 = pe.Node(interface=fsl.GLM(out_file="beta", demean=True),
name="glm0")
glm0.inputs.design = componentsfile
# second step, calculate the temporal regression of the time series
# from the first step on to the bold file
glm1 = pe.Node(interface=fsl.GLM(out_file="beta.nii.gz",
out_cope="cope.nii.gz",
out_varcb_name="varcope.nii.gz",
out_z_name="zstat.nii.gz",
demean=True),
name="glm1")
# split regression outputs into individual images
splitimgsimage = pe.Node(interface=fsl.Split(dimension="t"),
name="splitimgsimage")
splitvarcopesimage = pe.Node(interface=fsl.Split(dimension="t"),
name="splitvarcopesimage")
splitzstatsimage = pe.Node(interface=fsl.Split(dimension="t"),
name="splitzstatsimage")
# generate dof text file
gendoffile = pe.Node(interface=Dof(num_regressors=1), name="gendoffile")
# outputs are cope, varcope and zstat for each ICA component and a dof_file
outputnode = pe.Node(niu.IdentityInterface(fields=sum([[
"%s_img" % componentname,
"%s_varcope" % componentname,
"%s_zstat" % componentname
] for componentname in componentnames], []) + ["dof_file"]),
name="outputnode")
# split regression outputs by name
splitimgs = pe.Node(
interface=niu.Split(splits=[1 for componentname in componentnames]),
name="splitimgs")
splitvarcopes = pe.Node(
interface=niu.Split(splits=[1 for componentname in componentnames]),
name="splitvarcopes")
splitzstats = pe.Node(
interface=niu.Split(splits=[1 for componentname in componentnames]),
name="splitzstats")
workflow.connect([
(inputnode, glm0, [("bold_file", "in_file"), ("mask_file", "mask")]),
(inputnode, glm1, [("bold_file", "in_file"), ("mask_file", "mask")]),
(glm0, glm1, [("out_file", "design")]),
(glm1, splitimgsimage, [
("out_cope", "in_file"),
]),
(glm1, splitvarcopesimage, [
("out_varcb", "in_file"),
]),
(glm1, splitzstatsimage, [
("out_z", "in_file"),
]),
(splitimgsimage, splitimgs, [
("out_files", "inlist"),
]),
(splitvarcopesimage, splitvarcopes, [
("out_files", "inlist"),
]),
(splitzstatsimage, splitzstats, [
("out_files", "inlist"),
]),
(inputnode, gendoffile, [
("bold_file", "in_file"),
]),
(gendoffile, outputnode, [
("out_file", "dof_file"),
]),
])
# connect outputs named for the ICA components
for i, componentname in enumerate(componentnames):
workflow.connect(splitimgs, "out%i" % (i + 1), outputnode,
"%s_img" % componentname)
workflow.connect(splitvarcopes, "out%i" % (i + 1), outputnode,
"%s_varcope" % componentname)
workflow.connect(splitzstats, "out%i" % (i + 1), outputnode,
"%s_zstat" % componentname)
return workflow, componentnames
def l1(preprocessing_dir,
bf_path = '~/ni_data/irfs/chr_beta1.txt',
debug=False,
exclude={},
habituation='confound',
highpass_sigma=225,
lowpass_sigma=False,
include={},
keep_work=False,
out_base="",
mask="",
match={},
tr=1,
workflow_name="generic",
modality="cbv",
n_jobs_percentage=1,
invert=False,
):
"""Calculate subject level GLM statistic scores.
Parameters
----------
bf_path : str, optional
Basis set path. It should point to a text file in the so-called FEAT/FSL "#2" format (1 entry per volume).
exclude : dict
A dictionary with any combination of "sessions", "subjects", "tasks" as keys and corresponding identifiers as values.
If this is specified matching entries will be excluded in the analysis.
debug : bool, optional
Whether to enable nipype debug mode.
This increases logging.
habituation : {"", "confound", "separate_contrast", "in_main_contrast"}, optional
How the habituation regressor should be handled.
Anything which evaluates as False (though we recommend "") means no habituation regressor will be introduced.
highpass_sigma : int, optional
Highpass threshold (in seconds).
include : dict
A dictionary with any combination of "sessions", "subjects", "tasks" as keys and corresponding identifiers as values.
If this is specified only matching entries will be included in the analysis.
invert : bool
If true the values will be inverted with respect to zero.
This is commonly used for iron nano-particle Cerebral Blood Volume (CBV) measurements.
keep_work : bool, optional
Whether to keep the work directory (containing all the intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
out_base : str, optional
Path to the directory inside which both the working directory and the output directory will be created.
mask : str, optional
Path to the brain mask which shall be used to define the brain volume in the analysis.
This has to point to an existing NIfTI file containing zero and one values only.
n_jobs_percentage : float, optional
Percentage of the cores present on the machine which to maximally use for deploying jobs in parallel.
tr : int, optional
Repetition time, in seconds.
workflow_name : str, optional
Name of the workflow; this will also be the name of the final output directory produced under `out_dir`.
"""
from samri.pipelines.utils import bids_data_selection
preprocessing_dir = path.abspath(path.expanduser(preprocessing_dir))
out_base = path.abspath(path.expanduser(out_base))
data_selection = bids_data_selection(preprocessing_dir, structural_match=False, functional_match=match, subjects=False, sessions=False)
ind = data_selection.index.tolist()
out_dir = path.join(out_base,workflow_name)
workdir_name = workflow_name+'_work'
workdir = path.join(out_base,workdir_name)
if not os.path.exists(workdir):
os.makedirs(workdir)
data_selection.to_csv(path.join(workdir,'data_selection.csv'))
get_scan = pe.Node(name='get_scan', interface=util.Function(function=get_bids_scan,input_names=inspect.getargspec(get_bids_scan)[0], output_names=['scan_path','scan_type','task', 'nii_path', 'nii_name', 'events_name', 'subject_session', 'metadata_filename', 'dict_slice']))
get_scan.inputs.ignore_exception = True
get_scan.inputs.data_selection = data_selection
get_scan.inputs.bids_base = preprocessing_dir
get_scan.iterables = ("ind_type", ind)
eventfile = pe.Node(name='eventfile', interface=util.Function(function=corresponding_eventfile,input_names=inspect.getargspec(corresponding_eventfile)[0], output_names=['eventfile']))
if invert:
invert = pe.Node(interface=fsl.ImageMaths(), name="invert")
invert.inputs.op_string = '-mul -1'
specify_model = pe.Node(interface=SpecifyModel(), name="specify_model")
specify_model.inputs.input_units = 'secs'
specify_model.inputs.time_repetition = tr
specify_model.inputs.high_pass_filter_cutoff = highpass_sigma
level1design = pe.Node(interface=Level1Design(), name="level1design")
level1design.inputs.interscan_interval = tr
if bf_path:
bf_path = path.abspath(path.expanduser(bf_path))
level1design.inputs.bases = {"custom": {"bfcustompath":bf_path}}
else:
# We are not adding derivatives here, as these conflict with the habituation option.
# !!! This is not difficult to solve, and would only require the addition of an elif condition to the habituator definition, which would add multiple column copies for each of the derivs.
level1design.inputs.bases = {'gamma': {'derivs':True, 'gammasigma':30, 'gammadelay':10}}
level1design.inputs.model_serial_correlations = True
modelgen = pe.Node(interface=fsl.FEATModel(), name='modelgen')
#modelgen.inputs.ignore_exception = True
glm = pe.Node(interface=fsl.GLM(), name='glm', iterfield='design')
# glm.inputs.out_cope = "cope.nii.gz"
# glm.inputs.out_varcb_name = "varcb.nii.gz"
# #not setting a betas output file might lead to beta export in lieu of COPEs
# glm.inputs.out_file = "betas.nii.gz"
# glm.inputs.out_t_name = "t_stat.nii.gz"
# glm.inputs.out_p_name = "p_stat.nii.gz"
if mask == 'mouse':
mask = '/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii'
else:
glm.inputs.mask = path.abspath(path.expanduser(mask))
glm.interface.mem_gb = 6
#glm.inputs.ignore_exception = True
out_file_name_base = 'sub-{{subject}}_ses-{{session}}_task-{{task}}_acq-{{acquisition}}_run-{{run}}_{{modality}}_{}.{}'
betas_filename = pe.Node(name='betas_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
betas_filename.inputs.source_format = out_file_name_base.format('betas','nii.gz')
cope_filename = pe.Node(name='cope_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
cope_filename.inputs.source_format = out_file_name_base.format('cope','nii.gz')
varcb_filename = pe.Node(name='varcb_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
varcb_filename.inputs.source_format = out_file_name_base.format('varcb','nii.gz')
tstat_filename = pe.Node(name='tstat_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
tstat_filename.inputs.source_format = out_file_name_base.format('tstat','nii.gz')
zstat_filename = pe.Node(name='zstat_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
zstat_filename.inputs.source_format = out_file_name_base.format('zstat','nii.gz')
pstat_filename = pe.Node(name='pstat_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
pstat_filename.inputs.source_format = out_file_name_base.format('pstat','nii.gz')
pfstat_filename = pe.Node(name='pfstat_filename', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
pfstat_filename.inputs.source_format = out_file_name_base.format('pfstat','nii.gz')
design_filename = pe.Node(name='design', interface=util.Function(function=bids_dict_to_source,input_names=inspect.getargspec(bids_dict_to_source)[0], output_names=['filename']))
design_filename.inputs.source_format = out_file_name_base.format('design','mat')
design_rename = pe.Node(interface=util.Rename(), name='design_rename')
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = path.join(out_base,workflow_name)
datasink.inputs.parameterization = False
workflow_connections = [
(get_scan, eventfile, [('nii_path', 'timecourse_file')]),
(specify_model, level1design, [('session_info', 'session_info')]),
(level1design, modelgen, [('ev_files', 'ev_files')]),
(level1design, modelgen, [('fsf_files', 'fsf_file')]),
(modelgen, glm, [('design_file', 'design')]),
(modelgen, glm, [('con_file', 'contrasts')]),
(get_scan, datasink, [(('dict_slice',bids_dict_to_dir), 'container')]),
(get_scan, betas_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, cope_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, varcb_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, tstat_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, zstat_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, pstat_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, pfstat_filename, [('dict_slice', 'bids_dictionary')]),
(get_scan, design_filename, [('dict_slice', 'bids_dictionary')]),
(betas_filename, glm, [('filename', 'out_file')]),
(cope_filename, glm, [('filename', 'out_cope')]),
(varcb_filename, glm, [('filename', 'out_varcb_name')]),
(tstat_filename, glm, [('filename', 'out_t_name')]),
(zstat_filename, glm, [('filename', 'out_z_name')]),
(pstat_filename, glm, [('filename', 'out_p_name')]),
(pfstat_filename, glm, [('filename', 'out_pf_name')]),
(modelgen, design_rename, [('design_file', 'in_file')]),
(design_filename, design_rename, [('filename', 'format_string')]),
(glm, datasink, [('out_pf', '@pfstat')]),
(glm, datasink, [('out_p', '@pstat')]),
(glm, datasink, [('out_z', '@zstat')]),
(glm, datasink, [('out_t', '@tstat')]),
(glm, datasink, [('out_cope', '@cope')]),
(glm, datasink, [('out_varcb', '@varcb')]),
(glm, datasink, [('out_file', '@betas')]),
(design_rename, datasink, [('out_file', '@design')]),
]
if habituation:
level1design.inputs.orthogonalization = {1: {0:0,1:0,2:0}, 2: {0:1,1:1,2:0}}
specify_model.inputs.bids_condition_column = 'samri_l1_regressors'
specify_model.inputs.bids_amplitude_column = 'samri_l1_amplitude'
add_habituation = pe.Node(name='add_habituation', interface=util.Function(function=eventfile_add_habituation,input_names=inspect.getargspec(eventfile_add_habituation)[0], output_names=['out_file']))
# Regressor names need to be prefixed with "e" plus a numerator so that Level1Design will be certain to conserve the order.
add_habituation.inputs.original_stimulation_value='1stim'
add_habituation.inputs.habituation_value='2habituation'
workflow_connections.extend([
(eventfile, add_habituation, [('eventfile', 'in_file')]),
(add_habituation, specify_model, [('out_file', 'bids_event_file')]),
])
if not habituation:
specify_model.inputs.bids_condition_column = ''
level1design.inputs.contrasts = [('allStim','T', ['ev0'],[1])]
workflow_connections.extend([
(eventfile, specify_model, [('eventfile', 'bids_event_file')]),
])
#condition names as defined in eventfile_add_habituation:
elif habituation=="separate_contrast":
level1design.inputs.contrasts = [('stim','T', ['1stim','2habituation'],[1,0]),('hab','T', ['1stim','2habituation'],[0,1])]
elif habituation=="in_main_contrast":
level1design.inputs.contrasts = [('all','T', ['1stim','2habituation'],[1,1])]
elif habituation=="confound":
level1design.inputs.contrasts = [('stim','T', ["1stim", "2habituation"],[1,0])]
else:
print(habituation)
raise ValueError('The value you have provided for the `habituation` parameter, namely "{}", is invalid. Please choose one of: {{None, False,"","confound","in_main_contrast","separate_contrast"}}'.format(habituation))
if highpass_sigma or lowpass_sigma:
bandpass = pe.Node(interface=fsl.maths.TemporalFilter(), name="bandpass")
bandpass.inputs.highpass_sigma = highpass_sigma
bandpass.interface.mem_gb = 16
if lowpass_sigma:
bandpass.inputs.lowpass_sigma = lowpass_sigma
else:
bandpass.inputs.lowpass_sigma = tr
if invert:
workflow_connections.extend([
(get_scan, invert, [('nii_path', 'in_file')]),
(invert, bandpass, [('out_file', 'in_file')]),
(bandpass, specify_model, [('out_file', 'functional_runs')]),
(bandpass, glm, [('out_file', 'in_file')]),
(bandpass, datasink, [('out_file', '@ts_file')]),
(get_scan, bandpass, [('nii_name', 'out_file')]),
])
else:
workflow_connections.extend([
(get_scan, bandpass, [('nii_path', 'in_file')]),
(bandpass, specify_model, [('out_file', 'functional_runs')]),
(bandpass, glm, [('out_file', 'in_file')]),
(bandpass, datasink, [('out_file', '@ts_file')]),
(get_scan, bandpass, [('nii_name', 'out_file')]),
])
else:
if invert:
workflow_connections.extend([
(get_scan, invert, [('nii_path', 'in_file')]),
(invert, specify_model, [('out_file', 'functional_runs')]),
(invert, glm, [('out_file', 'in_file')]),
(invert, datasink, [('out_file', '@ts_file')]),
(get_scan, invert, [('nii_name', 'out_file')]),
])
else:
workflow_connections.extend([
(get_scan, specify_model, [('nii_path', 'functional_runs')]),
(get_scan, glm, [('nii_path', 'in_file')]),
(get_scan, datasink, [('nii_path', '@ts_file')]),
])
workflow_config = {'execution': {'crashdump_dir': path.join(out_base,'crashdump'),}}
if debug:
workflow_config['logging'] = {
'workflow_level':'DEBUG',
'utils_level':'DEBUG',
'interface_level':'DEBUG',
'filemanip_level':'DEBUG',
'log_to_file':'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = out_base
workflow.config = workflow_config
workflow.write_graph(dotfilename=path.join(workflow.base_dir,workdir_name,"graph.dot"), graph2use="hierarchical", format="png")
n_jobs = max(int(round(mp.cpu_count()*n_jobs_percentage)),2)
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_jobs})
if not keep_work:
shutil.rmtree(path.join(out_base,workdir_name))
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_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 get_spatial_map_timeseries(wf_name='spatial_map_timeseries'):
"""
Workflow to regress each provided spatial
map to the subjects functional 4D file in order
to return a timeseries for each of the maps
Parameters
----------
wf_name : string
name of the workflow
Returns
-------
wflow : workflow object
workflow object
Notes
-----
`Source <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/timeseries/timeseries_analysis.py>`_
Workflow Inputs::
inputspec.subject_rest : string (nifti file)
path to input functional data
inputspec.subject_mask : string (nifti file)
path to subject functional mask
inputspec.spatial_map : string (nifti file)
path to Spatial Maps
inputspec.demean : Boolean
control whether to demean model and data
Workflow Outputs::
outputspec.subject_timeseries: string (txt file)
list of time series stored in a space separated
txt file
the columns are spatial maps, rows are timepoints
Example
-------
>>> import CPAC.timeseries.timeseries_analysis as t
>>> wf = t.get_spatial_map_timeseries()
>>> wf.inputs.inputspec.subject_rest = '/home/data/rest.nii.gz'
>>> wf.inputs.inputspec.subject_mask = '/home/data/rest_mask.nii.gz'
>>> wf.inputs.inputspec.ICA_map = '/home/data/spatialmaps/spatial_map.nii.gz'
>>> wf.inputs.inputspec.demean = True
>>> wf.base_dir = './'
>>> wf.run()
"""
wflow = pe.Workflow(name=wf_name)
inputNode = pe.Node(util.IdentityInterface
(fields=['subject_rest',
'subject_mask',
'spatial_map',
'demean']),
name='inputspec')
outputNode = pe.Node(util.IdentityInterface
(fields=['subject_timeseries']),
name='outputspec')
spatialReg = pe.Node(interface=fsl.GLM(),
name='spatial_regression')
spatialReg.inputs.out_file = 'spatial_map_timeseries.txt'
wflow.connect(inputNode, 'subject_rest',
spatialReg, 'in_file')
wflow.connect(inputNode, 'subject_mask',
spatialReg, 'mask')
wflow.connect(inputNode, 'spatial_map',
spatialReg, 'design')
wflow.connect(inputNode, 'demean',
spatialReg, 'demean')
wflow.connect(spatialReg, 'out_file',
outputNode, 'subject_timeseries')
return wflow
def l1(
preprocessing_dir,
highpass_sigma=225,
include={},
exclude={},
keep_work=False,
l1_dir="",
nprocs=10,
mask="/home/chymera/ni_data/templates/ds_QBI_chr_bin.nii.gz",
per_stimulus_contrast=False,
habituation="",
tr=1,
workflow_name="generic",
):
"""Calculate subject level GLM statistics.
