def create_confound_extraction_workflow(name="confounds", wm_components=6):
"""Extract nuisance variables from anatomical sources."""
inputnode = Node(IdentityInterface(["timeseries", "brain_mask", "reg_file", "subject_id"]), "inputs")
# Find the subject's Freesurfer segmentation
# Grab the Freesurfer aparc+aseg file as an anatomical brain mask
getaseg = Node(
io.SelectFiles({"aseg": "{subject_id}/mri/aseg.mgz"}, base_directory=os.environ["SUBJECTS_DIR"]), "getaseg"
)
# Select and erode the white matter to get deep voxels
selectwm = Node(fs.Binarize(erode=3, wm=True), "selectwm")
# Transform the mask into functional space
transform = MapNode(fs.ApplyVolTransform(inverse=True, interp="nearest"), ["reg_file", "source_file"], "transform")
# Extract eigenvariates of the timeseries from WM and whole brain
extract = MapNode(ExtractConfounds(n_components=wm_components), ["timeseries", "brain_mask", "wm_mask"], "extract")
outputnode = Node(IdentityInterface(["confound_file"]), "outputs")
confounds = Workflow(name)
confounds.connect(
[
(inputnode, getaseg, [("subject_id", "subject_id")]),
(getaseg, selectwm, [("aseg", "in_file")]),
(selectwm, transform, [("binary_file", "target_file")]),
(inputnode, transform, [("reg_file", "reg_file"), ("timeseries", "source_file")]),
(transform, extract, [("transformed_file", "wm_mask")]),
(inputnode, extract, [("timeseries", "timeseries"), ("brain_mask", "brain_mask")]),
(extract, outputnode, [("out_file", "confound_file")]),
]
)
return confounds
def create_reg_workflow(name="reg", space="mni", regtype="model"):
"""Flexibly register files into one of several common spaces."""
if regtype == "model":
fields = ["copes", "varcopes", "ss_files"]
elif regtype == "timeseries":
fields = ["timeseries"]
fields.extend(["masks", "affines"])
if space == "mni":
fields.append("warpfield")
inputnode = Node(IdentityInterface(fields), "inputnode")
func = globals()["%s_%s_transform" % (space, regtype)]
transform = Node(Function(fields, ["out_files"],
func, imports),
"transform")
regflow = Workflow(name=name)
outputnode = Node(IdentityInterface(["out_files"]), "outputnode")
for field in fields:
regflow.connect(inputnode, field, transform, field)
regflow.connect(transform, "out_files", outputnode, "out_files")
return regflow, inputnode, outputnode
def create_bbregister_workflow(name="bbregister",
contrast_type="t2",
partial_brain=False):
"""Find a linear transformation to align the EPI file with the anatomy."""
in_fields = ["subject_id", "source_file"]
if partial_brain:
in_fields.append("whole_brain_template")
inputnode = Node(IdentityInterface(in_fields), "inputs")
# Estimate the registration to Freesurfer conformed space
func2anat = MapNode(fs.BBRegister(contrast_type=contrast_type,
init="fsl",
epi_mask=True,
registered_file=True,
out_reg_file="func2anat_tkreg.dat",
out_fsl_file="func2anat_flirt.mat"),
"source_file",
"func2anat")
# Make an image for quality control on the registration
report = MapNode(Function(["subject_id", "in_file"],
["out_file"],
write_coreg_plot,
imports),
"in_file",
"coreg_report")
# Define the workflow outputs
outputnode = Node(IdentityInterface(["tkreg_mat", "flirt_mat", "report"]),
"outputs")
bbregister = Workflow(name=name)
# Connect the registration
bbregister.connect([
(inputnode, func2anat,
[("subject_id", "subject_id"),
("source_file", "source_file")]),
(inputnode, report,
[("subject_id", "subject_id")]),
(func2anat, report,
[("registered_file", "in_file")]),
(func2anat, outputnode,
[("out_reg_file", "tkreg_mat")]),
(func2anat, outputnode,
[("out_fsl_file", "flirt_mat")]),
(report, outputnode,
[("out_file", "report")]),
])
# Possibly connect the full_fov image
if partial_brain:
bbregister.connect([
(inputnode, func2anat,
[("whole_brain_template", "intermediate_file")]),
])
return bbregister
def create_surface_projection_workflow(name="surfproj", exp_info=None):
"""Project the group mask and thresholded zstat file onto the surface."""
if exp_info is None:
exp_info = lyman.default_experiment_parameters()
inputnode = Node(IdentityInterface(["zstat_file", "mask_file"]), "inputs")
# Sample the zstat image to the surface
hemisource = Node(IdentityInterface(["mni_hemi"]), "hemisource")
hemisource.iterables = ("mni_hemi", ["lh", "rh"])
zstatproj = Node(freesurfer.SampleToSurface(
sampling_method=exp_info["sampling_method"],
sampling_range=exp_info["sampling_range"],
sampling_units=exp_info["sampling_units"],
smooth_surf=exp_info["surf_smooth"],
subject_id="fsaverage",
mni152reg=True,
target_subject="fsaverage"),
"zstatproj")
# Sample the mask to the surface
maskproj = Node(freesurfer.SampleToSurface(
sampling_range=exp_info["sampling_range"],
sampling_units=exp_info["sampling_units"],
subject_id="fsaverage",
mni152reg=True,
target_subject="fsaverage"),
"maskproj")
if exp_info["sampling_method"] == "point":
maskproj.inputs.sampling_method = "point"
else:
maskproj.inputs.sampling_method = "max"
outputnode = Node(IdentityInterface(["surf_zstat",
"surf_mask"]), "outputs")
# Define and connect the workflow
proj = Workflow(name)
proj.connect([
(inputnode, zstatproj,
[("zstat_file", "source_file")]),
(inputnode, maskproj,
[("mask_file", "source_file")]),
(hemisource, zstatproj,
[("mni_hemi", "hemi")]),
(hemisource, maskproj,
[("mni_hemi", "hemi")]),
(zstatproj, outputnode,
[("out_file", "surf_zstat")]),
(maskproj, outputnode,
[("out_file", "surf_mask")]),
])
return proj
def test_serial_input(tmpdir):
tmpdir.chdir()
wd = os.getcwd()
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1, 2, 3]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.add_nodes([n1])
# set local check
w1.config['execution'] = {'stop_on_first_crash': 'true',
'local_hash_check': 'true',
'crashdump_dir': wd,
'poll_sleep_duration': 2}
# test output of num_subnodes method when serial is default (False)
assert n1.num_subnodes() == len(n1.inputs.in1)
# test running the workflow on default conditions
w1.run(plugin='MultiProc')
# test output of num_subnodes method when serial is True
n1._serial = True
assert n1.num_subnodes() == 1
# test running the workflow on serial conditions
w1.run(plugin='MultiProc')
def create_bbregister_workflow(name="bbregister", contrast_type="t2", partial_brain=False, init_with="fsl"):
"""Find a linear transformation to align the EPI file with the anatomy."""