Parameters
----------
include : dict
A dictionary with any combination of "sessions", "subjects", "trials" as keys and corresponding identifiers as values.
If this is specified ony matching entries will be included in the analysis.
exclude : dict
A dictionary with any combination of "sessions", "subjects", "trials" as keys and corresponding identifiers as values.
If this is specified ony non-matching entries will be included in the analysis.
habituation : string
One value of "confound", "in_main_contrast", "separate_contrast", "" indicating how the habituation regressor should be handled.
"" or any other value which evaluates to False will mean no habituation regressor is used int he model
"""
preprocessing_dir = path.expanduser(preprocessing_dir)
if not l1_dir:
l1_dir = path.abspath(path.join(preprocessing_dir, "..", "..", "l1"))
datafind = nio.DataFinder()
datafind.inputs.root_paths = preprocessing_dir
datafind.inputs.match_regex = '.+/sub-(?P<sub>.+)/ses-(?P<ses>.+)/func/.*?_trial-(?P<scan>.+)\.nii.gz'
datafind_res = datafind.run()
iterfields = zip(*[
datafind_res.outputs.sub, datafind_res.outputs.ses,
datafind_res.outputs.scan
])
if include:
iterfields = iterfield_selector(iterfields, include, "include")
if exclude:
iterfields = iterfield_selector(iterfields, exclude, "exclude")
infosource = pe.Node(
interface=util.IdentityInterface(fields=['subject_session_scan']),
name="infosource")
infosource.iterables = [('subject_session_scan', iterfields)]
datafile_source = pe.Node(
name='datafile_source',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['out_file']))
datafile_source.inputs.base_directory = preprocessing_dir
datafile_source.inputs.source_format = "sub-{0}/ses-{1}/func/sub-{0}_ses-{1}_trial-{2}.nii.gz"
eventfile_source = pe.Node(
name='eventfile_source',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['out_file']))
eventfile_source.inputs.base_directory = preprocessing_dir
eventfile_source.inputs.source_format = "sub-{0}/ses-{1}/func/sub-{0}_ses-{1}_trial-{2}_events.tsv"
specify_model = pe.Node(interface=SpecifyModel(), name="specify_model")
specify_model.inputs.input_units = 'secs'
specify_model.inputs.time_repetition = tr
specify_model.inputs.high_pass_filter_cutoff = highpass_sigma
specify_model.inputs.one_condition_file = not per_stimulus_contrast
specify_model.inputs.habituation_regressor = bool(habituation)
level1design = pe.Node(interface=Level1Design(), name="level1design")
level1design.inputs.interscan_interval = tr
level1design.inputs.bases = {
"custom": {
"bfcustompath": "/mnt/data/ni_data/irfs/chr_beta1.txt"
}
}
# level1design.inputs.bases = {'gamma': {'derivs':False, 'gammasigma':10, 'gammadelay':5}}
level1design.inputs.orthogonalization = {
1: {
0: 0,
1: 0,
2: 0
},
2: {
0: 1,
1: 1,
2: 0
}
}
level1design.inputs.model_serial_correlations = True
if per_stimulus_contrast:
level1design.inputs.contrasts = [
('allStim', 'T', ["e0", "e1", "e2", "e3", "e4",
"e5"], [1, 1, 1, 1, 1, 1])
] #condition names as defined in specify_model
elif habituation == "separate_contrast":
level1design.inputs.contrasts = [
('allStim', 'T', ["e0"], [1]), ('allStim', 'T', ["e1"], [1])
] #condition names as defined in specify_model
elif habituation == "in_main_contrast":
level1design.inputs.contrasts = [
('allStim', 'T', ["e0", "e1"], [1, 1])
] #condition names as defined in specify_model
elif habituation == "confound":
level1design.inputs.contrasts = [
('allStim', 'T', ["e0"], [1])
] #condition names as defined in specify_model
else:
level1design.inputs.contrasts = [
('allStim', 'T', ["e0"], [1])
] #condition names as defined in specify_model
modelgen = pe.Node(interface=fsl.FEATModel(), name='modelgen')
glm = pe.Node(interface=fsl.GLM(), name='glm', iterfield='design')
glm.inputs.out_cope = "cope.nii.gz"
glm.inputs.out_varcb_name = "varcb.nii.gz"
#not setting a betas output file might lead to beta export in lieu of COPEs
glm.inputs.out_file = "betas.nii.gz"
glm.inputs.out_t_name = "t_stat.nii.gz"
glm.inputs.out_p_name = "p_stat.nii.gz"
if mask:
glm.inputs.mask = mask
cope_filename = pe.Node(
name='cope_filename',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['filename']))
cope_filename.inputs.source_format = "sub-{0}_ses-{1}_trial-{2}_cope.nii.gz"
varcb_filename = pe.Node(
name='varcb_filename',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['filename']))
varcb_filename.inputs.source_format = "sub-{0}_ses-{1}_trial-{2}_varcb.nii.gz"
tstat_filename = pe.Node(
name='tstat_filename',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['filename']))
tstat_filename.inputs.source_format = "sub-{0}_ses-{1}_trial-{2}_tstat.nii.gz"
zstat_filename = pe.Node(
name='zstat_filename',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['filename']))
zstat_filename.inputs.source_format = "sub-{0}_ses-{1}_trial-{2}_zstat.nii.gz"
pstat_filename = pe.Node(
name='pstat_filename',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['filename']))
pstat_filename.inputs.source_format = "sub-{0}_ses-{1}_trial-{2}_pstat.nii.gz"
pfstat_filename = pe.Node(
name='pfstat_filename',
interface=util.Function(
function=sss_to_source,
input_names=inspect.getargspec(sss_to_source)[0],
output_names=['filename']))
pfstat_filename.inputs.source_format = "sub-{0}_ses-{1}_trial-{2}_pfstat.nii.gz"
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = path.join(l1_dir, workflow_name)
datasink.inputs.parameterization = False
workflow_connections = [
(infosource, datafile_source, [('subject_session_scan',
'subject_session_scan')]),
(infosource, eventfile_source, [('subject_session_scan',
'subject_session_scan')]),
(eventfile_source, specify_model, [('out_file', 'event_files')]),
(datafile_source, specify_model, [('out_file', 'functional_runs')]),
(specify_model, level1design, [('session_info', 'session_info')]),
(level1design, modelgen, [('ev_files', 'ev_files')]),
(level1design, modelgen, [('fsf_files', 'fsf_file')]),
(datafile_source, glm, [('out_file', 'in_file')]),
(modelgen, glm, [('design_file', 'design')]),
(modelgen, glm, [('con_file', 'contrasts')]),
(infosource, datasink, [(('subject_session_scan', ss_to_path),
'container')]),
(infosource, cope_filename, [('subject_session_scan',
'subject_session_scan')]),
(infosource, varcb_filename, [('subject_session_scan',
'subject_session_scan')]),
(infosource, tstat_filename, [('subject_session_scan',
'subject_session_scan')]),
(infosource, zstat_filename, [('subject_session_scan',
'subject_session_scan')]),
(infosource, pstat_filename, [('subject_session_scan',
'subject_session_scan')]),
(infosource, pfstat_filename, [('subject_session_scan',
'subject_session_scan')]),
(cope_filename, glm, [('filename', 'out_cope')]),
(varcb_filename, glm, [('filename', 'out_varcb_name')]),
(tstat_filename, glm, [('filename', 'out_t_name')]),
(zstat_filename, glm, [('filename', 'out_z_name')]),
(pstat_filename, glm, [('filename', 'out_p_name')]),
(pfstat_filename, glm, [('filename', 'out_pf_name')]),
(glm, datasink, [('out_pf', '@pfstat')]),
(glm, datasink, [('out_p', '@pstat')]),
(glm, datasink, [('out_z', '@zstat')]),
(glm, datasink, [('out_t', '@tstat')]),
(glm, datasink, [('out_cope', '@cope')]),
(glm, datasink, [('out_varcb', '@varcb')]),
]
workdir_name = workflow_name + "_work"
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = l1_dir
workflow.config = {
"execution": {
"crashdump_dir": path.join(l1_dir, "crashdump")
}
}
workflow.write_graph(dotfilename=path.join(workflow.base_dir, workdir_name,
"graph.dot"),
graph2use="hierarchical",
format="png")
workflow.run(plugin="MultiProc", plugin_args={'n_procs': nprocs})
if not keep_work:
shutil.rmtree(path.join(l1_dir, workdir_name))
def denoise(subject, sessions, data_dir, wd, sink, TR):
#initiate min func preproc workflow
wf = pe.Workflow(name='DENOISE_aCompCor')
wf.base_dir = wd
wf.config['execution']['crashdump_dir'] = wf.base_dir + "/crash_files"
## set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# I/O nodes
inputnode = pe.Node(util.IdentityInterface(fields=['subjid']),
name='inputnode')
inputnode.inputs.subjid = subject
ds = pe.Node(nio.DataSink(base_directory=sink, parameterization=False),
name='sink')
#infosource to interate over sessions: COND, EXT1, EXT2
sessions_infosource = pe.Node(util.IdentityInterface(fields=['session']),
name='session')
sessions_infosource.iterables = [('session', sessions)]
#select files
templates = {
'prefiltered': 'MPP/{subject}/{session}/prefiltered_func_data.nii.gz',
'prefiltered_detrend':
'MPP/{subject}/{session}/prefiltered_func_data_detrend.nii.gz',
'prefiltered_detrend_Tmean':
'MPP/{subject}/{session}/QC/prefiltered_func_data_detrend_Tmean.nii.gz',
'prefiltered_mask':
'MPP/{subject}/{session}/prefiltered_func_data_mask.nii.gz',
'WM_msk': 'MASKS/{subject}/aparc_asec.WMmask_ero2EPI.nii.gz',
'CSF_msk': 'MASKS/{subject}/aparc_asec.CSFmask_ero0EPI.nii.gz',
'motion_par': 'MPP/{subject}/{session}/MOCO/func_data_stc_moco.par'
}
selectfiles = pe.Node(nio.SelectFiles(templates, base_directory=data_dir),
name='selectfiles')
wf.connect(inputnode, 'subjid', selectfiles, 'subject')
wf.connect(sessions_infosource, 'session', selectfiles, 'session')
wf.connect(sessions_infosource, 'session', ds, 'container')
##########################################################################
######################## START ######################################
##########################################################################
###########################################################################
######################## No. 1 ######################################
#the script outputs only std DVARS
DVARS = pe.Node(util.Function(
input_names=['in_file', 'in_mask', 'out_std_name'],
output_names=['out_std', 'out_nstd', 'out_vx_std'],
function=compute_dvars),
name='DVARS')
DVARS.inputs.out_std_name = 'stdDVARS_pre.txt'
wf.connect(selectfiles, 'prefiltered_detrend', DVARS, 'in_file')
wf.connect(selectfiles, 'prefiltered_mask', DVARS, 'in_mask')
wf.connect(DVARS, 'out_std', ds, 'QC.@DVARS')
###########################################################################
######################## No. 2 ######################################
# DEMAN and DETREND the data, which are used to get nuisance regressors
def run_demean_detrend(in_file):
import nibabel as nb
import numpy as np
import os
from scipy.signal import detrend
img = nb.load(in_file)
imgseries = img.get_data().astype(np.float32)
imgseries_new = detrend(imgseries, type='linear')
new = nb.nifti1.Nifti1Image(imgseries_new,
header=img.get_header(),
affine=img.get_affine())
out_file = os.path.join(os.getcwd(),
'prefiltered_func_data_demean_detrend.nii.gz')
new.to_filename(out_file)
del imgseries, imgseries_new, new
return out_file
demean_detrend = pe.Node(util.Function(input_names=['in_file'],
output_names=['out_file'],
function=run_demean_detrend),
name='demean_detrend')
wf.connect(selectfiles, 'prefiltered', demean_detrend, 'in_file')
wf.connect(demean_detrend, 'out_file', ds, 'TEMP.@demean_detrend')
###########################################################################
######################## No. 3A ######################################
#PREPARE WM_CSF MASK
WM_CSF_msk = pe.Node(fsl.BinaryMaths(operation='add'), name='wm_csf_msk')
wf.connect(selectfiles, 'WM_msk', WM_CSF_msk, 'in_file')
wf.connect(selectfiles, 'CSF_msk', WM_CSF_msk, 'operand_file')
#take the coverage of the masks from functional data (essentially multiply by the mask from functional data)
func_msk = pe.Node(fsl.BinaryMaths(operation='mul',
out_file='WM_CSFmsk.nii.gz'),
name='func_masking')
wf.connect(WM_CSF_msk, 'out_file', func_msk, 'in_file')
wf.connect(selectfiles, 'prefiltered_mask', func_msk, 'operand_file')
wf.connect(func_msk, 'out_file', ds, 'TEMP.@masks')
###########################################################################
######################## No. 3B ######################################
#PREPARE MOTION REGRESSSORS FRISTON 24 AND TRENDS
friston24 = pe.Node(util.Function(input_names=['in_file'],
output_names=['out_file'],
function=calc_friston_twenty_four),
name='friston24')
wf.connect(selectfiles, 'motion_par', friston24, 'in_file')
wf.connect(friston24, 'out_file', ds, 'TEMP.@friston24')
# linear and quadratic trends
trends = pe.Node(util.Function(input_names=['nr_vols'],
output_names=['out_file'],
function=calc_trends),
name='trends')
def get_nr_vols(in_file):
import nibabel as nb
img = nb.load(in_file)
return img.shape[3]
wf.connect(demean_detrend, ('out_file', get_nr_vols), trends, 'nr_vols')
wf.connect(trends, 'out_file', ds, 'TEMP.@trends')
###########################################################################
######################## No. 3C ######################################
#aCOMP_COR
aCompCor = pe.Node(util.Function(input_names=['in_file', 'in_mask'],
output_names=['out_file'],
function=calc_compcor),
name='aCompCor')
wf.connect(demean_detrend, 'out_file', aCompCor, 'in_file')
wf.connect(func_msk, 'out_file', aCompCor, 'in_mask')
wf.connect(aCompCor, 'out_file', ds, 'TEMP.@aCompCor')
###########################################################################
######################## No. 4 ######################################
#PREP the nuisance model
#A is with Global Signal, and B is CompCor
def mergetxt(filelist, fname):
import pandas as pd
import os
for n, f in enumerate(filelist):
if n == 0:
data = pd.read_csv(f, header=None, sep='\t')
else:
data_new = pd.read_csv(f, header=None, sep='\t')
data = pd.concat([data, data_new], axis=1)
out_file = os.path.join(os.getcwd(), 'nuisance' + fname + '.mat')
data.to_csv(out_file, index=False, header=None, sep='\t')
return out_file
merge_nuisance = pe.Node(util.Merge(3),
infields=['in1', 'in2', 'in3'],
name='merge_nuisance')
wf.connect(aCompCor, 'out_file', merge_nuisance, 'in1')
wf.connect(friston24, 'out_file', merge_nuisance, 'in2')
wf.connect(trends, 'out_file', merge_nuisance, 'in3')
nuisance_txt = pe.Node(util.Function(input_names=['filelist', 'fname'],
output_names=['out_file'],
function=mergetxt),
name='nuisance_txt')
nuisance_txt.inputs.fname = '_model'
wf.connect(merge_nuisance, 'out', nuisance_txt, 'filelist')
wf.connect(nuisance_txt, 'out_file', ds, 'TEMP.@nuisance_txt')
###########################################################################
######################## No. 5 ######################################
#run nuisance regression on prefiltered raw data
regression = pe.Node(fsl.GLM(demean=True), name='regression')
regression.inputs.out_res_name = 'residuals.nii.gz'
regression.inputs.out_f_name = 'residuals_fstats.nii.gz'
regression.inputs.out_pf_name = 'residuals_pstats.nii.gz'
regression.inputs.out_z_name = 'residuals_zstats.nii.gz'
wf.connect(nuisance_txt, 'out_file', regression, 'design')
wf.connect(selectfiles, 'prefiltered', regression, 'in_file')
wf.connect(selectfiles, 'prefiltered_mask', regression, 'mask')
wf.connect(regression, 'out_f', ds, 'REGRESSION.@out_f_name')
wf.connect(regression, 'out_pf', ds, 'REGRESSION.@out_pf_name')
wf.connect(regression, 'out_z', ds, 'REGRESSION.@out_z_name')
######################## FIX HEADER TR AFTER FSL_GLM #################
fixhd = pe.Node(fsl.utils.CopyGeom(), name='fixhd')
wf.connect(regression, 'out_res', fixhd, 'dest_file')
wf.connect(selectfiles, 'prefiltered', fixhd, 'in_file')
wf.connect(fixhd, 'out_file', ds, 'REGRESSION.@res_out')
###########################################################################
######################## No. 6 ######################################
#apply HP FILTER of 0.01Hz
#100/1.96/2 = 25.51
hp_filter = pe.Node(fsl.maths.TemporalFilter(
highpass_sigma=25.51, out_file='residuals_hp01.nii.gz'),
name='highpass')
wf.connect(fixhd, 'out_file', hp_filter, 'in_file')
wf.connect(hp_filter, 'out_file', ds, 'TEMP.@hp')
#add the mean back for smoothing
addmean = pe.Node(fsl.BinaryMaths(
operation='add', out_file='filtered_func_data_hp01.nii.gz'),
name='addmean')
wf.connect(hp_filter, 'out_file', addmean, 'in_file')
wf.connect(selectfiles, 'prefiltered_detrend_Tmean', addmean,
'operand_file')
wf.connect(addmean, 'out_file', ds, '@out')
###########################################################################
######################## No. 7 ######################################
## COMPUTE POST DVARS
DVARSpost = pe.Node(util.Function(
input_names=['in_file', 'in_mask', 'out_std_name'],
output_names=['out_std', 'out_nstd', 'out_vx_std'],
function=compute_dvars),
name='DVARSpost')
DVARSpost.inputs.out_std_name = 'stdDVARS_post.txt'
wf.connect(addmean, 'out_file', DVARSpost, 'in_file')
wf.connect(selectfiles, 'prefiltered_mask', DVARSpost, 'in_mask')
wf.connect(DVARSpost, 'out_std', ds, 'QC.@DVARSpost')
###########################################################################
######################## No. 8 ######################################
#SMOOTHING of 6fwhm
merge_datasets = pe.Node(util.Merge(2),
infields=['in1', 'in2'],
name='merge_datasets')
wf.connect(addmean, 'out_file', merge_datasets, 'in1')
wf.connect(selectfiles, 'prefiltered_detrend', merge_datasets, 'in2')
median = pe.MapNode(fsl.utils.ImageStats(op_string='-k %s -p 50'),
name='median',
iterfield=['in_file'])
wf.connect(merge_datasets, 'out', median, 'in_file')
wf.connect(selectfiles, 'prefiltered_mask', median, 'mask_file')
smooth = pe.MapNode(
fsl.SUSAN(fwhm=6.0),
name='smooth',
iterfield=['in_file', 'brightness_threshold', 'usans', 'out_file'])
smooth.inputs.out_file = [
'filtered_func_data_hp01_sm6fwhm.nii.gz',
'prefiltered_func_data_detrend_sm6fwhm.nii.gz'
]
merge_usans = pe.MapNode(util.Merge(2),
infields=['in1', 'in2'],
name='merge_usans',
iterfield=['in2'])
wf.connect(selectfiles, 'prefiltered_detrend_Tmean', merge_usans, 'in1')
wf.connect(median, 'out_stat', merge_usans, 'in2')
def getbtthresh(medianvals):
return [0.75 * val for val in medianvals]
def getusans(x):
return [[tuple([val[0], 0.75 * val[1]])] for val in x]
wf.connect(merge_datasets, 'out', smooth, 'in_file')
wf.connect(median, ('out_stat', getbtthresh), smooth,
'brightness_threshold')
wf.connect(merge_usans, ('out', getusans), smooth, 'usans')
wf.connect(smooth, 'smoothed_file', ds, '@smoothout')
###########################################################################
######################## RUN ######################################
wf.write_graph(dotfilename='wf.dot',
graph2use='colored',
format='pdf',
simple_form=True)
wf.run(plugin='MultiProc', plugin_args={'n_procs': 2})
#wf.run()
return
def init_dualregression_wf(analysis, memcalc=MemoryCalculator()):
"""
create a workflow to calculate dual regression for ICA seeds
"""
assert isinstance(analysis, Analysis)
assert isinstance(analysis.tags, Tags)
# make bold file variant specification
confoundsfilefields = []
varianttupls = [("space", analysis.tags.space)]
if analysis.tags.grand_mean_scaled is not None:
assert isinstance(analysis.tags.grand_mean_scaled, GrandMeanScaledTag)
varianttupls.append(analysis.tags.grand_mean_scaled.as_tupl())
if analysis.tags.band_pass_filtered is not None:
assert isinstance(analysis.tags.band_pass_filtered,
BandPassFilteredTag)
varianttupls.append(analysis.tags.band_pass_filtered.as_tupl())
if analysis.tags.confounds_removed is not None:
assert isinstance(analysis.tags.confounds_removed, ConfoundsRemovedTag)
confounds_removed_names = tuple(
name for name in analysis.tags.confounds_removed.names
if "aroma_motion" in name)
varianttupls.append(("confounds_removed", confounds_removed_names))
confounds_extract_names = tuple(
name for name in analysis.tags.confounds_removed.names
if "aroma_motion" not in name)
if len(confounds_extract_names) > 0:
confoundsfilefields.append("confounds_file")
varianttupls.append(("confounds_extract", confounds_extract_names))
if analysis.tags.smoothed is not None:
assert isinstance(analysis.tags.smoothed, SmoothedTag)
varianttupls.append(analysis.tags.smoothed.as_tupl())
boldfilevariant = (("bold_file", *confoundsfilefields),
tuple(varianttupls))
assert analysis.name is not None
workflow = pe.Workflow(name=analysis.name)
# input
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"bold_file",
*confoundsfilefields,
"mask_file",
"map_files",
"map_components",
"metadata",
]),
name="inputnode",
)
resampleifneeded = pe.MapNode(
interface=ResampleIfNeeded(method="continuous"),
name="resampleifneeded",
iterfield=["in_file"],
mem_gb=memcalc.series_std_gb,
)
workflow.connect(inputnode, "map_files", resampleifneeded, "in_file")
workflow.connect(inputnode, "bold_file", resampleifneeded, "ref_file")
# Delete zero voxels for mean time series
applymask = pe.MapNode(
interface=fsl.ApplyMask(),
name="applymask",
iterfield="in_file",
mem_gb=memcalc.volume_std_gb,
)
workflow.connect([
(inputnode, applymask, [("mask_file", "mask_file")]),
(resampleifneeded, applymask, [("out_file", "in_file")]),
])
# first step, calculate spatial regression of ICA components on to the
# bold file
glm0 = pe.MapNode(
interface=fsl.GLM(
out_file="beta",
demean=True,
),
name="glm0",
iterfield="design",
mem_gb=memcalc.series_std_gb * 10,
)
workflow.connect([
(applymask, glm0, [("out_file", "design")]),
(inputnode, glm0, [("bold_file", "in_file"), ("mask_file", "mask")]),
])
# second step, calculate the temporal regression of the time series
# from the first step on to the bold file
def make_contrastmat(map_file=None, confounds_file=None):
"""
extract number of ICA components from 4d image and name them
"""
import os
from os import path as op
from pipeline.utils import nvol, ncol
import numpy as np
ncomponents = nvol(map_file)
if confounds_file is not None:
nconfounds = ncol(confounds_file)
else:
nconfounds = 0
contrastmat = np.zeros((ncomponents, ncomponents + nconfounds))
contrastmat[:ncomponents, :ncomponents] = np.eye(ncomponents)
out_file = op.join(os.getcwd(), "contrasts.tsv")
np.savetxt(out_file, contrastmat, delimiter="\t")
return out_file
contrastmat = pe.MapNode(
interface=niu.Function(
input_names=["map_file", *confoundsfilefields],
output_names=["out_file"],
function=make_contrastmat,
),
iterfield="map_file",
name="contrastmat",
)
workflow.connect([(inputnode, contrastmat, [("map_files", "map_file")])])
if confoundsfilefields:
workflow.connect([(inputnode, contrastmat, [(*confoundsfilefields,
*confoundsfilefields)])])
designnode = pe.Node(niu.IdentityInterface(fields=["design"]),
name="designnode")
if confoundsfilefields:
mergecolumns = pe.MapNode(
interface=MergeColumnsTSV(2),
name="mergecolumns",
mem_gb=memcalc.min_gb,
iterfield="in1",
run_without_submitting=True,
)
workflow.connect([
(glm0, mergecolumns, [("out_file", "in1")]),
(inputnode, mergecolumns, [(*confoundsfilefields, "in2")]),
(mergecolumns, designnode, [("out_file", "design")]),
])
else:
workflow.connect([(glm0, designnode, [("out_file", "design")])])
glm1 = pe.MapNode(
interface=fsl.GLM(
out_file="beta.nii.gz",
out_cope="cope.nii.gz",
out_varcb_name="varcope.nii.gz",
out_z_name="zstat.nii.gz",
demean=True,
),
name="glm1",
iterfield=["design", "contrasts"],
mem_gb=memcalc.series_std_gb * 10,
)
workflow.connect([
(inputnode, glm1, [("bold_file", "in_file"), ("mask_file", "mask")]),
(contrastmat, glm1, [("out_file", "contrasts")]),
(designnode, glm1, [("design", "design")]),
])
splitcopesimages = pe.MapNode(interface=fsl.Split(dimension="t"),
iterfield="in_file",
name="splitcopesimages")
splitvarcopesimage = pe.MapNode(interface=fsl.Split(dimension="t"),
iterfield="in_file",
name="splitvarcopesimage")
splitzstatsimage = pe.MapNode(interface=fsl.Split(dimension="t"),
iterfield="in_file",
name="splitzstatsimage")
workflow.connect([
(glm1, splitcopesimages, [("out_cope", "in_file")]),
(glm1, splitvarcopesimage, [("out_varcb", "in_file")]),
(glm1, splitzstatsimage, [("out_z", "in_file")]),
])
# make dof volume
makedofvolume = pe.MapNode(
interface=MakeDofVolume(),
iterfield=["design"],
name="makedofvolume",
)
workflow.connect([
(inputnode, makedofvolume, [("bold_file", "bold_file")]),
(designnode, makedofvolume, [("design", "design")]),
])
# output
outputnode = pe.Node(
interface=MakeResultdicts(keys=[
"firstlevelanalysisname",
"firstlevelfeaturename",
"cope",
"varcope",
"zstat",
"dof_file",
"mask_file",
]),
name="outputnode",
)
outputnode.inputs.firstlevelanalysisname = analysis.name
workflow.connect([
(
inputnode,
outputnode,
[
("metadata", "basedict"),
("mask_file", "mask_file"),
(("map_components", ravel), "firstlevelfeaturename"),
],
),
(makedofvolume, outputnode, [("out_file", "dof_file")]),
(splitcopesimages, outputnode, [(("out_files", ravel), "cope")]),
(splitvarcopesimage, outputnode, [(("out_files", ravel), "varcope")]),
(splitzstatsimage, outputnode, [(("out_files", ravel), "zstat")]),
])
return workflow, (boldfilevariant, )
# prepare the nuisance factors
df = pd.concat([
dread['X'], dread['Y'], dread['Z'], dread['RotX'], dread['RotY'],
dread['RotZ'], dread['FramewiseDisplacement'], dread['aCompCor00'],
dread['aCompCor01'], dread['aCompCor02'], dread['aCompCor03'],
dread['aCompCor04'], dread['aCompCor05']
],
axis=1)
design_out = conf_fil[:-4] + '_small.csv'
print(design_out)
df.to_csv(design_out, sep='\t', index=False, header=False)
# regress out nuisance factors using fls_glm
glm = fsl.GLM(in_file=img_removed,
mask=img_mask,
design=design_out,
demean=True,
out_res_name=img_removed[:-7] + '_denois.nii.gz',
output_type='NIFTI_GZ')
glm.run()
# detrend timeseries using afni-3dDetrend
detrend = afni.Detrend()
detrend.inputs.in_file = img_removed[:-7] + '_denois.nii.gz'
detrend.inputs.args = '-polort 2'
detrend.inputs.outputtype = 'NIFTI_GZ'
detrend.inputs.out_file = img_removed[:-7] + '_denois_detrend.nii.gz'
print(detrend.cmdline)
detrend.run()
def seed_fc(
preprocessing_dir,
exclude={},
habituation='confound',
highpass_sigma=225,
lowpass_sigma=False,
include={},
keep_work=False,
out_dir="",
mask="",
match_regex='sub-(?P<sub>[a-zA-Z0-9]+)/ses-(?P<ses>[a-zA-Z0-9]+)/func/.*?_task-(?P<task>[a-zA-Z0-9]+)_acq-(?P<acq>[a-zA-Z0-9]+)_(?P<mod>[a-zA-Z0-9]+)\.(?:tsv|nii|nii\.gz)',
nprocs=N_PROCS,
tr=1,
workflow_name="generic",
modality="cbv",
):
"""Calculate subject level seed-based functional connectivity via the `fsl_glm` command.
Parameters
----------
exclude : dict
A dictionary with any combination of "sessions", "subjects", "tasks" as keys and corresponding identifiers as values.
If this is specified matching entries will be excluded in the analysis.
habituation : {"", "confound", "separate_contrast", "in_main_contrast"}, optional
How the habituation regressor should be handled.
Anything which evaluates as False (though we recommend "") means no habituation regressor will be introduced.
highpass_sigma : int, optional
Highpass threshold (in seconds).
include : dict
A dictionary with any combination of "sessions", "subjects", "tasks" as keys and corresponding identifiers as values.