in_fields = ["subject_id", "timeseries"]
if partial_brain:
in_fields.append("whole_brain_template")
inputnode = Node(IdentityInterface(in_fields), "inputs")
# Take the mean over time to get a target volume
meanvol = MapNode(fsl.MeanImage(), "in_file", "meanvol")
# Do a rough skullstrip using BET
skullstrip = MapNode(fsl.BET(), "in_file", "bet")
# Estimate the registration to Freesurfer conformed space
func2anat = MapNode(
fs.BBRegister(
contrast_type=contrast_type,
init=init_with,
epi_mask=True,
registered_file=True,
out_reg_file="func2anat_tkreg.dat",
out_fsl_file="func2anat_flirt.mat",
),
"source_file",
"func2anat",
)
# Make an image for quality control on the registration
report = MapNode(CoregReport(), "in_file", "coreg_report")
# Define the workflow outputs
outputnode = Node(IdentityInterface(["tkreg_mat", "flirt_mat", "report"]), "outputs")
bbregister = Workflow(name=name)
# Connect the registration
bbregister.connect(
[
(inputnode, func2anat, [("subject_id", "subject_id")]),
(inputnode, report, [("subject_id", "subject_id")]),
(inputnode, meanvol, [("timeseries", "in_file")]),
(meanvol, skullstrip, [("out_file", "in_file")]),
(skullstrip, func2anat, [("out_file", "source_file")]),
(func2anat, report, [("registered_file", "in_file")]),
(func2anat, outputnode, [("out_reg_file", "tkreg_mat")]),
(func2anat, outputnode, [("out_fsl_file", "flirt_mat")]),
(report, outputnode, [("out_file", "report")]),
]
)
# Possibly connect the full_fov image
if partial_brain:
bbregister.connect([(inputnode, func2anat, [("whole_brain_template", "intermediate_file")])])
return bbregister
def create_filtering_workflow(name="filter",
hpf_cutoff=128,
TR=2,
output_name="timeseries"):
"""Scale and high-pass filter the timeseries."""
inputnode = Node(IdentityInterface(["timeseries", "mask_file"]),
"inputs")
# Grand-median scale within the brain mask
scale = MapNode(ScaleTimeseries(statistic="median", target=10000),
["in_file", "mask_file"],
"scale")
# Gaussian running-line filter
hpf_sigma = (hpf_cutoff / 2.0) / TR
filter = MapNode(fsl.TemporalFilter(highpass_sigma=hpf_sigma),
"in_file",
"filter")
# Possibly replace the mean
# (In later versions of FSL, the highpass filter removes the
# mean component. Put it back, but be flexible so this isn't
# broken on older versions of FSL).
replacemean = MapNode(ReplaceMean(output_name=output_name),
["orig_file", "filtered_file"],
"replacemean")
# Compute a final mean functional volume
meanfunc = MapNode(fsl.MeanImage(out_file="mean_func.nii.gz"),
"in_file", "meanfunc")
outputnode = Node(IdentityInterface(["timeseries",
"mean_file"]), "outputs")
filtering = Workflow(name)
filtering.connect([
(inputnode, scale,
[("timeseries", "in_file"),
("mask_file", "mask_file")]),
(scale, filter,
[("out_file", "in_file")]),
(scale, replacemean,
[("out_file", "orig_file")]),
(filter, replacemean,
[("out_file", "filtered_file")]),
(replacemean, meanfunc,
[("out_file", "in_file")]),
(replacemean, outputnode,
[("out_file", "timeseries")]),
(meanfunc, outputnode,
[("out_file", "mean_file")]),
])
return filtering
def workflow_spec(name="{workflow_name}", exp_info=None):
"""Return a Nipype workflow for MR processing.
Parameters
----------
name : string
workflow object name
exp_info : dict
dictionary with experimental information
"""
workflow = Workflow(name)
if exp_info is None:
exp_info = fitz.default_experiment_parameters()
# Define the inputs for the preprocessing workflow
in_fields = [""] # "timeseries"]
inputnode = Node(IdentityInterface(in_fields), "inputs")
"""
# Define Actual Nipype Nodes, Workflows, etc.
# e.g. The start of an example SPM preproc workflow
# --------------------------------------------------
slicetiming = pe.Node(interface=spm.SliceTiming(), name="slicetiming")
slicetiming.inputs.ref_slice = 1
realign = pe.Node(interface=spm.Realign(), name="realign")
realign.inputs.register_to_mean = True
"""
workflow.connect([
"""
(inputnode, slicetiming,
[('timeseries', 'in_files')]),
(slicetiming, realign,
[('timecorrected_files', 'in_files')]),
"""
])
output_fields = [""] # realigned_files", "realignment_parameters"]
outputnode = Node(IdentityInterface(output_fields), "outputs")
workflow.connect([
"""
(realign, outputnode,
[("realigned_files", "realigned_files"),
("realignment_parameters", "realignment_parameters")]),
"""
])
# Return the workflow itself and input and output nodes.
return workflow, inputnode, outputnode
def test_execute(self, lyman_dir, execdir):
info = frontend.info(lyman_dir=lyman_dir)
def f(x):
return x ** 2
assert f(2) == 4
n1 = Node(Function("x", "y", f), "n1")
n2 = Node(Function("x", "y", f), "n2")
wf = Workflow("test", base_dir=info.cache_dir)
wf.connect(n1, "y", n2, "x")
wf.inputs.n1.x = 2
cache_dir = execdir.join("cache").join("test")
class args(object):
graph = False
n_procs = 1
debug = False
clear_cache = True
execute = True
frontend.execute(wf, args, info)
assert not cache_dir.exists()
args.debug = True
frontend.execute(wf, args, info)
assert cache_dir.exists()
args.debug = False
info.remove_cache = False
frontend.execute(wf, args, info)
assert cache_dir.exists()
args.execute = False
res = frontend.execute(wf, args, info)
assert res is None
args.execute = True
fname = str(execdir.join("graph").join("workflow.dot"))
args.graph = fname
res = frontend.execute(wf, args, info)
assert res == fname[:-4] + ".svg"
args.graph = True
args.stage = "preproc"
res = frontend.execute(wf, args, info)
assert res == cache_dir.join("preproc.svg")
def create_unwarp_workflow(name="unwarp", fieldmap_pe=("y", "y-")):
"""Unwarp functional timeseries using reverse phase-blipped images."""
inputnode = Node(IdentityInterface(["timeseries", "fieldmap"]), "inputs")
# Calculate the shift field
# Note that setting readout_times to 1 will give a fine
# map of the field, but the units will be off
# Since we don't write out the map of the field itself, it does
# not seem worth it to add another parameter for the readout times.
# (It does require that they are the same, but when wouldn't they be?)
topup = MapNode(
fsl.TOPUP(encoding_direction=fieldmap_pe, readout_times=[1] * len(fieldmap_pe)), ["in_file"], "topup"
)
# Unwarp the timeseries
applytopup = MapNode(
fsl.ApplyTOPUP(method="jac", in_index=[1]),
["in_files", "in_topup_fieldcoef", "in_topup_movpar", "encoding_file"],
"applytopup",
)
# Make a figure summarize the unwarping
report = MapNode(UnwarpReport(), ["orig_file", "corrected_file"], "unwarp_report")
# Define the outputs
outputnode = Node(IdentityInterface(["timeseries", "report"]), "outputs")
# Define and connect the workflow
unwarp = Workflow(name)
unwarp.connect(
[
(inputnode, topup, [("fieldmap", "in_file")]),
(inputnode, applytopup, [("timeseries", "in_files")]),
(
topup,
applytopup,
[
("out_fieldcoef", "in_topup_fieldcoef"),
("out_movpar", "in_topup_movpar"),
("out_enc_file", "encoding_file"),
],
),
(inputnode, report, [("fieldmap", "orig_file")]),
(topup, report, [("out_corrected", "corrected_file")]),
(applytopup, outputnode, [("out_corrected", "timeseries")]),
(report, outputnode, [("out_file", "report")]),
]
)
return unwarp
def create_reg_workflow(name="reg", space="mni",
regtype="model", method="fsl",
residual=False, cross_exp=False):
"""Flexibly register files into one of several common spaces."""