If this is specified only matching entries will be included in the analysis.
keep_work : bool, optional
Whether to keep the work directory (containing all the intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
out_dir : str, optional
Path to the directory inside which both the working directory and the output directory will be created.
mask : str, optional
Path to the brain mask which shall be used to define the brain volume in the analysis.
This has to point to an existing NIfTI file containing zero and one values only.
match_regex : str, optional
Regex matching pattern by which to select input files. Has to contain groups named "sub", "ses", "acq", "task", and "mod".
n_procs : int, optional
Maximum number of processes which to simultaneously spawn for the workflow.
If not explicitly defined, this is automatically calculated from the number of available cores and under the assumption that the workflow will be the main process running for the duration that it is running.
tr : int, optional
Repetition time, in seconds.
workflow_name : str, optional
Name of the workflow; this will also be the name of the final output directory produced under `out_dir`.
"""
preprocessing_dir = path.abspath(path.expanduser(preprocessing_dir))
if not out_dir:
out_dir = path.join(bids_base, 'l1')
else:
out_dir = path.abspath(path.expanduser(out_dir))
datafind = nio.DataFinder()
datafind.inputs.root_paths = preprocessing_dir
datafind.inputs.match_regex = match_regex
datafind_res = datafind.run()
out_paths = [
path.abspath(path.expanduser(i))
for i in datafind_res.outputs.out_paths
]
data_selection = zip(*[
datafind_res.outputs.sub, datafind_res.outputs.ses,
datafind_res.outputs.acq, datafind_res.outputs.task,
datafind_res.outputs.mod, out_paths
])
data_selection = [list(i) for i in data_selection]
data_selection = pd.DataFrame(data_selection,
columns=('subject', 'session', 'acquisition',
'task', 'modality', 'path'))
if exclude:
for key in exclude:
data_selection = data_selection[~data_selection[key].
isin(exclude[key])]
if include:
for key in include:
data_selection = data_selection[data_selection[key].isin(
include[key])]
bids_dictionary = data_selection[
data_selection['modality'] ==
modality].drop_duplicates().T.to_dict().values()
infosource = pe.Node(
interface=util.IdentityInterface(fields=['bids_dictionary']),
name="infosource")
infosource.iterables = [('bids_dictionary', bids_dictionary)]
datafile_source = pe.Node(
name='datafile_source',
interface=util.Function(
function=select_from_datafind_df,
input_names=inspect.getargspec(select_from_datafind_df)[0],
output_names=['out_file']))
datafile_source.inputs.bids_dictionary_override = {'modality': modality}
datafile_source.inputs.df = data_selection
seed_timecourse = pe.Node(
name='seed_timecourse',
interface=util.Function(
function=select_from_datafind_df,
input_names=inspect.getargspec(select_from_datafind_df)[0],
output_names=['out_file']))
specify_model = pe.Node(interface=SpecifyModel(), name="specify_model")
specify_model.inputs.input_units = 'secs'
specify_model.inputs.time_repetition = tr
specify_model.inputs.high_pass_filter_cutoff = highpass_sigma
specify_model.inputs.habituation_regressor = bool(habituation)
level1design = pe.Node(interface=Level1Design(), name="level1design")
level1design.inputs.interscan_interval = tr
if bf_path:
bf_path = path.abspath(path.expanduser(bf_path))
level1design.inputs.bases = {"custom": {"bfcustompath": bf_path}}
# level1design.inputs.bases = {'gamma': {'derivs':False, 'gammasigma':10, 'gammadelay':5}}
level1design.inputs.orthogonalization = {
1: {
0: 0,
1: 0,
2: 0
},
2: {
0: 1,
1: 1,
2: 0
}
}
level1design.inputs.model_serial_correlations = True
if habituation == "separate_contrast":
level1design.inputs.contrasts = [
('allStim', 'T', ["e0"], [1]), ('allStim', 'T', ["e1"], [1])
] #condition names as defined in specify_model
elif habituation == "in_main_contrast":
level1design.inputs.contrasts = [
('allStim', 'T', ["e0", "e1"], [1, 1])
] #condition names as defined in specify_model
elif habituation == "confound" or not habituation:
level1design.inputs.contrasts = [
('allStim', 'T', ["e0"], [1])
] #condition names as defined in specify_model
else:
raise ValueError(
'The value you have provided for the `habituation` parameter, namely "{}", is invalid. Please choose one of: {"confound","in_main_contrast","separate_contrast"}'
.format(habituation))
modelgen = pe.Node(interface=fsl.FEATModel(), name='modelgen')
modelgen.inputs.ignore_exception = True
glm = pe.Node(interface=fsl.GLM(), name='glm', iterfield='design')
glm.inputs.out_cope = "cope.nii.gz"
glm.inputs.out_varcb_name = "varcb.nii.gz"
#not setting a betas output file might lead to beta export in lieu of COPEs
glm.inputs.out_file = "betas.nii.gz"
glm.inputs.out_t_name = "t_stat.nii.gz"
glm.inputs.out_p_name = "p_stat.nii.gz"
if mask:
glm.inputs.mask = path.abspath(path.expanduser(mask))
glm.inputs.ignore_exception = True
cope_filename = pe.Node(
name='cope_filename',
interface=util.Function(
function=bids_dict_to_source,
input_names=inspect.getargspec(bids_dict_to_source)[0],
output_names=['filename']))
cope_filename.inputs.source_format = "sub-{subject}_ses-{session}_task-{task}_acq-{acquisition}_{modality}_cope.nii.gz"
varcb_filename = pe.Node(
name='varcb_filename',
interface=util.Function(
function=bids_dict_to_source,
input_names=inspect.getargspec(bids_dict_to_source)[0],
output_names=['filename']))
varcb_filename.inputs.source_format = "sub-{subject}_ses-{session}_task-{task}_acq-{acquisition}_{modality}_varcb.nii.gz"
tstat_filename = pe.Node(
name='tstat_filename',
interface=util.Function(
function=bids_dict_to_source,
input_names=inspect.getargspec(bids_dict_to_source)[0],
output_names=['filename']))
tstat_filename.inputs.source_format = "sub-{subject}_ses-{session}_task-{task}_acq-{acquisition}_{modality}_tstat.nii.gz"
zstat_filename = pe.Node(
name='zstat_filename',
interface=util.Function(
function=bids_dict_to_source,
input_names=inspect.getargspec(bids_dict_to_source)[0],
output_names=['filename']))
zstat_filename.inputs.source_format = "sub-{subject}_ses-{session}_task-{task}_acq-{acquisition}_{modality}_zstat.nii.gz"
pstat_filename = pe.Node(
name='pstat_filename',
interface=util.Function(
function=bids_dict_to_source,
input_names=inspect.getargspec(bids_dict_to_source)[0],
output_names=['filename']))
pstat_filename.inputs.source_format = "sub-{subject}_ses-{session}_task-{task}_acq-{acquisition}_{modality}_pstat.nii.gz"
pfstat_filename = pe.Node(
name='pfstat_filename',
interface=util.Function(
function=bids_dict_to_source,
input_names=inspect.getargspec(bids_dict_to_source)[0],
output_names=['filename']))
pfstat_filename.inputs.source_format = "sub-{subject}_ses-{session}_task-{task}_acq-{acquisition}_{modality}_pfstat.nii.gz"
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = path.join(out_dir, workflow_name)
datasink.inputs.parameterization = False
workflow_connections = [
(infosource, datafile_source, [('bids_dictionary', 'bids_dictionary')
]),
(infosource, eventfile_source, [('bids_dictionary', 'bids_dictionary')
]),
(eventfile_source, specify_model, [('out_file', 'event_files')]),
(specify_model, level1design, [('session_info', 'session_info')]),
(level1design, modelgen, [('ev_files', 'ev_files')]),
(level1design, modelgen, [('fsf_files', 'fsf_file')]),
(modelgen, glm, [('design_file', 'design')]),
(modelgen, glm, [('con_file', 'contrasts')]),
(infosource, datasink, [(('bids_dictionary', bids_dict_to_dir),
'container')]),
(infosource, cope_filename, [('bids_dictionary', 'bids_dictionary')]),
(infosource, varcb_filename, [('bids_dictionary', 'bids_dictionary')]),
(infosource, tstat_filename, [('bids_dictionary', 'bids_dictionary')]),
(infosource, zstat_filename, [('bids_dictionary', 'bids_dictionary')]),
(infosource, pstat_filename, [('bids_dictionary', 'bids_dictionary')]),
(infosource, pfstat_filename, [('bids_dictionary', 'bids_dictionary')
]),
(cope_filename, glm, [('filename', 'out_cope')]),
(varcb_filename, glm, [('filename', 'out_varcb_name')]),
(tstat_filename, glm, [('filename', 'out_t_name')]),
(zstat_filename, glm, [('filename', 'out_z_name')]),
(pstat_filename, glm, [('filename', 'out_p_name')]),
(pfstat_filename, glm, [('filename', 'out_pf_name')]),
(glm, datasink, [('out_pf', '@pfstat')]),
(glm, datasink, [('out_p', '@pstat')]),
(glm, datasink, [('out_z', '@zstat')]),
(glm, datasink, [('out_t', '@tstat')]),
(glm, datasink, [('out_cope', '@cope')]),
(glm, datasink, [('out_varcb', '@varcb')]),
]
if highpass_sigma or lowpass_sigma:
bandpass = pe.Node(interface=fsl.maths.TemporalFilter(),
name="bandpass")
bandpass.inputs.highpass_sigma = highpass_sigma
if lowpass_sigma:
bandpass.inputs.lowpass_sigma = lowpass_sigma
else:
bandpass.inputs.lowpass_sigma = tr
workflow_connections.extend([
(datafile_source, bandpass, [('out_file', 'in_file')]),
(bandpass, specify_model, [('out_file', 'functional_runs')]),
(bandpass, glm, [('out_file', 'in_file')]),
])
else:
workflow_connections.extend([
(datafile_source, specify_model, [('out_file', 'functional_runs')
]),
(datafile_source, glm, [('out_file', 'in_file')]),
])
workdir_name = workflow_name + "_work"
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = out_dir
workflow.config = {
"execution": {
"crashdump_dir": path.join(out_dir, "crashdump")
}
}
workflow.write_graph(dotfilename=path.join(workflow.base_dir, workdir_name,
"graph.dot"),
graph2use="hierarchical",
format="png")
workflow.run(plugin="MultiProc", plugin_args={'n_procs': nprocs})
if not keep_work:
shutil.rmtree(path.join(out_dir, workdir_name))
def create_denoise_pipeline(name='denoise'):
# workflow
denoise = Workflow(name='denoise')
# Define nodes
inputnode = Node(interface=util.IdentityInterface(fields=[
'anat_brain', 'brain_mask', 'flirt_mat', 'unwarped_mean', 'epi_coreg',
'highpass_sigma', 'tr'
]),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(fields=[
'wmcsf_mask', 'brain2epi', 'wmcsf_mask2epi', 'combined_motion',
'comp_regressor', 'comp_F', 'comp_pF', 'out_betas', 'ts_fullspectrum',
'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]
# binarize tissue classes
binarize_tissue = MapNode(
fsl.ImageMaths(op_string='-nan -thr 0.99 -ero -bin'),
iterfield=['in_file'],
name='binarize_tissue')
denoise.connect([
(fast, binarize_tissue, [(('partial_volume_files', selectindex,
[0, 2]), 'in_file')]),
])
# combine tissue classes to noise mask
wmcsf_mask = Node(fsl.BinaryMaths(operation='add',
out_file='wmcsf_mask.nii'),
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')])])
# project wm_csf mask from anatomical to original epi space using inverse FLIRT-matrix
invmat = Node(fsl.ConvertXFM(), name='invmat')
invmat.inputs.invert_xfm = True
apply_inv = Node(fsl.ApplyXfm(), name='apply_inv')
apply_inv.inputs.apply_xfm = True
denoise.connect([(inputnode, invmat, [('flirt_mat', 'in_file')]),
(invmat, apply_inv, [('out_file', 'in_matrix_file')]),
(inputnode, apply_inv, [('unwarped_mean', 'reference')]),
(wmcsf_mask, apply_inv, [('out_file', 'in_file')]),
(apply_inv, outputnode, [('out_file', 'wmcsf_mask2epi')])
])
#project brain to epi space as a checkup
apply_inv_brain = Node(fsl.ApplyXfm(), name='apply_inv_brain')
apply_inv_brain.inputs.apply_xfm = True
denoise.connect([
(invmat, apply_inv_brain, [('out_file', 'in_matrix_file')]),
(inputnode, apply_inv_brain, [('unwarped_mean', 'reference')]),
(inputnode, apply_inv_brain, [('anat_brain', 'in_file')]),
(apply_inv_brain, outputnode, [('out_file', 'brain2epi')])
])
#no artifact detection and motion regression done because of AROMA
# 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.inputs.extra_regressors = None
createfilter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([
(inputnode, createfilter2, [('epi_coreg', 'realigned_file')]),
(apply_inv, 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',
output_type='NIFTI_GZ',
demean=True),
name='filternoise')
filter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, filter2, [('epi_coreg', 'in_file')]),
(createfilter2, filter2, [('out_files', 'design')]),
(inputnode, filter2, [('brain_mask', 'mask')]),
(filter2, outputnode, [('out_f', 'comp_F'),
('out_pf', 'comp_pF'),
('out_file', 'out_betas')])])
# write TR into header again (glms remove it)
# do not use mri_convert interface as it has a bug (already fixed in niyppe master)
fix_tr = Node(util.Function(input_names=['in_file', 'TR_sec'],
output_names=['out_file'],
function=fix_TR_fs),
name='fix_tr')
denoise.connect(inputnode, 'tr', fix_tr, 'TR_sec')
denoise.connect(filter2, 'out_res', fix_tr, 'in_file')
#use only highpass filter (because high-frequency content (otherwise filtered by lowpass is already considered in AROMA))
highpass_filter = Node(
fsl.TemporalFilter(out_file='rest_denoised_highpassed.nii'),
name='highpass_filter')
highpass_filter.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, highpass_filter, [('highpass_sigma',
'highpass_sigma')]),
(fix_tr, highpass_filter, [('out_file', 'in_file')]),
(fix_tr, outputnode, [('out_file', 'ts_fullspectrum')])])
# time-normalize scans (could be set to percent change etc. but here NO normalization is used
# http://nipy.org/nitime/api/generated/nitime.fmri.io.html)
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')]),
(highpass_filter, normalize_time, [('out_file', 'in_file')]),
(normalize_time, outputnode, [('out_file', 'normalized_file')])
])
return denoise
def dr_stage2(self, **kwargs):
regress_moco = True
desnorm = True
for i in kwargs.keys():
if i == 'regress_moco':
if kwargs[i]:
regress_moco = True
else:
regress_moco = False
if i == 'desnorm':
if kwargs[i]:
desnorm = True
else:
desnorm = False
for subj in self.subjects:
dr_s1_txt = os.path.join(self.outdir, 'stage1',
'dr_stage1_idc_' + subj + '.txt')
moco_txt = os.path.join(os.path.dirname(self.indir), subj,
'idc_' + subj + self.featdir_sfix, 'mc',
'prefiltered_func_data_mcf.par')
dr_s1 = read_txt_file(dr_s1_txt)
if regress_moco:
moco_pars = read_txt_file(moco_txt)
for i in range(0, len(dr_s1)):
for j in range(0, 6):
dr_s1[i].append(moco_pars[i][j])
dr_s1_moco_txt = os.path.join(
self.outdir, 'stage1',
'dr_stage1_moco_idc_' + subj + '.txt')
write_txt_file(dr_s1, dr_s1_moco_txt)
designFile = dr_s1_moco_txt
else:
designFile = dr_s1_txt
iFile = os.path.join(os.path.dirname(self.indir), subj,
'idc_' + subj + self.featdir_sfix,
self.ff_data_name)
oFile = os.path.join(self.outdir, 'stage2',
'dr_stage2_idc_' + subj + '.nii.gz')
ozFile = os.path.join(self.outdir, 'stage2',
'dr_stage2_Z_idc_' + subj + '.nii.gz')
mask = os.path.join(self.outdir, 'stage1', 'mask.nii.gz')
if desnorm:
opts_str = '--demean --des_norm'
else:
opst_str = '--demean'
fsl_glm = fsl.GLM(in_file=iFile,
design=designFile,
terminal_output='stream',
out_file=oFile,
mask=mask,
options=opts_str,
output_type='NIFTI_GZ')
fsl_glm.run()
obname = os.path.join(self.outdir, 'stage2',
'dr_stage2_idc_' + subj + '_ic')
fslsplit = fsl.Split(dimension='t',
in_file=oFile,
out_base_name=obname,
terminal_output='stream',
output_type='NIFTI_GZ')
fslsplit.run()
def init_seedbasedconnectivity_wf(analysis, memcalc=MemoryCalculator()):
"""
create workflow to calculate seed connectivity maps
"""
assert isinstance(analysis, Analysis)
assert isinstance(analysis.tags, Tags)
# make bold file variant specification
confoundsfilefields = []
varianttupls = [("space", analysis.tags.space)]
if analysis.tags.grand_mean_scaled is not None:
assert isinstance(analysis.tags.grand_mean_scaled, GrandMeanScaledTag)
varianttupls.append(analysis.tags.grand_mean_scaled.as_tupl())
if analysis.tags.band_pass_filtered is not None:
assert isinstance(analysis.tags.band_pass_filtered,
BandPassFilteredTag)
varianttupls.append(analysis.tags.band_pass_filtered.as_tupl())
if analysis.tags.confounds_removed is not None:
assert isinstance(analysis.tags.confounds_removed, ConfoundsRemovedTag)
confounds_removed_names = tuple(
name for name in analysis.tags.confounds_removed.names
if "aroma_motion" in name)
varianttupls.append(("confounds_removed", confounds_removed_names))
confounds_extract_names = tuple(
name for name in analysis.tags.confounds_removed.names
if "aroma_motion" not in name)
if len(confounds_extract_names) > 0:
confoundsfilefields.append("confounds_file")
varianttupls.append(("confounds_extract", confounds_extract_names))
if analysis.tags.smoothed is not None:
assert isinstance(analysis.tags.smoothed, SmoothedTag)
varianttupls.append(analysis.tags.smoothed.as_tupl())
boldfilevariant = (("bold_file", *confoundsfilefields),
tuple(varianttupls))
assert analysis.name is not None
workflow = pe.Workflow(name=analysis.name)
# input
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"bold_file",
*confoundsfilefields,
"mask_file",
"seed_files",
"seed_names",
"metadata",
]),
name="inputnode",
)
resampleifneeded = pe.MapNode(
interface=ResampleIfNeeded(method="nearest"),
name="resampleifneeded",
iterfield=["in_file"],
mem_gb=memcalc.series_std_gb,
)
workflow.connect(inputnode, "seed_files", resampleifneeded, "in_file")
workflow.connect(inputnode, "bold_file", resampleifneeded, "ref_file")
# Delete zero voxels for the seeds
applymask = pe.MapNode(
interface=fsl.ApplyMask(),
name="applymask",
iterfield="in_file",
mem_gb=memcalc.volume_std_gb,
)
workflow.connect([
(inputnode, applymask, [("mask_file", "mask_file")]),
(resampleifneeded, applymask, [("out_file", "in_file")]),
])
# calculate the mean time series of the region defined by each mask
meants = pe.MapNode(
interface=fsl.ImageMeants(),
name="meants",
iterfield="mask",
mem_gb=memcalc.series_std_gb,
)
workflow.connect([
(inputnode, meants, [("bold_file", "in_file")]),
(applymask, meants, [("out_file", "mask")]),
])
def make_contrastmat(confounds_file=None):
import os
from os import path as op
from pipeline.utils import ncol
import numpy as np
if confounds_file is not None:
nconfounds = ncol(confounds_file)
else:
nconfounds = 0
contrastmat = np.zeros((1, 1 + nconfounds))
contrastmat[0, 0] = 1
out_file = op.join(os.getcwd(), "contrasts.tsv")
np.savetxt(out_file, contrastmat, delimiter="\t")
return out_file
contrastmat = pe.Node(
interface=niu.Function(
input_names=[*confoundsfilefields],
output_names=["out_file"],
function=make_contrastmat,
),
name="contrastmat",
)
if confoundsfilefields:
workflow.connect([(inputnode, contrastmat, [(*confoundsfilefields,
*confoundsfilefields)])])
designnode = pe.Node(niu.IdentityInterface(fields=["design"]),
name="designnode")
if confoundsfilefields:
mergecolumns = pe.MapNode(
interface=MergeColumnsTSV(2),
name="mergecolumns",
mem_gb=memcalc.min_gb,
iterfield="in1",
run_without_submitting=True,
)
workflow.connect([
(meants, mergecolumns, [("out_file", "in1")]),
(inputnode, mergecolumns, [(*confoundsfilefields, "in2")]),
(mergecolumns, designnode, [("out_file", "design")]),
])
else:
workflow.connect([(meants, designnode, [("out_file", "design")])])
# calculate the regression of the mean time series
# onto the functional image.
# the result is the seed connectivity map
glm = pe.MapNode(
interface=fsl.GLM(
out_file="beta.nii.gz",
out_cope="cope.nii.gz",
out_varcb_name="varcope.nii.gz",
out_z_name="zstat.nii.gz",
demean=True,
),
name="glm",
iterfield="design",
mem_gb=memcalc.series_std_gb * 5,
)
workflow.connect([
(inputnode, glm, [("bold_file", "in_file")]),
(contrastmat, glm, [("out_file", "contrasts")]),
(designnode, glm, [("design", "design")]),
])
# make dof volume
makedofvolume = pe.MapNode(
interface=MakeDofVolume(),
iterfield=["design"],
name="makedofvolume",
)
workflow.connect([
(inputnode, makedofvolume, [("bold_file", "bold_file")]),
(designnode, makedofvolume, [("design", "design")]),
])
outputnode = pe.Node(
interface=MakeResultdicts(keys=[
"firstlevelanalysisname",
"firstlevelfeaturename",
"cope",
"varcope",
"zstat",
"dof_file",
"mask_file",
]),
name="outputnode",
)
outputnode.inputs.firstlevelanalysisname = analysis.name
workflow.connect([
(
inputnode,
outputnode,
[
("metadata", "basedict"),
("mask_file", "mask_file"),
("seed_names", "firstlevelfeaturename"),
],
),
(makedofvolume, outputnode, [("out_file", "dof_file")]),
(
glm,
outputnode,
[
(("out_cope", ravel), "cope"),
(("out_varcb", ravel), "varcope"),
(("out_z", ravel), "zstat"),
],
),
])
return workflow, (boldfilevariant, )
def create_temporal_reg(wflow_name='temporal_reg', which='SR'):
"""
Temporal multiple regression workflow
Provides a spatial map of parameter estimates corresponding to each
provided timeseries in a timeseries.txt file as regressors
Parameters
----------
wflow_name : a string
Name of the temporal regression workflow
which: a string
SR: Spatial Regression, RT: ROI Timeseries
NOTE: If you set (which = 'RT'), the output of this workflow will be
renamed based on the header information provided in the
timeseries.txt file.
If you run the temporal regression workflow manually, don\'t set
(which = 'RT') unless you provide a timeseries.txt file with a header
containing the names of the timeseries.
Returns
-------
wflow : workflow
temporal multiple regression Workflow
Notes
-----
`Source <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/sca/sca.py>`_
Workflow Inputs::
inputspec.subject_rest : string (existing nifti file)
Band passed Image with Global Signal , white matter, csf and
motion regression. Recommended bandpass filter (0.001,0.1) )
inputspec.subject_timeseries : string (existing txt file)
text file containing the timeseries to be regressed on the subjects
functional file
timeseries are organized by columns, timepoints by rows
inputspec.subject_mask : string (existing nifti file)
path to subject functional mask
inputspec.demean : Boolean
control whether to demean model and data
inputspec.normalize : Boolean
control whether to normalize the input timeseries to unit standard deviation
Workflow Outputs::
outputspec.temp_reg_map : string (nifti file)
GLM parameter estimate image for each timeseries in the input file
outputspec.temp_reg_map_zstat : string (nifti file)
Normalized version of the GLM parameter estimates
Temporal Regression Workflow Procedure:
Enter all timeseries into a general linear model and regress these
timeseries to the subjects functional file to get spatial maps of voxels
showing activation patterns related to those in the timeseries.
.. exec::
from CPAC.sca import create_temporal_reg
wf = create_temporal_reg()
wf.write_graph(
graph2use='orig',
dotfilename='./images/generated/create_temporal_regression.dot'
)
Workflow:
.. image:: ../../images/generated/create_temporal_regression.png
:width: 500
Detailed Workflow:
.. image:: ../../images/generated/create_temporal_regression_detailed.png
:width: 500
References
----------
`http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression/UserGuide <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression/UserGuide>`_
Examples
--------
>>> tr_wf = create_temporal_reg('temporal regression')
>>> tr_wf.inputs.inputspec.subject_rest = '/home/data/subject/func/rest_bandpassed.nii.gz'
>>> tr_wf.inputs.inputspec.subject_timeseries = '/home/data/subject/func/timeseries.txt'
>>> tr_wf.inputs.inputspec.subject_mask = '/home/data/spatialmaps/spatial_map.nii.gz'
>>> tr_wf.inputs.inputspec.demean = True
>>> tr_wf.inputs.inputspec.normalize = True
>>> tr_wf.run() # doctest: +SKIP
"""
wflow = pe.Workflow(name=wflow_name)
inputNode = pe.Node(util.IdentityInterface(fields=[
'subject_rest', 'subject_timeseries', 'subject_mask', 'demean',
'normalize'
]),
name='inputspec')
outputNode = pe.Node(util.IdentityInterface(fields=[
'temp_reg_map', 'temp_reg_map_files', 'temp_reg_map_z',
'temp_reg_map_z_files'
]),
name='outputspec')
check_timeseries = pe.Node(util.Function(input_names=['in_file'],
output_names=['out_file'],
function=check_ts),
name='check_timeseries')
wflow.connect(inputNode, 'subject_timeseries', check_timeseries, 'in_file')
temporalReg = pe.Node(interface=fsl.GLM(),
name='temporal_regression',
mem_gb=4.0)
temporalReg.inputs.out_file = 'temp_reg_map.nii.gz'
temporalReg.inputs.out_z_name = 'temp_reg_map_z.nii.gz'
wflow.connect(inputNode, 'subject_rest', temporalReg, 'in_file')
wflow.connect(check_timeseries, 'out_file', temporalReg, 'design')
wflow.connect(inputNode, 'demean', temporalReg, 'demean')
wflow.connect(inputNode, 'normalize', temporalReg, 'des_norm')
wflow.connect(inputNode, 'subject_mask', temporalReg, 'mask')
wflow.connect(temporalReg, 'out_file', outputNode, 'temp_reg_map')
wflow.connect(temporalReg, 'out_z', outputNode, 'temp_reg_map_z')
'''
split = pe.Node(interface=fsl.Split(), name='split_raw_volumes')
split.inputs.dimension = 't'
split.inputs.out_base_name = 'temp_reg_map_'
wflow.connect(temporalReg, 'out_file', split, 'in_file')
split_zstat = pe.Node(interface=fsl.Split(), name='split_zstat_volumes')
split_zstat.inputs.dimension = 't'
split_zstat.inputs.out_base_name = 'temp_reg_map_z_'
wflow.connect(temporalReg, 'out_z',
split_zstat, 'in_file')
if which == 'SR':
wflow.connect(split, 'out_files',
outputNode, 'temp_reg_map_files')
wflow.connect(split_zstat, 'out_files',
outputNode, 'temp_reg_map_z_files')
elif which == 'RT':
map_roi_imports = ['import os', 'import numpy as np']
# get roi order and send to output node for raw outputs
get_roi_order = pe.Node(util.Function(input_names=['maps',
'timeseries'],
output_names=['labels',
'maps'],
function=map_to_roi,
imports=map_roi_imports),
name='get_roi_order')
wflow.connect(split, 'out_files', get_roi_order, 'maps')
wflow.connect(inputNode, 'subject_timeseries',
get_roi_order, 'timeseries')
rename_maps = pe.MapNode(interface=util.Rename(),
name='rename_maps',
iterfield=['in_file',
'format_string'])
rename_maps.inputs.keep_ext = True
wflow.connect(get_roi_order, 'labels', rename_maps, 'format_string')
wflow.connect(get_roi_order, 'maps', rename_maps, 'in_file')
wflow.connect(rename_maps, 'out_file',
outputNode, 'temp_reg_map_files')
# get roi order and send to output node for z-stat outputs
get_roi_order_zstat = pe.Node(util.Function(input_names=['maps',
'timeseries'],
output_names=['labels',
'maps'],
function=map_to_roi,
imports=map_roi_imports),
name='get_roi_order_zstat')
wflow.connect(split_zstat, 'out_files', get_roi_order_zstat, 'maps')
wflow.connect(inputNode, 'subject_timeseries',
get_roi_order_zstat, 'timeseries')
rename_maps_zstat = pe.MapNode(interface=util.Rename(),
name='rename_maps_zstat',
iterfield=['in_file',
'format_string'])
rename_maps_zstat.inputs.keep_ext = True
wflow.connect(get_roi_order_zstat, 'labels',
rename_maps_zstat, 'format_string')
wflow.connect(get_roi_order_zstat, 'maps',
rename_maps_zstat, 'in_file')
wflow.connect(rename_maps_zstat, 'out_file',
outputNode, 'temp_reg_map_z_files')
'''
return wflow
def runglmperun(self, subject, trtimeinsec):
s = SpecifyModel()
# loop on all runs and models within each run
modelfiles = subject._modelfiles
for model in modelfiles:
# Make directory results to store the results of the model
results_dir = os.path.join(subject._path, 'model', model[0],
'results', model[1])
dir_util.mkpath(results_dir)
os.chdir(results_dir)
s.inputs.event_files = model[2]
s.inputs.input_units = 'secs'
s.inputs.functional_runs = os.path.join(subject._path, 'BOLD',
model[1],
'bold_mcf_hp.nii.gz')
# use nibable to get the tr of from the .nii file
s.inputs.time_repetition = trtimeinsec
s.inputs.high_pass_filter_cutoff = 128.
# find par file that has motion
motionfiles = glob(
os.path.join(subject._path, 'BOLD', model[1], "*.par"))
s.inputs.realignment_parameters = motionfiles
#info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], durations=[[1]]), Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], durations=[[1]])]
#s.inputs.subject_info = None
res = s.run()
res.runtime.cwd
print ">>>> preparing evs for model " + model[
1] + "and run " + model[0]
sessionInfo = res.outputs.session_info
level1design = Level1Design()
level1design.inputs.interscan_interval = trtimeinsec
level1design.inputs.bases = {'dgamma': {'derivs': False}}
level1design.inputs.session_info = sessionInfo
level1design.inputs.model_serial_correlations = True
#TODO: add contrasts to level 1 design so that I have just condition vs rest for each ev
#TODO: Look into changign this to FILM instead of FEAT - this also has the option of setting output directory
# http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#Contrasts
#http://nipy.org/nipype/interfaces/generated/nipype.interfaces.fsl.model.html#filmgls
resLevel = level1design.run()
featModel = FEATModel()
featModel.inputs.fsf_file = resLevel.outputs.fsf_files
featModel.inputs.ev_files = resLevel.outputs.ev_files
resFeat = featModel.run()
print ">>>> creating fsf design files for " + model[
1] + "and run " + model[0]
# TODO: give mask here
glm = fsl.GLM(in_file=s.inputs.functional_runs[0],
design=resFeat.outputs.design_file,
output_type='NIFTI')
print ">>>> running glm for " + model[1] + "and run " + model[0]
resGlm = glm.run()
print ">>>> finished running glm for " + model[
1] + "and run " + model[0]
def create_indnet_workflow(hp_cutoff=100,
smoothing=5,
smm_threshold=0.5,
binarise_threshold=0.5,
melodic_seed=None,
aggr_aroma=False,
name="indnet"):
indnet = Workflow(name=name)
# Input node
inputspec = Node(utility.IdentityInterface(
fields=['anat_file', 'func_file', 'templates', 'networks']),
name='inputspec')
# T1 skullstrip
anat_bet = Node(fsl.BET(), name="anat_bet")
# EPI preprocessing
func_realignsmooth = create_featreg_preproc(highpass=False,
whichvol='first',
name='func_realignsmooth')
func_realignsmooth.inputs.inputspec.fwhm = smoothing
# Transform EPI to MNI space
func_2mni = create_reg_workflow(name='func_2mni')
func_2mni.inputs.inputspec.target_image = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
func_2mni.inputs.inputspec.target_image_brain = fsl.Info.standard_image(
'MNI152_T1_2mm_brain.nii.gz')
func_2mni.inputs.inputspec.config_file = 'T1_2_MNI152_2mm'
# Segmentation of T1
anat_segmentation = Node(fsl.FAST(output_biascorrected=True),
name='anat_segmentation')
# Transfrom segments to EPI space
segments_2func = create_segments_2func_workflow(
threshold=binarise_threshold, name='segments_2func')
# Transform templates to EPI space
templates_2func = create_templates_2func_workflow(
threshold=binarise_threshold, name='templates_2func')
# Mask network templates with GM
gm_mask_templates = MapNode(fsl.ImageMaths(op_string='-mul'),
iterfield=['in_file2'],
name='gm_mask_templates')
# Mask for ICA-AROMA and statistics
func_brainmask = Node(fsl.BET(frac=0.3,
mask=True,
no_output=True,
robust=True),
name='func_brainmask')
# Melodic ICA
if melodic_seed != None:
func_melodic = Node(fsl.MELODIC(args='--seed={}'.format(melodic_seed),
out_stats=True),
name='func_melodic')
# ICA-AROMA
func_aroma = Node(fsl.ICA_AROMA(), name='func_aroma')
if aggr_aroma:
func_aroma.inputs.denoise_type = 'aggr'
else:
func_aroma.inputs.denoise_type = 'nonaggr'
# Highpass filter ICA results
func_highpass = create_highpass_filter(cutoff=hp_cutoff,
name='func_highpass')
# Calculate mean CSF sgnal
csf_meansignal = Node(fsl.ImageMeants(), name='csf_meansignal')
# Calculate mean WM signal
wm_meansignal = Node(fsl.ImageMeants(), name='wm_meansignal')
# Calculate mean non-brain signal
nonbrain_meansignal = create_nonbrain_meansignal(
name='nonbrain_meansignal')
# Calculate first Eigenvariates
firsteigenvariates = MapNode(fsl.ImageMeants(show_all=True, eig=True),
iterfield=['mask'],
name='firsteigenvariates')
# Combine first eigenvariates and wm/csf/non-brain signals
regressors = Node(utility.Merge(4), name='regressors')
# z-transform regressors
ztransform = MapNode(Ztransform(),
iterfield=['in_file'],
name='ztransform')
# Create design matrix
designmatrix = Node(DesignMatrix(), name='designmatrix')
# Create contrasts
contrasts = Node(Contrasts(), name='contrasts')
# GLM
glm = Node(fsl.GLM(), name='glm')
glm.inputs.out_z_name = 'z_stats.nii.gz'
glm.inputs.demean = True
# Split z-maps
zmaps = Node(fsl.Split(), name='zmaps')
zmaps.inputs.dimension = 't'
# Spatial Mixture Modelling
smm = MapNode(fsl.SMM(), iterfield=['spatial_data_file'], name='smm')
# Transform probability maps to native (anat) space
actmaps_2anat = MapNode(fsl.ApplyXFM(),
iterfield=['in_file'],
name='actmaps_2anat')
# Transform probability maps to MNI space
actmaps_2mni = MapNode(fsl.ApplyWarp(),
iterfield=['in_file'],
name='actmaps_2mni')
actmaps_2mni.inputs.ref_file = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
# Create network masks in native (func) space
network_masks_func = create_network_masks_workflow(
name='network_masks_func', smm_threshold=smm_threshold)
# Create network masks in native (anat) space
network_masks_anat = create_network_masks_workflow(
name='network_masks_anat', smm_threshold=smm_threshold)
# Create network masks in MNI space
network_masks_mni = create_network_masks_workflow(
name='network_masks_mni', smm_threshold=smm_threshold)
# Output node
outputspec = Node(utility.IdentityInterface(fields=[
'network_masks_func_main', 'network_masks_func_exclusive',
'network_masks_anat_main', 'network_masks_anat_exclusive',
'network_masks_mni_main', 'network_masks_mni_exclusive',
'preprocessed_func_file', 'preprocessed_anat_file',
'motion_parameters', 'func2anat_transform', 'anat2mni_transform'
]),
name='outputspec')
# Helper functions
def get_first_item(x):
try:
return x[0]
except:
return x
def get_second_item(x):
return x[1]
def get_third_item(x):
return x[2]
def get_components(x):
return [y['components'] for y in x]
# Connect the nodes
# anat_bet
indnet.connect(inputspec, 'anat_file', anat_bet, 'in_file')
# func_realignsmooth
indnet.connect(inputspec, 'func_file', func_realignsmooth,
'inputspec.func')
# func_2mni
indnet.connect(func_realignsmooth,
('outputspec.smoothed_files', get_first_item), func_2mni,
'inputspec.source_files')
indnet.connect(inputspec, 'anat_file', func_2mni,
'inputspec.anatomical_image')
indnet.connect(func_realignsmooth, 'outputspec.reference', func_2mni,
'inputspec.mean_image')
# anat_segmentation
indnet.connect(anat_bet, 'out_file', anat_segmentation, 'in_files')
# segments_2func
indnet.connect(anat_segmentation, 'partial_volume_files', segments_2func,
'inputspec.segments')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', segments_2func,
'inputspec.premat')
indnet.connect(func_realignsmooth, 'outputspec.mean', segments_2func,
'inputspec.func_file')
# templates_2func
indnet.connect(func_realignsmooth, 'outputspec.mean', templates_2func,
'inputspec.func_file')
indnet.connect(func_2mni, 'outputspec.func2anat_transform',
templates_2func, 'inputspec.premat')
indnet.connect(func_2mni, 'outputspec.anat2target_transform',
templates_2func, 'inputspec.warp')
indnet.connect(inputspec, 'templates', templates_2func,
'inputspec.templates')
# gm_mask_templates
indnet.connect(segments_2func,
('outputspec.segments_2func_files', get_second_item),
gm_mask_templates, 'in_file')
indnet.connect(templates_2func, 'outputspec.templates_2func_files',
gm_mask_templates, 'in_file2')
# func_brainmask
indnet.connect(func_realignsmooth, 'outputspec.mean', func_brainmask,
'in_file')
# func_melodic
if melodic_seed != None:
indnet.connect(func_realignsmooth,
('outputspec.smoothed_files', get_first_item),
func_melodic, 'in_files')
indnet.connect(func_brainmask, 'mask_file', func_melodic, 'mask')
# func_aroma
indnet.connect(func_realignsmooth,
('outputspec.smoothed_files', get_first_item), func_aroma,
'in_file')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', func_aroma,
'mat_file')
indnet.connect(func_2mni, 'outputspec.anat2target_transform', func_aroma,
'fnirt_warp_file')
indnet.connect(func_realignsmooth,
('outputspec.motion_parameters', get_first_item),
func_aroma, 'motion_parameters')
indnet.connect(func_brainmask, 'mask_file', func_aroma, 'mask')
if melodic_seed != None:
indnet.connect(func_melodic, 'out_dir', func_aroma, 'melodic_dir')
# func_highpass
if aggr_aroma:
indnet.connect(func_aroma, 'aggr_denoised_file', func_highpass,
'inputspec.in_file')
else:
indnet.connect(func_aroma, 'nonaggr_denoised_file', func_highpass,
'inputspec.in_file')
# csf_meansignal
indnet.connect(segments_2func,
('outputspec.segments_2func_files', get_first_item),
csf_meansignal, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file', csf_meansignal,
'in_file')
# wm_meansignal
indnet.connect(segments_2func,
('outputspec.segments_2func_files', get_third_item),
wm_meansignal, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file', wm_meansignal,
'in_file')
# nonbrain_meansignal
indnet.connect(inputspec, 'func_file', nonbrain_meansignal,
'inputspec.func_file')
# firsteigenvariates
indnet.connect(gm_mask_templates, 'out_file', firsteigenvariates, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file',
firsteigenvariates, 'in_file')
# regressors
indnet.connect(firsteigenvariates, 'out_file', regressors, 'in1')
indnet.connect(wm_meansignal, 'out_file', regressors, 'in2')
indnet.connect(csf_meansignal, 'out_file', regressors, 'in3')
indnet.connect(nonbrain_meansignal, 'outputspec.nonbrain_regressor',
regressors, 'in4')
# ztransform
indnet.connect(regressors, 'out', ztransform, 'in_file')
# designmatrix
indnet.connect(ztransform, 'out_file', designmatrix, 'in_files')
# contrasts
indnet.connect(inputspec, ('networks', get_components), contrasts,
'in_list')
indnet.connect(designmatrix, 'out_file', contrasts, 'design')
# glm
indnet.connect(designmatrix, 'out_file', glm, 'design')
indnet.connect(contrasts, 'out_file', glm, 'contrasts')
indnet.connect(func_brainmask, 'mask_file', glm, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file', glm, 'in_file')
# zmaps
indnet.connect(glm, 'out_z', zmaps, 'in_file')
# smm
indnet.connect(zmaps, 'out_files', smm, 'spatial_data_file')
indnet.connect(func_brainmask, 'mask_file', smm, 'mask')
# actmaps_2anat
indnet.connect(smm, 'activation_p_map', actmaps_2anat, 'in_file')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', actmaps_2anat,
'in_matrix_file')
indnet.connect(anat_bet, 'out_file', actmaps_2anat, 'reference')
# actmaps_2mni
indnet.connect(smm, 'activation_p_map', actmaps_2mni, 'in_file')
indnet.connect(templates_2func, 'outputspec.func_2mni_warp', actmaps_2mni,
'field_file')
# network_masks_func
indnet.connect(smm, 'activation_p_map', network_masks_func,
'inputspec.actmaps')
indnet.connect(inputspec, 'networks', network_masks_func,
'inputspec.networks')
# network_masks_anat
indnet.connect(actmaps_2anat, 'out_file', network_masks_anat,
'inputspec.actmaps')
indnet.connect(inputspec, 'networks', network_masks_anat,
'inputspec.networks')
# network_masks_mni
indnet.connect(actmaps_2mni, 'out_file', network_masks_mni,
'inputspec.actmaps')
indnet.connect(inputspec, 'networks', network_masks_mni,
'inputspec.networks')
# output node
indnet.connect(network_masks_func, 'outputspec.main_masks', outputspec,
'network_masks_func_main')
indnet.connect(network_masks_func, 'outputspec.exclusive_masks',
outputspec, 'network_masks_func_exclusive')
indnet.connect(network_masks_anat, 'outputspec.main_masks', outputspec,
'network_masks_anat_main')
indnet.connect(network_masks_anat, 'outputspec.exclusive_masks',
outputspec, 'network_masks_anat_exclusive')
indnet.connect(network_masks_mni, 'outputspec.main_masks', outputspec,
'network_masks_mni_main')
indnet.connect(network_masks_mni, 'outputspec.exclusive_masks', outputspec,
'network_masks_mni_exclusive')
indnet.connect(func_highpass, 'outputspec.filtered_file', outputspec,
'preprocessed_func_file')
indnet.connect(anat_segmentation, 'restored_image', outputspec,
'preprocessed_anat_file')
indnet.connect(func_realignsmooth,
('outputspec.motion_parameters', get_first_item),
outputspec, 'motion_parameters')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', outputspec,
'func2anat_transform')
indnet.connect(func_2mni, 'outputspec.anat2target_transform', outputspec,
'anat2mni_transform')
return indnet
def init_seedbasedconnectivity_wf(workdir=None,
feature=None,
seed_files=None,
seed_spaces=None,
memcalc=MemoryCalculator()):
"""
create workflow to calculate seed connectivity maps
"""
if feature is not None:
name = f"{formatlikebids(feature.name)}_wf"
else:
name = "seedbasedconnectivity_wf"
workflow = pe.Workflow(name=name)
# input
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"tags",
"vals",
"metadata",
"bold",
"mask",
"confounds_selected",
"seed_names",
"seed_files",
"seed_spaces",
]),
name="inputnode",
)
outputnode = pe.Node(niu.IdentityInterface(fields=["resultdicts"]),
name="outputnode")
min_seed_coverage = 1
if feature is not None:
inputnode.inputs.seed_names = feature.seeds
if hasattr(feature, "min_seed_coverage"):
min_seed_coverage = feature.min_seed_coverage
if seed_files is not None:
inputnode.inputs.seed_files = seed_files
if seed_spaces is not None:
inputnode.inputs.seed_spaces = seed_spaces
#
statmaps = ["effect", "variance", "z", "dof", "mask"]
make_resultdicts = pe.Node(
MakeResultdicts(
tagkeys=["feature", "seed"],
imagekeys=[*statmaps, "design_matrix", "contrast_matrix"],
metadatakeys=["mean_t_s_n_r", "coverage"],
),
name="make_resultdicts",
)
if feature is not None:
make_resultdicts.inputs.feature = feature.name
workflow.connect(inputnode, "tags", make_resultdicts, "tags")
workflow.connect(inputnode, "vals", make_resultdicts, "vals")
workflow.connect(inputnode, "metadata", make_resultdicts, "metadata")
workflow.connect(inputnode, "mask", make_resultdicts, "mask")
workflow.connect(make_resultdicts, "resultdicts", outputnode,
"resultdicts")
#
resultdict_datasink = pe.Node(ResultdictDatasink(base_directory=workdir),
name="resultdict_datasink")
workflow.connect(make_resultdicts, "resultdicts", resultdict_datasink,
"indicts")
#
reference_dict = dict(reference_space=constants.reference_space,
reference_res=constants.reference_res)
resample = pe.MapNode(
Resample(interpolation="MultiLabel", **reference_dict),
name="resample",
iterfield=["input_image", "input_space"],
n_procs=config.nipype.omp_nthreads,
mem_gb=memcalc.series_std_gb,
)
workflow.connect(inputnode, "seed_files", resample, "input_image")
workflow.connect(inputnode, "seed_spaces", resample, "input_space")
# Delete zero voxels for the seeds
maskseeds = pe.Node(
MaskCoverage(keys=["names"], min_coverage=min_seed_coverage),
name="maskseeds",
mem_gb=memcalc.volume_std_gb,
)
workflow.connect(inputnode, "mask", maskseeds, "mask_file")
workflow.connect(inputnode, "seed_names", maskseeds, "names")
workflow.connect(resample, "output_image", maskseeds, "in_files")
workflow.connect(maskseeds, "names", make_resultdicts, "seed")
workflow.connect(maskseeds, "coverage", make_resultdicts, "coverage")
# calculate the mean time series of the region defined by each mask
meants = pe.MapNode(
fsl.ImageMeants(),
name="meants",
iterfield="mask",
mem_gb=memcalc.series_std_gb,
)
workflow.connect(inputnode, "bold", meants, "in_file")
workflow.connect(maskseeds, "out_files", meants, "mask")
#
design = pe.MapNode(MergeColumns(2),
iterfield=["in1", "column_names1"],
name="design")
workflow.connect(meants, "out_file", design, "in1")
workflow.connect(maskseeds, "names", design, "column_names1")
workflow.connect(inputnode, "confounds_selected", design, "in2")
workflow.connect(design, "out_with_header", make_resultdicts,
"design_matrix")
contrasts = pe.MapNode(
niu.Function(
input_names=["design_file"],
output_names=["out_with_header", "out_no_header"],
function=_contrasts,
),
iterfield="design_file",
name="contrasts",
)
workflow.connect(design, "out_with_header", contrasts, "design_file")
workflow.connect(contrasts, "out_with_header", make_resultdicts,
"contrast_matrix")
fillna = pe.MapNode(FillNA(), iterfield="in_tsv", name="fillna")
workflow.connect(design, "out_no_header", fillna, "in_tsv")