# Define the input fields flexibly
if regtype == "model":
fields = ["copes", "varcopes", "sumsquares"]
elif regtype == "timeseries":
fields = ["timeseries"]
if cross_exp:
fields.extend(["first_rigid"])
fields.extend(["means", "masks", "rigids"])
if space == "mni":
fields.extend(["affine", "warpfield"])
else:
fields.extend(["tkreg_rigid"])
inputnode = Node(IdentityInterface(fields), "inputnode")
# Grap the correct interface class dynamically
interface_name = "{}{}Registration".format(space.upper(),
regtype.capitalize())
reg_interface = globals()[interface_name]
transform = Node(reg_interface(method=method), "transform")
# Sanity check on inputs
if regtype == "model" and residual:
raise ValueError("residual and regtype=model does not make sense")
# Set the kind of timeseries
if residual:
transform.inputs.residual = True
outputnode = Node(IdentityInterface(["out_files"]), "outputnode")
# Define the workflow
regflow = Workflow(name=name)
# Connect the inputs programatically
for field in fields:
regflow.connect(inputnode, field, transform, field)
# The transform node only ever has one output
regflow.connect(transform, "out_files", outputnode, "out_files")
return regflow, inputnode, outputnode
def make_simple_workflow():
wf = Workflow(name="test")
node1 = Node(IdentityInterface(fields=["foo"]), name="node1")
node2 = MapNode(IdentityInterface(fields=["foo"]),
name="node2", iterfield=["foo"])
node3 = Node(IdentityInterface(fields=["foo"]), name="node3")
wf.connect([
(node1, node2, [("foo", "foo")]),
(node2, node3, [("foo", "foo")]),
])
return wf, node1, node2, node3
def test_serial_input():
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1, 2, 3]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.add_nodes([n1])
# set local check
w1.config['execution'] = {'stop_on_first_crash': 'true',
'local_hash_check': 'true',
'crashdump_dir': wd,
'poll_sleep_duration': 2}
# test output of num_subnodes method when serial is default (False)
yield assert_equal, n1.num_subnodes(), len(n1.inputs.in1)
# test running the workflow on default conditions
error_raised = False
try:
w1.run(plugin='MultiProc')
except Exception as e:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_false, error_raised
# test output of num_subnodes method when serial is True
n1._serial = True
yield assert_equal, n1.num_subnodes(), 1
# test running the workflow on serial conditions
error_raised = False
try:
w1.run(plugin='MultiProc')
except Exception as e:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_false, error_raised
os.chdir(cwd)
rmtree(wd)
def create_realignment_workflow(name="realignment", temporal_interp=True, TR=2, slice_order="up", interleaved=True):
"""Motion and slice-time correct the timeseries and summarize."""
inputnode = Node(IdentityInterface(["timeseries"]), "inputs")
# Get the middle volume of each run for motion correction
extractref = MapNode(ExtractRealignmentTarget(), "in_file", "extractref")
# Motion correct to middle volume of each run
mcflirt = MapNode(
fsl.MCFLIRT(cost="normcorr", interpolation="spline", save_mats=True, save_rms=True, save_plots=True),
["in_file", "ref_file"],
"mcflirt",
)
# Optionally emoporally interpolate to correct for slice time differences
if temporal_interp:
slicetime = MapNode(fsl.SliceTimer(time_repetition=TR), "in_file", "slicetime")
if slice_order == "down":
slicetime.inputs.index_dir = True
elif slice_order != "up":
raise ValueError("slice_order must be 'up' or 'down'")
if interleaved:
slicetime.inputs.interleaved = True
# Generate a report on the motion correction
mcreport = MapNode(RealignmentReport(), ["target_file", "realign_params", "displace_params"], "mcreport")
# Define the outputs
outputnode = Node(IdentityInterface(["timeseries", "example_func", "report", "motion_file"]), "outputs")
# Define and connect the sub workflow
realignment = Workflow(name)
realignment.connect(
[
(inputnode, extractref, [("timeseries", "in_file")]),
(inputnode, mcflirt, [("timeseries", "in_file")]),
(extractref, mcflirt, [("out_file", "ref_file")]),
(extractref, mcreport, [("out_file", "target_file")]),
(mcflirt, mcreport, [("par_file", "realign_params"), ("rms_files", "displace_params")]),
(extractref, outputnode, [("out_file", "example_func")]),
(mcreport, outputnode, [("realign_report", "report"), ("motion_file", "motion_file")]),
]
)
if temporal_interp:
realignment.connect(
[
(mcflirt, slicetime, [("out_file", "in_file")]),
(slicetime, outputnode, [("slice_time_corrected_file", "timeseries")]),
]
)
else:
realignment.connect([(mcflirt, outputnode, [("out_file", "timeseries")])])
return realignment
def create_filtering_workflow(name="filter",
hpf_cutoff=128,
TR=2,
output_name="timeseries"):
"""Scale and high-pass filter the timeseries."""
inputnode = Node(IdentityInterface(["timeseries", "mask_file"]),
"inputs")
# Grand-median scale within the brain mask
scale = MapNode(Function(["in_file",
"mask_file"],
["out_file"],
scale_timeseries,
imports),
["in_file", "mask_file"],
"scale")
# Gaussian running-line filter
hpf_sigma = (hpf_cutoff / 2.0) / TR
filter = MapNode(fsl.TemporalFilter(highpass_sigma=hpf_sigma,
out_file=output_name + ".nii.gz"),
"in_file",
"filter")
outputnode = Node(IdentityInterface(["timeseries"]), "outputs")
filtering = Workflow(name)
filtering.connect([
(inputnode, scale,
[("timeseries", "in_file"),
("mask_file", "mask_file")]),
(scale, filter,
[("out_file", "in_file")]),
(filter, outputnode,
[("out_file", "timeseries")]),
])
return filtering
def create_workflow_to_resample_baw_files(name="ResampleBAWOutputs"):
"""
This function...
:param name:
:return:
"""
workflow = Workflow(name)
inputs_to_resample = ["t1_file", "t2_file", "hncma_file", "abc_file"]
other_inputs = ["reference_file", "acpc_transform"]
label_maps = ["hncma_file", "abc_file"]
input_spec = Node(
IdentityInterface(inputs_to_resample + other_inputs), name="input_spec"
)
output_spec = Node(IdentityInterface(inputs_to_resample), name="output_spec")
for input in inputs_to_resample:
node = Node(BRAINSResample(), "Resample_{0}".format(input))
node.inputs.pixelType = "short"
node.inputs.inverseTransform = True
node.inputs.outputVolume = input + ".nii.gz"
if input in label_maps:
node.inputs.interpolationMode = "NearestNeighbor"
workflow.connect(
[
(
input_spec,
node,
[
("reference_file", "referenceVolume"),
("acpc_transform", "warpTransform"),
("{0}".format(input), "inputVolume"),
],
),
(node, output_spec, [("outputVolume", "{0}".format(input))]),
]
)
return workflow
def workflow_spec(name="onset", exp_info=None):
# Default experiment parameters
if exp_info is None:
exp_info = fitz.default_experiment_parameters
# Define constant inputs
inputs = ["design_file"]
# Define the workflow inputs
inputnode = Node(IdentityInterface(inputs), "inputs")
onsetsetup = Node(OnsetSetup(), "onsetsetup")
onsetsetup.inputs.exp_info = exp_info
onsetsetup.inputs.conditions = exp_info['conditions']
onsetsetup.inputs.condition_col = exp_info['condition_col']
onsetsetup.inputs.duration_col = exp_info['duration_col']
onsetsetup.inputs.onset_col = exp_info['onset_col']
onsetsetup.inputs.run_col = exp_info['run_col']
onsetsetup.inputs.pmod_cols = exp_info['pmod_cols']
onsetsetup.inputs.pmod_conditions = exp_info['pmod_conditions']
onsetsetup.inputs.concatenate_runs = exp_info['concatenate_runs']
# Define the workflow outputs
outputnode = Node(IdentityInterface(["design_mats"]),
"outputs")
# Define the workflow and connect the nodes
onsetFlow = Workflow(name=name)
onsetFlow.connect([
(inputnode, onsetsetup,
[("design_file", "design_file")]),
(onsetsetup, outputnode,
[("design_mats", "design_mats")])
])
return onsetFlow, inputnode, outputnode
def create_workflow_to_mask_white_matter(name):
"""
This function...