# calculate the regression of the mean time series
# onto the functional image.
# the result is the seed connectivity map
glm = pe.MapNode(
fsl.GLM(
out_file="beta.nii.gz",
out_cope="cope.nii.gz",
out_varcb_name="varcope.nii.gz",
out_z_name="zstat.nii.gz",
demean=True,
),
name="glm",
iterfield=["design", "contrasts"],
mem_gb=memcalc.series_std_gb * 5,
)
workflow.connect(inputnode, "bold", glm, "in_file")
workflow.connect(inputnode, "mask", glm, "mask")
workflow.connect(fillna, "out_no_header", glm, "design")
workflow.connect(contrasts, "out_no_header", glm, "contrasts")
# make dof volume
makedofvolume = pe.MapNode(MakeDofVolume(),
iterfield=["design"],
name="makedofvolume")
workflow.connect(inputnode, "bold", makedofvolume, "bold_file")
workflow.connect(fillna, "out_no_header", makedofvolume, "design")
workflow.connect(glm, "out_cope", make_resultdicts, "effect")
workflow.connect(glm, "out_varcb", make_resultdicts, "variance")
workflow.connect(glm, "out_z", make_resultdicts, "z")
workflow.connect(makedofvolume, "out_file", make_resultdicts, "dof")
#
tsnr = pe.Node(nac.TSNR(), name="tsnr", mem_gb=memcalc.series_std_gb)
workflow.connect(inputnode, "bold", tsnr, "in_file")
calcmean = pe.MapNode(CalcMean(),
iterfield="mask",
name="calcmean",
mem_gb=memcalc.series_std_gb)
workflow.connect(maskseeds, "out_files", calcmean, "mask")
workflow.connect(tsnr, "tsnr_file", calcmean, "in_file")
workflow.connect(calcmean, "mean", make_resultdicts, "mean_t_s_n_r")
return workflow
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 init_dualregression_wf(workdir=None,
feature=None,
map_files=None,
map_spaces=None,
memcalc=MemoryCalculator()):
"""
create a workflow to calculate dual regression for ICA seeds
"""
if feature is not None:
name = f"{formatlikebids(feature.name)}_wf"
else:
name = "dualregression_wf"
workflow = pe.Workflow(name=name)
# input
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"tags",
"vals",
"metadata",
"bold",
"mask",
"confounds_selected",
"map_names",
"map_files",
"map_spaces",
]),
name="inputnode",
)
outputnode = pe.Node(niu.IdentityInterface(fields=["resultdicts"]),
name="outputnode")
if feature is not None:
inputnode.inputs.map_names = feature.maps
if map_files is not None:
inputnode.inputs.map_files = map_files
if map_spaces is not None:
inputnode.inputs.map_spaces = map_spaces
#
statmaps = ["effect", "variance", "z", "dof", "mask"]
make_resultdicts_a = pe.Node(
MakeResultdicts(tagkeys=["feature", "map"],
imagekeys=["design_matrix", "contrast_matrix"]),
name="make_resultdicts_a",
)
if feature is not None:
make_resultdicts_a.inputs.feature = feature.name
workflow.connect(inputnode, "tags", make_resultdicts_a, "tags")
workflow.connect(inputnode, "vals", make_resultdicts_a, "vals")
workflow.connect(inputnode, "metadata", make_resultdicts_a, "metadata")
workflow.connect(inputnode, "map_names", make_resultdicts_a, "map")
make_resultdicts_b = pe.Node(
MakeResultdicts(
tagkeys=["feature", "map", "component"],
imagekeys=statmaps,
metadatakeys=["sources", "mean_t_s_n_r"],
),
name="make_resultdicts_b",
)
if feature is not None:
make_resultdicts_b.inputs.feature = feature.name
workflow.connect(inputnode, "tags", make_resultdicts_b, "tags")
workflow.connect(inputnode, "vals", make_resultdicts_b, "vals")
workflow.connect(inputnode, "metadata", make_resultdicts_b, "metadata")
workflow.connect(inputnode, "map_names", make_resultdicts_b, "map")
workflow.connect(inputnode, "mask", make_resultdicts_b, "mask")
workflow.connect(make_resultdicts_b, "resultdicts", outputnode,
"resultdicts")
#
merge_resultdicts = pe.Node(niu.Merge(2), name="merge_resultdicts")
workflow.connect(make_resultdicts_a, "resultdicts", merge_resultdicts,
"in1")
workflow.connect(make_resultdicts_b, "resultdicts", merge_resultdicts,
"in2")
resultdict_datasink = pe.Node(ResultdictDatasink(base_directory=workdir),
name="resultdict_datasink")
workflow.connect(merge_resultdicts, "out", resultdict_datasink, "indicts")
#
reference_dict = dict(reference_space=constants.reference_space,
reference_res=constants.reference_res)
resample = pe.MapNode(
Resample(interpolation="LanczosWindowedSinc", **reference_dict),
name="resample",
iterfield=["input_image", "input_space"],
n_procs=config.nipype.omp_nthreads,
mem_gb=memcalc.series_std_gb,
)
workflow.connect(inputnode, "map_files", resample, "input_image")
workflow.connect(inputnode, "map_spaces", resample, "input_space")
# Delete zero voxels for the maps
applymask = pe.MapNode(
fsl.ApplyMask(),
name="applymask",
iterfield="in_file",
mem_gb=memcalc.volume_std_gb,
)
workflow.connect(inputnode, "mask", applymask, "mask_file")
workflow.connect(resample, "output_image", applymask, "in_file")
# first step, calculate spatial regression of ICA components on to the
# bold file
spatialglm = pe.MapNode(
fsl.GLM(out_file="beta", demean=True),
name="spatialglm",
iterfield="design",
mem_gb=memcalc.series_std_gb * 5,
)
workflow.connect(applymask, "out_file", spatialglm, "design")
workflow.connect(inputnode, "bold", spatialglm, "in_file")
workflow.connect(inputnode, "mask", spatialglm, "mask")
# second step, calculate the temporal regression of the time series
# from the first step on to the bold file
contrasts = pe.MapNode(
niu.Function(
input_names=["map_timeseries_file", "confounds_file"],
output_names=[
"out_with_header", "out_no_header", "map_component_names"
],
function=_contrasts,
),
iterfield="map_timeseries_file",
name="contrasts",
)
workflow.connect(spatialglm, "out_file", contrasts, "map_timeseries_file")
workflow.connect(inputnode, "confounds_selected", contrasts,
"confounds_file")
workflow.connect(contrasts, "out_with_header", make_resultdicts_a,
"contrast_matrix")
workflow.connect(contrasts, "map_component_names", make_resultdicts_b,
"component")
design = pe.MapNode(MergeColumns(2),
iterfield=["in1", "column_names1"],
name="design")
workflow.connect(spatialglm, "out_file", design, "in1")
workflow.connect(contrasts, "map_component_names", design, "column_names1")
workflow.connect(inputnode, "confounds_selected", design, "in2")
workflow.connect(design, "out_with_header", make_resultdicts_a,
"design_matrix")
fillna = pe.MapNode(FillNA(), iterfield="in_tsv", name="fillna")
workflow.connect(design, "out_no_header", fillna, "in_tsv")
temporalglm = pe.MapNode(
fsl.GLM(
out_file="beta.nii.gz",
out_cope="cope.nii.gz",
out_varcb_name="varcope.nii.gz",
out_z_name="zstat.nii.gz",
demean=True,
),
name="temporalglm",
iterfield=["design", "contrasts"],
mem_gb=memcalc.series_std_gb * 5,
)
workflow.connect(inputnode, "bold", temporalglm, "in_file")
workflow.connect(inputnode, "mask", temporalglm, "mask")
workflow.connect(fillna, "out_no_header", temporalglm, "design")
workflow.connect(contrasts, "out_no_header", temporalglm, "contrasts")
# make dof volume
makedofvolume = pe.MapNode(
MakeDofVolume(),
iterfield=["design"],
name="makedofvolume",
)
workflow.connect(inputnode, "bold", makedofvolume, "bold_file")
workflow.connect(fillna, "out_no_header", makedofvolume, "design")
for glmattr, resultattr in (("cope", "effect"), ("varcb", "variance"),
("z", "z")):
split = pe.MapNode(fsl.Split(dimension="t"),
iterfield="in_file",
name=f"split{resultattr}images")
workflow.connect(temporalglm, f"out_{glmattr}", split, "in_file")
workflow.connect(split, "out_files", make_resultdicts_b, resultattr)
workflow.connect(makedofvolume, "out_file", make_resultdicts_b, "dof")
#
tsnr = pe.Node(nac.TSNR(), name="tsnr", mem_gb=memcalc.series_std_gb)
workflow.connect(inputnode, "bold", tsnr, "in_file")
maxintensity = pe.MapNode(MaxIntensity(),
iterfield="in_file",
name="maxintensity",
mem_gb=memcalc.series_std_gb)
workflow.connect(resample, "output_image", maxintensity, "in_file")
calcmean = pe.MapNode(CalcMean(),
iterfield="parcellation",
name="calcmean",
mem_gb=memcalc.series_std_gb)
workflow.connect(maxintensity, "out_file", calcmean, "parcellation")
workflow.connect(tsnr, "tsnr_file", calcmean, "in_file")
workflow.connect(calcmean, "mean", make_resultdicts_b, "mean_t_s_n_r")
return workflow
def rest_noise_filter_wf(wf_name='rest_noise_removal'):
""" Create a resting-state fMRI noise removal node.
Nipype Inputs
-------------
rest_noise_input.in_file
rest_noise_input.brain_mask
rest_noise_input.wm_mask
rest_noise_input.csf_mask
rest_noise_input.motion_params
Nipy motion parameters.
Nipype Outputs
--------------
rest_noise_output.tsnr_file
A SNR estimation volume file for QA purposes.
rest_noise_output.motion_corrected
The fMRI motion corrected image.
rest_noise_output.nuis_corrected
The resulting nuisance corrected image.
This will be the same as 'motion_corrected' if compcor
is disabled.
rest_noise_output.motion_regressors
Motion regressors file.
rest_noise_output.compcor_regressors
CompCor regressors file.
rest_noise_output.art_displacement_files
One image file containing the voxel-displacement timeseries.
rest_noise_output.art_intensity_files
One file containing the global intensity values determined
from the brainmask.
rest_noise_output.art_norm_files
One file containing the composite norm.
rest_noise_output.art_outlier_files
One file containing a list of 0-based indices corresponding
to outlier volumes.
rest_noise_output.art_plot_files
One image file containing the detected outliers.
rest_noise_output.art_statistic_files
One file containing information about the different types of
artifacts and if design info is provided then details of
stimulus correlated motion and a listing or artifacts by
event type.
Returns
-------
rm_nuisance_wf: nipype Workflow
"""
# Create the workflow object
wf = pe.Workflow(name=wf_name)
in_fields = [
"in_file",
"brain_mask",
"wm_mask",
"csf_mask",
"motion_params",
]
out_fields = [
"tsnr_file",
"motion_corrected",
"nuis_corrected",
"motion_regressors",
"compcor_regressors",
"gsr_regressors",
"art_displacement_files",
"art_intensity_files",
"art_norm_files",
"art_outlier_files",
"art_plot_files",
"art_statistic_files",
]
# input identities
rest_noise_input = setup_node(IdentityInterface(fields=in_fields,
mandatory_inputs=True),
name="rest_noise_input")
# get the settings for filters
filters = _get_params_for('rest_filter')
# Compute TSNR on realigned data regressing polynomial up to order 2
tsnr = setup_node(TSNR(regress_poly=2), name='tsnr')
# 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 = setup_node(rapidart_fmri_artifact_detection(),
name="detect_artifacts")
# Compute motion regressors
motion_regs = setup_node(Function(
input_names=[
'motion_params',
'order',
'derivatives',
],
output_names=['out_files'],
function=motion_regressors,
),
name='motion_regressors')
# Create a filter to remove motion and art confounds
motart_pars = setup_node(Function(
input_names=['motion_params', 'comp_norm', 'outliers', 'detrend_poly'],
output_names=['out_files'],
function=create_regressors),
name='motart_parameters')
motion_filter = setup_node(fsl.GLM(out_f_name='F_mcart.nii.gz',
out_pf_name='pF_mcart.nii.gz',
demean=True),
name='motion_filter')
# Noise confound regressors
compcor_pars = setup_node(Function(
input_names=[
'realigned_file', 'mask_file', 'num_components', 'extra_regressors'
],
output_names=['out_files'],
function=extract_noise_components,
),
name='compcor_pars')
#compcor_pars = setup_node(ACompCor(), name='compcor_pars')
#compcor_pars.inputs.components_file = 'noise_components.txt'
compcor_filter = setup_node(fsl.GLM(out_f_name='F.nii.gz',
out_pf_name='pF.nii.gz',
demean=True),
name='compcor_filter')
# Global signal regression
gsr_pars = setup_node(Function(
input_names=[
'realigned_file', 'mask_file', 'num_components', 'extra_regressors'
],
output_names=['out_files'],
function=extract_noise_components,
),
name='gsr_pars')
gsr_filter = setup_node(fsl.GLM(out_f_name='F_gsr.nii.gz',
out_pf_name='pF_gsr.nii.gz',
demean=True),
name='gsr_filter')
# output identities
rest_noise_output = setup_node(IdentityInterface(fields=out_fields,
mandatory_inputs=True),
name="rest_noise_output")
# Connect the nodes
wf.connect([
# tsnr
(rest_noise_input, tsnr, [("in_file", "in_file")]),
# artifact detection
(rest_noise_input, art, [
("in_file", "realigned_files"),
("motion_params", "realignment_parameters"),
("brain_mask", "mask_file"),
]),
# calculte motion regressors
(rest_noise_input, motion_regs, [("motion_params", "motion_params")]),
# create motion and confound regressors parameters file
(art, motart_pars, [
("norm_files", "comp_norm"),
("outlier_files", "outliers"),
]),
(motion_regs, motart_pars, [("out_files", "motion_params")]),
# motion filtering
(rest_noise_input, motion_filter, [
("in_file", "in_file"),
(("in_file", rename, "_filtermotart"), "out_res_name"),
]),
(motart_pars, motion_filter, [(("out_files", selectindex, [0]),
"design")]),
# output
(tsnr, rest_noise_output, [("tsnr_file", "tsnr_file")]),
(motart_pars, rest_noise_output, [("out_files", "motion_regressors")]),
(motion_filter, rest_noise_output, [("out_res", "motion_corrected")]),
(art, rest_noise_output, [
("displacement_files", "art_displacement_files"),
("intensity_files", "art_intensity_files"),
("norm_files", "art_norm_files"),
("outlier_files", "art_outlier_files"),
("plot_files", "art_plot_files"),
("statistic_files", "art_statistic_files"),
]),
])
last_filter = motion_filter
# compcor filter
if filters['compcor_csf'] or filters['compcor_wm']:
wf.connect([
# calculate compcor regressor and parameters file
(motart_pars, compcor_pars, [
(("out_files", selectindex, [0]), "extra_regressors"),
]),
(motion_filter, compcor_pars, [
("out_res", "realigned_file"),
]),
# the compcor filter
(motion_filter, compcor_filter, [
("out_res", "in_file"),
(("out_res", rename, "_cleaned"), "out_res_name"),
]),
(compcor_pars, compcor_filter, [(("out_files", selectindex, [0]),
"design")]),
#(compcor_pars, compcor_filter, [("components_file", "design")]),
(rest_noise_input, compcor_filter, [("brain_mask", "mask")]),
# output
(compcor_pars, rest_noise_output, [("out_files",
"compcor_regressors")]),
#(compcor_pars, rest_noise_output, [("components_file", "compcor_regressors")]),
])
last_filter = compcor_filter
# global signal regression
if filters['gsr']:
wf.connect([
# calculate gsr regressors parameters file
(last_filter, gsr_pars, [("out_res", "realigned_file")]),
(rest_noise_input, gsr_pars, [("brain_mask", "mask_file")]),
# the output file name
(rest_noise_input, gsr_filter, [("brain_mask", "mask")]),
(last_filter, gsr_filter, [
("out_res", "in_file"),
(("out_res", rename, "_gsr"), "out_res_name"),
]),
(gsr_pars, gsr_filter, [(("out_files", selectindex, [0]), "design")
]),
# output
(gsr_pars, rest_noise_output, [("out_files", "gsr_regressors")]),
])
last_filter = gsr_filter
# connect the final nuisance correction output node
wf.connect([
(last_filter, rest_noise_output, [("out_res", "nuis_corrected")]),
])
if filters['compcor_csf'] and filters['compcor_wm']:
mask_merge = setup_node(Merge(2), name="mask_merge")
wf.connect([
## the mask for the compcor filter
(rest_noise_input, mask_merge, [("wm_mask", "in1")]),
(rest_noise_input, mask_merge, [("csf_mask", "in2")]),
(mask_merge, compcor_pars, [("out", "mask_file")]),
])
elif filters['compcor_csf']:
wf.connect([
## the mask for the compcor filter
(rest_noise_input, compcor_pars, [("csf_mask", "mask_file")]),
])
elif filters['compcor_wm']:
wf.connect([
## the mask for the compcor filter
(rest_noise_input, compcor_pars, [("wm_mask", "mask_file")]),
])
return wf
def create_workflow(func_runs,
subject_id,
subjects_dir,
fwhm,
slice_times,
highpass_frequency,
lowpass_frequency,
TR,
sink_directory,
use_fsl_bp,
num_components,
whichvol,
name='wmaze'):
wf = pe.Workflow(name=name)
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run'],
outfields=['func']),
name='datasource')
datasource.inputs.subject_id = subject_id
datasource.inputs.run = func_runs
datasource.inputs.template = '/home/data/madlab/data/mri/wmaze/%s/rsfmri/rest_run%03d/rest.nii.gz'
datasource.inputs.sort_filelist = True
# Rename files in case they are named identically
name_unique = pe.MapNode(util.Rename(format_string='wmaze_rest_%(run)02d'),
iterfield=['in_file', 'run'],
name='rename')
name_unique.inputs.keep_ext = True
name_unique.inputs.run = func_runs
wf.connect(datasource, 'func', name_unique, 'in_file')
# Define the outputs for the preprocessing workflow
output_fields = [
'reference', 'motion_parameters', 'motion_parameters_plusDerivs',
'motionandoutlier_noise_file', 'noise_components', 'realigned_files',
'motion_plots', 'mask_file', 'smoothed_files', 'reg_file', 'reg_cost',
'reg_fsl_file', 'artnorm_files', 'artoutlier_files',
'artdisplacement_files', 'tsnr_file'
]
outputnode = pe.Node(util.IdentityInterface(fields=output_fields),
name='outputspec')
# Convert functional images to float representation
img2float = pe.MapNode(fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
wf.connect(name_unique, 'out_file', img2float, 'in_file')
# Run AFNI's despike. This is always run, however, whether this is fed to
# realign depends on the input configuration
despiker = pe.MapNode(afni.Despike(outputtype='NIFTI_GZ'),
iterfield=['in_file'],
name='despike')
num_threads = 4
despiker.inputs.environ = {'OMP_NUM_THREADS': '%d' % num_threads}
despiker.plugin_args = {'bsub_args': '-n %d' % num_threads}
despiker.plugin_args = {'bsub_args': '-R "span[hosts=1]"'}
wf.connect(img2float, 'out_file', despiker, 'in_file')
# Extract the first volume of the first run as the reference
extractref = pe.Node(fsl.ExtractROI(t_size=1),
iterfield=['in_file'],
name="extractref")
wf.connect(despiker, ('out_file', pickfirst), extractref, 'in_file')
wf.connect(despiker, ('out_file', pickvol, 0, whichvol), extractref,
't_min')
wf.connect(extractref, 'roi_file', outputnode, 'reference')
if slice_times is not None:
# Simultaneous motion and slice timing correction with Nipy algorithm
motion_correct = pe.Node(nipy.SpaceTimeRealigner(),
name='motion_correct')
motion_correct.inputs.tr = TR
motion_correct.inputs.slice_times = slice_times
motion_correct.inputs.slice_info = 2
motion_correct.plugin_args = {
'bsub_args': '-n %s' % os.environ['OMP_NUM_THREADS']
}
motion_correct.plugin_args = {'bsub_args': '-R "span[hosts=1]"'}
wf.connect(despiker, 'out_file', motion_correct, 'in_file')
wf.connect(motion_correct, 'par_file', outputnode, 'motion_parameters')
wf.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
else:
# Motion correct functional runs to the reference (1st volume of 1st run)
motion_correct = pe.MapNode(fsl.MCFLIRT(save_mats=True,
save_plots=True,
interpolation='sinc'),
name='motion_correct',
iterfield=['in_file'])
wf.connect(despiker, 'out_file', motion_correct, 'in_file')
wf.connect(extractref, 'roi_file', motion_correct, 'ref_file')
wf.connect(motion_correct, 'par_file', outputnode, 'motion_parameters')
wf.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
# Compute TSNR on realigned data regressing polynomials upto order 2
tsnr = pe.MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(motion_correct, 'out_file', tsnr, 'in_file')
wf.connect(tsnr, 'tsnr_file', outputnode, 'tsnr_file')
# Plot the estimated motion parameters
plot_motion = pe.MapNode(fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
wf.connect(motion_correct, 'par_file', plot_motion, 'in_file')
wf.connect(plot_motion, 'out_file', outputnode, 'motion_plots')
# Register a source file to fs space and create a brain mask in source space
fssource = pe.Node(nio.FreeSurferSource(), name='fssource')
fssource.inputs.subject_id = subject_id
fssource.inputs.subjects_dir = subjects_dir
# Extract aparc+aseg brain mask and binarize
fs_threshold = pe.Node(fs.Binarize(min=0.5, out_type='nii'),
name='fs_threshold')
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), fs_threshold,
'in_file')
# Calculate the transformation matrix from EPI space to FreeSurfer space
# using the BBRegister command
fs_register = pe.MapNode(fs.BBRegister(init='fsl'),
iterfield=['source_file'],
name='fs_register')
fs_register.inputs.contrast_type = 't2'
fs_register.inputs.out_fsl_file = True
fs_register.inputs.subject_id = subject_id
fs_register.inputs.subjects_dir = subjects_dir
wf.connect(extractref, 'roi_file', fs_register, 'source_file')
wf.connect(fs_register, 'out_reg_file', outputnode, 'reg_file')
wf.connect(fs_register, 'min_cost_file', outputnode, 'reg_cost')
wf.connect(fs_register, 'out_fsl_file', outputnode, 'reg_fsl_file')
# Extract wm+csf, brain masks by eroding freesurfer lables
wmcsf = pe.MapNode(fs.Binarize(),
iterfield=['match', 'binary_file', 'erode'],
name='wmcsfmask')
#wmcsf.inputs.wm_ven_csf = True
wmcsf.inputs.match = [[2, 41], [4, 5, 14, 15, 24, 31, 43, 44, 63]]
wmcsf.inputs.binary_file = ['wm.nii.gz', 'csf.nii.gz']
wmcsf.inputs.erode = [2, 2] #int(np.ceil(slice_thickness))
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), wmcsf, 'in_file')
# Now transform the wm and csf masks to 1st volume of 1st run
wmcsftransform = pe.MapNode(fs.ApplyVolTransform(inverse=True,
interp='nearest'),
iterfield=['target_file'],
name='wmcsftransform')
wmcsftransform.inputs.subjects_dir = subjects_dir
wf.connect(extractref, 'roi_file', wmcsftransform, 'source_file')
wf.connect(fs_register, ('out_reg_file', pickfirst), wmcsftransform,
'reg_file')
wf.connect(wmcsf, 'binary_file', wmcsftransform, 'target_file')
# Transform the binarized aparc+aseg file to the 1st volume of 1st run space
fs_voltransform = pe.MapNode(fs.ApplyVolTransform(inverse=True),
iterfield=['source_file', 'reg_file'],
name='fs_transform')
fs_voltransform.inputs.subjects_dir = subjects_dir
wf.connect(extractref, 'roi_file', fs_voltransform, 'source_file')
wf.connect(fs_register, 'out_reg_file', fs_voltransform, 'reg_file')
wf.connect(fs_threshold, 'binary_file', fs_voltransform, 'target_file')
# Dilate the binarized mask by 1 voxel that is now in the EPI space
fs_threshold2 = pe.MapNode(fs.Binarize(min=0.5, out_type='nii'),
iterfield=['in_file'],
name='fs_threshold2')
fs_threshold2.inputs.dilate = 1
wf.connect(fs_voltransform, 'transformed_file', fs_threshold2, 'in_file')
wf.connect(fs_threshold2, ('binary_file', pickfirst), outputnode,
'mask_file')
# Use RapidART to detect motion/intensity outliers
art = pe.MapNode(ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
zintensity_threshold=3,
norm_threshold=1,
bound_by_brainmask=True,
mask_type="file"),
iterfield=["realignment_parameters", "realigned_files"],
name="art")
if slice_times is not None:
art.inputs.parameter_source = "NiPy"
else:
art.inputs.parameter_source = "FSL"
wf.connect(motion_correct, 'par_file', art, 'realignment_parameters')
wf.connect(motion_correct, 'out_file', art, 'realigned_files')
wf.connect(fs_threshold2, ('binary_file', pickfirst), art, 'mask_file')
wf.connect(art, 'norm_files', outputnode, 'artnorm_files')
wf.connect(art, 'outlier_files', outputnode, 'artoutlier_files')
wf.connect(art, 'displacement_files', outputnode, 'artdisplacement_files')
# Compute motion regressors (save file with 1st and 2nd derivatives)
motreg = pe.Node(util.Function(
input_names=['motion_params', 'order', 'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(motion_correct, 'par_file', motreg, 'motion_params')
wf.connect(motreg, 'out_files', outputnode, 'motion_parameters_plusDerivs')
# Create a filter text file to remove motion (+ derivatives), art confounds,
# and 1st, 2nd, and 3rd order legendre polynomials.
createfilter1 = pe.Node(util.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 = 3
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
wf.connect(createfilter1, 'out_files', outputnode,
'motionandoutlier_noise_file')
filter1 = pe.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(motion_correct, 'out_file', filter1, 'in_file')
wf.connect(motion_correct, ('out_file', rename, '_filtermotart'), filter1,
'out_res_name')
wf.connect(createfilter1, 'out_files', filter1, 'design')
# Create a filter to remove noise components based on white matter and CSF
createfilter2 = pe.MapNode(
util.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(motion_correct, 'out_file', createfilter2, 'realigned_file')
wf.connect(wmcsftransform, 'transformed_file', createfilter2, 'mask_file')
wf.connect(createfilter2, 'out_files', outputnode, 'noise_components')
filter2 = pe.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, 'out_files', filter2, 'design')
wf.connect(fs_threshold2, ('binary_file', pickfirst), filter2, 'mask')
# Band-pass filter the timeseries
if use_fsl_bp == 'True':
determine_bp_sigmas = pe.Node(util.Function(
input_names=['tr', 'highpass_freq', 'lowpass_freq'],
output_names=['out_sigmas'],
function=calc_fslbp_sigmas),
name='determine_bp_sigmas')
determine_bp_sigmas.inputs.tr = float(TR)
determine_bp_sigmas.inputs.highpass_freq = float(highpass_frequency)
determine_bp_sigmas.inputs.lowpass_freq = float(lowpass_frequency)
bandpass = pe.MapNode(fsl.ImageMaths(suffix='_tempfilt'),
iterfield=["in_file"],
name="bandpass")
wf.connect(determine_bp_sigmas, ('out_sigmas', highpass_operand),
bandpass, 'op_string')
wf.connect(filter2, 'out_res', bandpass, 'in_file')
wf.connect(bandpass, 'out_file', outputnode, 'bandpassed_files')
else:
bandpass = pe.Node(util.Function(
input_names=['files', 'lowpass_freq', 'highpass_freq', 'fs'],
output_names=['out_files'],
function=bandpass_filter,
imports=imports),
name='bandpass')
bandpass.inputs.fs = 1. / TR
if highpass_frequency < 0:
bandpass.inputs.highpass_freq = -1
else:
bandpass.inputs.highpass_freq = highpass_frequency
if lowpass_frequency < 0:
bandpass.inputs.lowpass_freq = -1
else:
bandpass.inputs.lowpass_freq = lowpass_frequency
wf.connect(filter2, 'out_res', bandpass, 'files')
wf.connect(bandpass, 'out_files', outputnode, 'bandpassed_files')
# Smooth each run using SUSAn with the brightness threshold set to 75%
# of the median value for each run and a mask constituting the mean functional
smooth_median = pe.MapNode(fsl.ImageStats(op_string='-k %s -p 50'),
iterfield=['in_file'],
name='smooth_median')
wf.connect(motion_correct, 'out_file', smooth_median, 'in_file')
wf.connect(fs_threshold2, ('binary_file', pickfirst), smooth_median,
'mask_file')
smooth_meanfunc = pe.MapNode(fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='smooth_meanfunc')
wf.connect(motion_correct, 'out_file', smooth_meanfunc, 'in_file')
smooth_merge = pe.Node(util.Merge(2, axis='hstack'), name='smooth_merge')
wf.connect(smooth_meanfunc, 'out_file', smooth_merge, 'in1')
wf.connect(smooth_median, 'out_stat', smooth_merge, 'in2')
smooth = pe.MapNode(fsl.SUSAN(),
iterfield=['in_file', 'brightness_threshold', 'usans'],
name='smooth')
smooth.inputs.fwhm = fwhm
wf.connect(bandpass, 'out_file', smooth, 'in_file')
wf.connect(smooth_median, ('out_stat', getbtthresh), smooth,
'brightness_threshold')
wf.connect(smooth_merge, ('out', getusans), smooth, 'usans')
wf.connect(smooth, 'smoothed_file', outputnode, 'smoothed_files')
# Save the relevant data into an output directory
datasink = pe.Node(nio.DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
wf.connect(outputnode, 'reference', datasink, 'wmaze_rest.ref')
wf.connect(outputnode, 'motion_parameters', datasink, 'wmaze_rest.motion')
wf.connect(outputnode, 'realigned_files', datasink,
'wmaze_rest.func.realigned')
wf.connect(outputnode, 'motion_plots', datasink,
'wmaze_rest.motion.@plots')
wf.connect(outputnode, 'mask_file', datasink, 'wmaze_rest.ref.@mask')
wf.connect(outputnode, 'smoothed_files', datasink,
'wmaze_rest.func.smoothed_bandpassed')
wf.connect(outputnode, 'reg_file', datasink, 'wmaze_rest.bbreg.@reg')
wf.connect(outputnode, 'reg_cost', datasink, 'wmaze_rest.bbreg.@cost')
wf.connect(outputnode, 'reg_fsl_file', datasink,
'wmaze_rest.bbreg.@regfsl')
wf.connect(outputnode, 'artnorm_files', datasink,
'wmaze_rest.art.@norm_files')
wf.connect(outputnode, 'artoutlier_files', datasink,
'wmaze_rest.art.@outlier_files')
wf.connect(outputnode, 'artdisplacement_files', datasink,
'wmaze_rest.art.@displacement_files')
wf.connect(outputnode, 'motion_parameters_plusDerivs', datasink,
'wmaze_rest.noise.@motionplusDerivs')
wf.connect(outputnode, 'motionandoutlier_noise_file', datasink,
'wmaze_rest.noise.@motionplusoutliers')
wf.connect(outputnode, 'noise_components', datasink, 'wmaze_rest.compcor')
wf.connect(outputnode, 'tsnr_file', datasink, 'wmaze_rest.tsnr')
return wf