:param name:
:return:
"""
workflow = Workflow(name)
input_spec = create_identity_interface_node(["t1_file", "white"], "input_spec")
mask_white_matter = Node(Mesh2Mask(), "MaskWhiteMatter")
mask_white_matter.inputs.output_image = "white.nii.gz"
workflow.connect(input_spec, "white", mask_white_matter, "input_mesh")
workflow.connect(input_spec, "t1_file", mask_white_matter, "input_image")
output_spec = create_identity_interface_node(["white_mask"], "output_spec")
workflow.connect(mask_white_matter, "output_image", output_spec, "white_mask")
return workflow
if delete_tmp_files is None:
os.remove(tck_file)
return output_file
convertNode = Node(Function(input_names = ['tck_file', 'image_file', 'output_file', 'delete_tmp_files'],
output_names = ['output_file'],
function = convert2trk),
name = 'tck2trk')
# ### Define the workflow
# In[16]:
wf = Workflow('MRTRIX_tracking')
wf.connect([
(inputNode, trackingNode, [('spherical_harmonics_image', 'in_file'),
('seedmask', 'seed_file'),
('targetmask', 'include_file'),
('wmmask_1mm', 'mask_file'),
('seed_count', 'desired_number_of_tracks'),
(('tracks_dir', fileNameBuild, 'seedmask'), 'out_file')]),
(trackingNode, convertNode, [('tracked', 'tck_file')]),
(inputNode, convertNode, [('seedmask', 'image_file'),
(('tracks_dir', fileNameBuildTRK, 'seedmask'), 'output_file')]),
(convertNode, outputNode, [('output_file', 'tck_file')])
])
def create_fs_reg_workflow(name="registration"):
"""Create a FEAT preprocessing workflow together with freesurfer
Parameters
----------
::
name : name of workflow (default: 'registration')
Inputs::
inputspec.source_files : files (filename or list of filenames to register)
inputspec.mean_image : reference image to use
inputspec.target_image : registration target
Outputs::
outputspec.func2anat_transform : FLIRT transform
outputspec.anat2target_transform : FLIRT+FNIRT transform
outputspec.transformed_files : transformed files in target space
outputspec.transformed_mean : mean image in target space
Example
-------
"""
register = Workflow(name=name)
inputnode = Node(
interface=IdentityInterface(
fields=["source_files", "mean_image", "subject_id", "subjects_dir", "target_image"]
),
name="inputspec",
)
outputnode = Node(
interface=IdentityInterface(
fields=[
"func2anat_transform",
"out_reg_file",
"anat2target_transform",
"transforms",
"transformed_mean",
"transformed_files",
"min_cost_file",
"anat2target",
"aparc",
"mean2anat_mask",
]
),
name="outputspec",
)
# Get the subject's freesurfer source directory
fssource = Node(FreeSurferSource(), name="fssource")
fssource.run_without_submitting = True
register.connect(inputnode, "subject_id", fssource, "subject_id")
register.connect(inputnode, "subjects_dir", fssource, "subjects_dir")
convert = Node(freesurfer.MRIConvert(out_type="nii"), name="convert")
register.connect(fssource, "T1", convert, "in_file")
# Coregister the median to the surface
bbregister = Node(freesurfer.BBRegister(registered_file=True), name="bbregister")
bbregister.inputs.init = "fsl"
bbregister.inputs.contrast_type = "t2"
bbregister.inputs.out_fsl_file = True
bbregister.inputs.epi_mask = True
register.connect(inputnode, "subject_id", bbregister, "subject_id")
register.connect(inputnode, "mean_image", bbregister, "source_file")
register.connect(inputnode, "subjects_dir", bbregister, "subjects_dir")
# Create a mask of the median coregistered to the anatomical image
mean2anat_mask = Node(fsl.BET(mask=True), name="mean2anat_mask")
register.connect(bbregister, "registered_file", mean2anat_mask, "in_file")
"""
use aparc+aseg's brain mask
"""
binarize = Node(fs.Binarize(min=0.5, out_type="nii.gz", dilate=1), name="binarize_aparc")
register.connect(fssource, ("aparc_aseg", get_aparc_aseg), binarize, "in_file")
stripper = Node(fsl.ApplyMask(), name="stripper")
register.connect(binarize, "binary_file", stripper, "mask_file")
register.connect(convert, "out_file", stripper, "in_file")
"""
Apply inverse transform to aparc file
"""
aparcxfm = Node(freesurfer.ApplyVolTransform(inverse=True, interp="nearest"), name="aparc_inverse_transform")
register.connect(inputnode, "subjects_dir", aparcxfm, "subjects_dir")
register.connect(bbregister, "out_reg_file", aparcxfm, "reg_file")
register.connect(fssource, ("aparc_aseg", get_aparc_aseg), aparcxfm, "target_file")
register.connect(inputnode, "mean_image", aparcxfm, "source_file")
"""
Convert the BBRegister transformation to ANTS ITK format
"""
convert2itk = Node(C3dAffineTool(), name="convert2itk")
convert2itk.inputs.fsl2ras = True
convert2itk.inputs.itk_transform = True
register.connect(bbregister, "out_fsl_file", convert2itk, "transform_file")
register.connect(inputnode, "mean_image", convert2itk, "source_file")
register.connect(stripper, "out_file", convert2itk, "reference_file")
"""
Compute registration between the subject's structural and MNI template
This is currently set to perform a very quick registration. However, the
registration can be made significantly more accurate for cortical
structures by increasing the number of iterations
All parameters are set using the example from:
#https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh
"""
reg = Node(ants.Registration(), name="antsRegister")
reg.inputs.output_transform_prefix = "output_"
reg.inputs.transforms = ["Rigid", "Affine", "SyN"]
reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.2, 3.0, 0.0)]
reg.inputs.number_of_iterations = [[10000, 11110, 11110]] * 2 + [[100, 30, 20]]
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = True
reg.inputs.initial_moving_transform_com = True
reg.inputs.metric = ["Mattes"] * 2 + [["Mattes", "CC"]]
reg.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
reg.inputs.sampling_strategy = ["Regular"] * 2 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
reg.inputs.convergence_threshold = [1.0e-8] * 2 + [-0.01]
reg.inputs.convergence_window_size = [20] * 2 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ["vox"] * 3
reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 3
reg.inputs.use_histogram_matching = [False] * 2 + [True]
reg.inputs.winsorize_lower_quantile = 0.005
reg.inputs.winsorize_upper_quantile = 0.995
reg.inputs.args = "--float"
reg.inputs.output_warped_image = "output_warped_image.nii.gz"
reg.inputs.num_threads = 4
reg.plugin_args = {"qsub_args": "-pe orte 4", "sbatch_args": "--mem=6G -c 4"}
register.connect(stripper, "out_file", reg, "moving_image")
register.connect(inputnode, "target_image", reg, "fixed_image")
"""
Concatenate the affine and ants transforms into a list
"""
pickfirst = lambda x: x[0]
merge = Node(Merge(2), iterfield=["in2"], name="mergexfm")
register.connect(convert2itk, "itk_transform", merge, "in2")
register.connect(reg, ("composite_transform", pickfirst), merge, "in1")
"""
Transform the mean image. First to anatomical and then to target
"""
warpmean = Node(ants.ApplyTransforms(), name="warpmean")
warpmean.inputs.input_image_type = 0
warpmean.inputs.interpolation = "Linear"
warpmean.inputs.invert_transform_flags = [False, False]
warpmean.inputs.terminal_output = "file"
warpmean.inputs.args = "--float"
# warpmean.inputs.num_threads = 4
# warpmean.plugin_args = {'sbatch_args': '--mem=4G -c 4'}
"""
Transform the remaining images. First to anatomical and then to target
"""
warpall = pe.MapNode(ants.ApplyTransforms(), iterfield=["input_image"], name="warpall")
warpall.inputs.input_image_type = 0
warpall.inputs.interpolation = "Linear"
warpall.inputs.invert_transform_flags = [False, False]
warpall.inputs.terminal_output = "file"
warpall.inputs.args = "--float"
warpall.inputs.num_threads = 2
warpall.plugin_args = {"sbatch_args": "--mem=6G -c 2"}
"""
Assign all the output files
"""
register.connect(warpmean, "output_image", outputnode, "transformed_mean")
register.connect(warpall, "output_image", outputnode, "transformed_files")
register.connect(inputnode, "target_image", warpmean, "reference_image")
register.connect(inputnode, "mean_image", warpmean, "input_image")
register.connect(merge, "out", warpmean, "transforms")
register.connect(inputnode, "target_image", warpall, "reference_image")
register.connect(inputnode, "source_files", warpall, "input_image")
register.connect(merge, "out", warpall, "transforms")
"""
Assign all the output files
"""
register.connect(reg, "warped_image", outputnode, "anat2target")
register.connect(aparcxfm, "transformed_file", outputnode, "aparc")
register.connect(bbregister, "out_fsl_file", outputnode, "func2anat_transform")
register.connect(bbregister, "out_reg_file", outputnode, "out_reg_file")
register.connect(bbregister, "min_cost_file", outputnode, "min_cost_file")
register.connect(mean2anat_mask, "mask_file", outputnode, "mean2anat_mask")
register.connect(reg, "composite_transform", outputnode, "anat2target_transform")
register.connect(merge, "out", outputnode, "transforms")
return register
def prep(zfrqs, dummies=0, pca_retain=0, name='CEST_prep'):
inputnode = Node(IdentityInterface(fields=['zspec_file', 'ref_file']),
name='inputnode')
outputnode = Node(IdentityInterface(
fields=['zspec_file', 'f0_map', 'mask_file', 'ref_file', 'DS', 'MT']),
name='outputnode')
moco = Node(MCFLIRT(cost='mutualinfo', mean_vol=True), name='moco')
mask = Node(BET(mask=True, no_output=True), name='mask')
if (dummies > 0):
ref_index = dummies - 1
zspec_select = Node(Select(volumes=list(range(dummies, len(zfrqs))),
out_file='zspec.nii.gz'),
name='zspec_select')
zfrqs = np.array(zfrqs[dummies:])
else:
ref_index = 0
zfrqs = np.array(zfrqs)
zspec_ref = Node(Select(volumes=[
ref_index,
], out_file='reference.nii.gz'),
name='zspec_ref')
zspec_norm = Node(ImageMaths(op_string='-div', out_file='zspec.nii.gz'),
name='zspec_norm')
f0_indices = (np.abs(zfrqs) > 7) | (np.abs(zfrqs) < 1.1)
sat_frqs = zfrqs[f0_indices]
sat_angles = np.repeat(180.0, len(f0_indices))
f0_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(),
out_file='background_zspec.nii.gz'),
name='f0_select')
sequence = {
'MTSat': {
'pulse': {
'p1': 0.4,
'p2': 0.3,
'bandwidth': 0.39
},
'Trf': 0.02,
'TR': 4,
'FA': 5,
'sat_f0': sat_frqs.tolist(),
'sat_angle': sat_angles.tolist()
}
}
two_pools = [{
'name': 'DS',
'df0': [0, -2.5, 2.5],
'fwhm': [1.0, 1.e-6, 3.0],
'A': [0.2, 1.e-3, 1.0],
'use_bandwidth': True
}, {
'name': 'MT',
'df0': [-2.5, -5.0, -0.5],
'fwhm': [50.0, 35.0, 200.0],
'A': [0.3, 1.e-3, 1.0]
}]
f0_fit = Node(Lorentzian(sequence=sequence, pools=two_pools, verbose=True),
name='f0_fit')
out_frqs = np.sort(zfrqs)
f0_correct = Node(ZSpec(in_freqs=zfrqs.tolist(),
out_freqs=out_frqs.tolist(),
verbose=True),
name='f0_correct')
prep = Workflow(name=name)
prep.connect([(inputnode, moco, [('zspec_file', 'in_file'),
('ref_file', 'ref_file')]),
(moco, zspec_ref, [('out_file', 'in_file')]),
(moco, mask, [('mean_img', 'in_file')]),
(zspec_ref, zspec_norm, [('out_file', 'in_file2')]),
(zspec_norm, f0_select, [('out_file', 'in_file')]),
(f0_select, f0_fit, [('out_file', 'in_file')]),
(mask, f0_fit, [('mask_file', 'mask_file')]),
(zspec_norm, f0_correct, [('out_file', 'in_file')]),
(f0_fit, f0_correct, [('DS_f0', 'f0_map')]),
(mask, f0_correct, [('mask_file', 'mask_file')]),
(moco, outputnode, [('mean_img', 'ref_file')]),
(mask, outputnode, [('out_file', 'mask_file')]),
(f0_fit, outputnode, [('DS_f0', 'f0_map'), ('DS_A', 'DS'),
('MT_A', 'MT')])])
if (dummies > 0):
prep.connect([(moco, zspec_select, [('out_file', 'in_file')]),
(zspec_select, zspec_norm, [('out_file', 'in_file')])])
else:
prep.connect([(moco, zspec_norm, [('out_file', 'in_file')])])
if pca_retain > 0:
f0_pca = Node(PCA(retain=pca_retain, projections_file='proj.nii.gz'),
name='f0_pca')
prep.connect([(f0_correct, f0_pca, [('out_file', 'in_file')]),
(f0_pca, outputnode, [('out_file', 'zspec_file')])])
else:
prep.connect([(f0_correct, outputnode, [('out_file', 'zspec_file')])])
return (prep, out_frqs)
def run_bianca_wf(masterfile,
out_dir,
wd_dir,
crash_dir,
df,
training_subject_idx,
query_subject_idx,
name="bianca",
n_cpu=4,
save_classifier=False,
trained_classifier_file=None):
"""
:param masterfile: str
:param out_dir:
:param wd_dir:
:param crash_dir:
:param df: df
:param training_subject_idx: training_subject_idx: list of ints, python-style 0-based; training subjects in df
:param query_subject_idx: list of ints, python-style 0-based; querysubjects in df
:param name:
:param n_cpu:
:param save_classifier: bool
:param trained_classifier_file: file previously saved with save_classifier; if given, training subjects
are ignored and classifier file is used in prediction
:return: None
"""
if save_classifier and trained_classifier_file:
raise RuntimeError(
"save_classifier and trained_classifier_file cannot be set at the same time"
)
if trained_classifier_file:
trained_classifier_file = str(trained_classifier_file)
#####
# masterfile information
expected_header = [
'flair', 't1w', 'manual_mask', 'mat', 'subject', 'session'
]
assert df.columns.tolist(
) == expected_header, f"masterfile columns are off. columns should be \
{expected_header} but are {df.columns}"
featuresubset = "1,2"
brainmaskfeaturenum = "2"
labelfeaturenum = "3"
matfeaturenum = "4"
######
# workflow
wf = Workflow(name=name)
######
# subject info
inputnode = Node(niu.IdentityInterface(fields=['query_subject_idx']),
name='inputnode')
inputnode.iterables = [("query_subject_idx", query_subject_idx)]
inputnode.synchronize = True
def get_query_info_fnc(df, query_subject_idx):
def get_subjects_info(df, idx):
return df.iloc[idx].subject.tolist()[0], df.iloc[
idx].session.tolist()[0], df.iloc[idx].flair.tolist()[0]
query_subject, query_session, query_flair = get_subjects_info(
df, [query_subject_idx])
query_subject_num = query_subject_idx + 1
return query_subject, query_session, query_flair, query_subject_num
query_info = Node(niu.Function(input_names=["df", "query_subject_idx"],
output_names=[
'query_subject', 'query_session',
'query_flair', 'query_subject_num'
],
function=get_query_info_fnc),
name="query_info")
query_info.inputs.df = df
wf.connect(inputnode, "query_subject_idx", query_info, "query_subject_idx")
def get_training_info_fnc(df, query_subject_idx, training_subject_idx):
import numpy as np
training_subject_idx_clean = training_subject_idx.tolist()
if query_subject_idx in training_subject_idx_clean:
training_subject_idx_clean.remove(query_subject_idx)
training_subjects = df.iloc[training_subject_idx_clean].subject.tolist(
)
training_sessions = df.iloc[training_subject_idx_clean].session.tolist(
)
training_subject_nums_str = ",".join(
(np.array(training_subject_idx_clean) + 1).astype(str).tolist())
return training_subject_idx_clean, training_subject_nums_str, training_subjects, training_sessions
training_info = Node(niu.Function(
input_names=["df", "query_subject_idx", "training_subject_idx"],
output_names=[
"training_subject_idx", "training_subject_nums_str",
"training_subjects", "training_sessions"
],
function=get_training_info_fnc),
name="training_info")
training_info.inputs.df = df
training_info.inputs.training_subject_idx = training_subject_idx
wf.connect(inputnode, "query_subject_idx", training_info,
"query_subject_idx")
bianca = Node(BIANCA(), name="bianca")
bianca.inputs.masterfile = str(masterfile)
bianca.inputs.featuresubset = featuresubset
bianca.inputs.brainmaskfeaturenum = brainmaskfeaturenum
bianca.inputs.matfeaturenum = matfeaturenum
bianca.inputs.save_classifier = save_classifier
wf.connect(query_info, "query_subject_num", bianca, "querysubjectnum")
if trained_classifier_file:
bianca.inputs.trained_classifier_file = trained_classifier_file
else:
bianca.inputs.labelfeaturenum = labelfeaturenum
wf.connect(training_info, "training_subject_nums_str", bianca,
"trainingnums")
def classifier_info_fct(masterfile,
query_subject,
query_session,
query_flair,
training_subjects=None,
training_sessions=None,
classifier_file=None):
d = {
"masterfile": str(masterfile),
"query_subject_session": [query_subject, query_session],
"query_flair": query_flair,
}
if training_subjects:
d["training_subjects_sessions"] = list(
zip(training_subjects, training_sessions))
else:
d["classifier_file"] = classifier_file
return d
classifier_info = Node(niu.Function(input_names=[
"masterfile", "query_subject", "query_session", "query_flair",
"training_subjects", "training_sessions", "classifier_file"
],
output_names=["meta_dict"],
function=classifier_info_fct),
name="classifier_info")
classifier_info.inputs.masterfile = masterfile
wf.connect(query_info, "query_subject", classifier_info, "query_subject")
wf.connect(query_info, "query_session", classifier_info, "query_session")
wf.connect(query_info, "query_flair", classifier_info, "query_flair")
if trained_classifier_file:
classifier_info.inputs.classifier_file = trained_classifier_file
else:
wf.connect(training_info, "training_subjects", classifier_info,
"training_subjects")
wf.connect(training_info, "training_sessions", classifier_info,
"training_sessions")
ds = Node(DerivativesDataSink(base_directory=str(out_dir.parent),
out_path_base=str(out_dir.name)),
name="ds")
ds.inputs.suffix = "LPM"
wf.connect(bianca, "out_file", ds, "in_file")
wf.connect(query_info, "query_flair", ds, "source_file")
wf.connect(classifier_info, "meta_dict", ds, "meta_dict")
if save_classifier:
ds_clf = Node(DerivativesDataSink(base_directory=str(out_dir.parent),
out_path_base=str(out_dir.name)),
name="ds_clf")
ds_clf.inputs.suffix = "classifier"
wf.connect(bianca, "classifier_file", ds_clf, "in_file")
wf.connect(query_info, "query_flair", ds_clf, "source_file")
ds_clf_labels = Node(DerivativesDataSink(
base_directory=str(out_dir.parent),
out_path_base=str(out_dir.name)),
name="ds_clf_labels")
ds_clf_labels.inputs.suffix = "classifier_labels"
wf.connect(bianca, "classifier_labels_file", ds_clf_labels, "in_file")
wf.connect(query_info, "query_flair", ds_clf_labels, "source_file")
wf.base_dir = wd_dir
wf.config.remove_unnecessary_outputs = False
wf.config["execution"]["crashdump_dir"] = crash_dir
wf.config["monitoring"]["enabled"] = "true"
# wf.write_graph("workflow_graph.png", graph2use="exec")
# wf.write_graph("workflow_graph_c.png", graph2use="colored")
wf.run(plugin='MultiProc', plugin_args={'n_procs': n_cpu})
def test_mapnode_json(tmpdir):
"""Tests that mapnodes don't generate excess jsons
"""
tmpdir.chdir()
wd = os.getcwd()
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
w1.add_nodes([n1])
w1.run()
n1.inputs.in1 = [2]
w1.run()
# should rerun
n1.inputs.in1 = [1]
eg = w1.run()
node = list(eg.nodes())[0]
outjson = glob(os.path.join(node.output_dir(), '_0x*.json'))
assert len(outjson) == 1
# check that multiple json's don't trigger rerun
with open(os.path.join(node.output_dir(), 'test.json'), 'wt') as fp:
fp.write('dummy file')
w1.config['execution'].update(**{'stop_on_first_rerun': True})
w1.run()
def amide_noe(zfrqs, name='Amide_NOE'):
inputnode = Node(IdentityInterface(fields=['zspec_file', 'mask_file']),
name='inputnode')
outputnode = Node(
IdentityInterface(fields=['diff_file', 'DS', 'MT', 'Amide', 'NOE']),
name='outputnode')
# Repeat 2-pool fit
f0_indices = (np.abs(zfrqs) > 9.9) | (np.abs(zfrqs) < 1.1)
sequence = {
'MTSat': {
'pulse': {
'p1': 0.4,
'p2': 0.3,
'bandwidth': 0.39
},
'Trf': 0.02,
'TR': 4,
'FA': 5,
'sat_f0': zfrqs[f0_indices].tolist(),
'sat_angle': np.repeat(180.0, len(f0_indices)).tolist()
}
}
two_pools = [{
'name': 'DS',
'df0': [0, -2.5, 2.5],
'fwhm': [1.0, 1.e-6, 3.0],
'A': [0.2, 1.e-3, 1.0],
'use_bandwidth': True
}, {
'name': 'MT',
'df0': [-2.5, -5.0, -0.5],
'fwhm': [50.0, 35.0, 200.0],
'A': [0.3, 1.e-3, 1.0]
}]
backg_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(),
out_file='bg_zspec.nii.gz'),
name='backg_select')
backg_fit = Node(Lorentzian(sequence=sequence,
pools=two_pools,
verbose=True),
name='backg_fit')
# Simulate data for all frequencies
sequence['MTSat']['sat_f0'] = zfrqs.tolist()
sequence['MTSat']['sat_angle'] = np.repeat(180.0, len(zfrqs)).tolist()
backg_sim = Node(LorentzianSim(sequence=sequence,
pools=two_pools,
noise=0,
in_file='backg_sim.nii.gz',
verbose=True),
name='backg_sim')
backg_sub = Node(ImageMaths(op_string='-sub',
out_file='no_backg_sub.nii.gz'),
name='backg_sub')
an_pools = [{
'name': 'Amide',
'df0': [3.5, 2.0, 6.0],
'fwhm': [2.0, 0.4, 4.0],
'A': [0.2, 1.e-3, 0.2],
'use_bandwidth': True
}, {
'name': 'NOE',
'df0': [-4.0, -6.0, -2.0],
'fwhm': [2.0, 0.4, 4.0],
'A': [0.2, 1.e-3, 0.2],
'use_bandwidth': True
}]
f0_indices = (np.abs(zfrqs) > 0.99) & (np.abs(zfrqs) < 10.1)
sequence['MTSat']['sat_f0'] = zfrqs[f0_indices].tolist()
sequence['MTSat']['sat_angle'] = np.repeat(180.0, len(f0_indices)).tolist()
an_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(),
out_file='fg_zspec.nii.gz'),
name='an_select')
an_fit = Node(Lorentzian(sequence=sequence,
pools=an_pools,
Zref=0.0,
additive=True,
verbose=True),
name='an_pool')
outputnode = Node(IdentityInterface(
fields=['zspec', 'f0_map', 'mask', 'DS', 'MT', 'Amide', 'NOE']),
name='outputnode')
wf = Workflow(name=name)
wf.connect([
(inputnode, backg_select, [('zspec_file', 'in_file')]),
(backg_select, backg_fit, [('out_file', 'in_file')]),
(inputnode, backg_fit, [('mask_file', 'mask_file')]),
(backg_fit, backg_sim, [('DS_f0', 'DS_f0'), ('DS_fwhm', 'DS_fwhm'),
('DS_A', 'DS_A'), ('MT_f0', 'MT_f0'),
('MT_fwhm', 'MT_fwhm'), ('MT_A', 'MT_A')]),
(inputnode, backg_sub, [('zspec_file', 'in_file2')]),
(backg_sim, backg_sub, [('out_file', 'in_file')]),
(backg_sub, an_select, [('out_file', 'in_file')]),
(an_select, an_fit, [('out_file', 'in_file')]),
(inputnode, an_fit, [('mask_file', 'mask_file')]),
(backg_sub, outputnode, [('out_file', 'diff_file')]),
(backg_fit, outputnode, [('DS_A', 'DS'), ('MT_A', 'MT')]),
(an_fit, outputnode, [('Amide_A', 'Amide'), ('NOE_A', 'NOE')])
])
return wf
modelspec.inputs.time_repetition = 1. # make sure its with a dot
modelspec.inputs.high_pass_filter_cutoff = 128.
################################################
#modelspec.inputs.subject_info = subjectinfo(subject_id) # run per subject
level1design = pe.Node(interface=spm.Level1Design(),
name="level1design") #, base_dir = '/media/Data/work')
level1design.inputs.timing_units = modelspec.inputs.output_units
level1design.inputs.interscan_interval = 1.
level1design.inputs.bases = {'hrf': {'derivs': [0, 0]}}
level1design.inputs.model_serial_correlations = 'AR(1)'
#######################################################################################################################
# Initiation of a workflow
wfSPM = Workflow(name="l1spm", base_dir=output_dir)
wfSPM.connect([
(infosource, selectfiles, [('subject_id', 'subject_id')]),
(selectfiles, runinfo, [('events', 'events_file'),
('regressors', 'regressors_file')]),
(selectfiles, extract, [('func', 'in_file')]),
(extract, smooth, [('roi_file', 'in_files')]),
(smooth, runinfo, [('smoothed_files', 'in_file')]),
(smooth, modelspec, [('smoothed_files', 'functional_runs')]),
(runinfo, modelspec, [('info', 'subject_info'),
('realign_file', 'realignment_parameters')]),
])
wfSPM.connect([(modelspec, level1design, [("session_info", "session_info")])])
##########################################################################3
# calculating the minimum across time points on merged mask image
minmask = Node(fsl.MinImage(), name="minmask")
# creating datasink to collect outputs
datasink = Node(
DataSink(base_directory=os.path.join(outDir, 'Flanker_Cope4_Level2')),
name='datasink')
###########
#
# SETTING UP THE WORKFLOW NODES
#
###########
# creating the workflow
secondLevel = Workflow(name="secondLevel", base_dir=outDir)
# connecting nodes
secondLevel.connect(level2design, 'design_mat', flameo, 'design_file')
secondLevel.connect(level2design, 'design_con', flameo, 't_con_file')
secondLevel.connect(level2design, 'design_grp', flameo, 'cov_split_file')
secondLevel.connect(copemerge, 'merged_file', flameo, 'cope_file')
secondLevel.connect(varcopemerge, 'merged_file', flameo, 'var_cope_file')
secondLevel.connect(maskmerge, 'merged_file', minmask, 'in_file')
secondLevel.connect(minmask, 'out_file', flameo, 'mask_file')
secondLevel.connect(flameo, 'stats_dir', datasink, 'stats_dir')
# running the workflow
secondLevel.run()
def create_dti():
# main workflow for preprocessing diffusion data
# fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# Initiation of a workflow
dwi_preproc = Workflow(name="dwi_preproc")
# inputnode
inputnode = Node(IdentityInterface(fields=[
'subject_id', 'freesurfer_dir', 'aseg', 'dwi', 'dwi_b0', 'dwi_mag',
'dwi_ph', 'bvals', 'bvecs', 'dwi_dwelltime', 'te_diff'
]),
name='inputnode')
# output node
outputnode = Node(IdentityInterface(fields=[
'bo_brain', "bo_brainmask", 'dwi_denoised', 'dwi_unringed',
"mag2b0mat", "mag2b0", "fmap", "eddy_corr", "rotated_bvecs",
"total_movement_rms", "outlier_report", "cnr_maps", "residuals",
"shell_params", "eddy_params", 'dti_fa', 'dti_md', 'dti_l1', 'dti_l2',
'dti_l3', 'dti_v1', 'dti_v2', 'dti_v3', 'fa2anat', 'fa2anat_mat',
'fa2anat_dat'
]),
name='outputnode')
'''
workflow to run distortion correction
-------------------------------------
'''
distor_corr = create_distortion_correct()
'''
tensor fitting
--------------
'''
dti = Node(fsl.DTIFit(), name='dti')
#connecting the nodes
dwi_preproc.connect([
(inputnode, distor_corr, [('dwi', 'inputnode.dwi')]),
(inputnode, distor_corr, [('dwi_b0', 'inputnode.dwi_b0')]),
(inputnode, distor_corr, [('dwi_mag', 'inputnode.dwi_mag')]),
(inputnode, distor_corr, [('dwi_ph', 'inputnode.dwi_ph')]),
(inputnode, distor_corr, [("bvals", "inputnode.bvals")]),
(inputnode, distor_corr, [("bvecs", "inputnode.bvecs")]),
(inputnode, distor_corr, [("dwi_dwelltime", "inputnode.dwi_dwelltime")
]),
(inputnode, distor_corr, [("te_diff", "inputnode.te_diff")]),
(distor_corr, outputnode, [('outputnode.bo_brain', 'bo_brain')]),
(distor_corr, outputnode, [('outputnode.bo_brainmask', 'bo_brainmask')
]),
(distor_corr, outputnode, [('outputnode.dwi_denoised', 'dwi_denoised')
]),
(distor_corr, outputnode, [('outputnode.dwi_unringed', 'dwi_unringed')
]),
(distor_corr, outputnode, [('outputnode.fmap', 'fmap')]),
(distor_corr, outputnode, [('outputnode.mag2b0mat', 'mag2b0mat')]),
(distor_corr, outputnode, [('outputnode.mag2b0', 'mag2b0')]),
(distor_corr, outputnode, [('outputnode.eddy_corr', 'eddy_corr')]),
(distor_corr, outputnode, [('outputnode.rotated_bvecs',
'rotated_bvecs')]),
(distor_corr, outputnode, [('outputnode.total_movement_rms',
'total_movement_rms')]),
(distor_corr, outputnode, [('outputnode.cnr_maps', 'cnr_maps')]),
(distor_corr, outputnode, [('outputnode.residuals', 'residuals')]),
(distor_corr, outputnode, [('outputnode.shell_params', 'shell_params')
]),
(distor_corr, outputnode, [('outputnode.eddy_params', 'eddy_params')]),
(distor_corr, outputnode, [('outputnode.outlier_report',
'outlier_report')]),
(distor_corr, dti, [("outputnode.rotated_bvecs", "bvecs")]),
(distor_corr, dti, [('outputnode.bo_brainmask', 'mask')]),
(distor_corr, dti, [('outputnode.eddy_corr', 'dwi')]),
(distor_corr, dti, [("outputnode.bvals", "bvals")]),
(dti, outputnode, [('FA', 'dti_fa')]),
(dti, outputnode, [('MD', 'dti_md')]),
(dti, outputnode, [('L1', 'dti_l1')]),
(dti, outputnode, [('L2', 'dti_l2')]),
(dti, outputnode, [('L3', 'dti_l3')]),
(dti, outputnode, [('V1', 'dti_v1')]),
(dti, outputnode, [('V2', 'dti_v2')]),
(dti, outputnode, [('V3', 'dti_v3')])
])
'''
coregistration of FA and T1
------------------------------------
'''
# linear registration with bbregister
bbreg = Node(fs.BBRegister(contrast_type='t1',
out_fsl_file='fa2anat.mat',
out_reg_file='fa2anat.dat',
registered_file='fa2anat_bbreg.nii.gz',
init='fsl'),
name='bbregister')
# connecting the nodes
dwi_preproc.connect([
(inputnode, bbreg, [('subject_id', 'subject_id')]),
(inputnode, bbreg, [('freesurfer_dir', 'subjects_dir')]),
(dti, bbreg, [("FA", "source_file")]),
(bbreg, outputnode, [('out_fsl_file', 'fa2anat_mat'),
('out_reg_file', 'fa2anat_dat'),
('registered_file', 'fa2anat')])
])
return dwi_preproc
def create_reg_workflow(name='registration'):
"""Create a FEAT preprocessing workflow together with freesurfer
Parameters
----------
name : name of workflow (default: 'registration')
Inputs:
inputspec.source_files : files (filename or list of filenames to register)
inputspec.mean_image : reference image to use
inputspec.anatomical_image : anatomical image to coregister to
inputspec.target_image : registration target
Outputs:
outputspec.func2anat_transform : FLIRT transform
outputspec.anat2target_transform : FLIRT+FNIRT transform
outputspec.transformed_files : transformed files in target space
outputspec.transformed_mean : mean image in target space
Example
-------
See code below
"""
register = Workflow(name=name)
inputnode = Node(
interface=IdentityInterface(fields=[
'source_files', 'mean_image', 'subject_id', 'subjects_dir',
'target_image'
]),
name='inputspec')
outputnode = Node(
interface=IdentityInterface(fields=[
'func2anat_transform', 'out_reg_file', 'anat2target_transform',
'transforms', 'transformed_mean', 'segmentation_files',
'anat2target', 'aparc', 'min_cost_file'
]),
name='outputspec')
# Get the subject's freesurfer source directory
fssource = Node(FreeSurferSource(), name='fssource')
fssource.run_without_submitting = True
register.connect(inputnode, 'subject_id', fssource, 'subject_id')
register.connect(inputnode, 'subjects_dir', fssource, 'subjects_dir')
convert = Node(freesurfer.MRIConvert(out_type='nii'), name="convert")
register.connect(fssource, 'T1', convert, 'in_file')
# Coregister the median to the surface
bbregister = Node(freesurfer.BBRegister(), name='bbregister')
bbregister.inputs.init = 'fsl'
bbregister.inputs.contrast_type = 't2'
bbregister.inputs.out_fsl_file = True
bbregister.inputs.epi_mask = True
register.connect(inputnode, 'subject_id', bbregister, 'subject_id')
register.connect(inputnode, 'mean_image', bbregister, 'source_file')
register.connect(inputnode, 'subjects_dir', bbregister, 'subjects_dir')
"""
Estimate the tissue classes from the anatomical image. But use aparc+aseg's brain mask
"""
binarize = Node(
fs.Binarize(min=0.5, out_type="nii.gz", dilate=1),
name="binarize_aparc")
register.connect(fssource, ("aparc_aseg", get_aparc_aseg), binarize,
"in_file")
stripper = Node(fsl.ApplyMask(), name='stripper')
register.connect(binarize, "binary_file", stripper, "mask_file")
register.connect(convert, 'out_file', stripper, 'in_file')
fast = Node(fsl.FAST(), name='fast')
register.connect(stripper, 'out_file', fast, 'in_files')
"""
Binarize the segmentation
"""
binarize = MapNode(
fsl.ImageMaths(op_string='-nan -thr 0.9 -ero -bin'),
iterfield=['in_file'],
name='binarize')
register.connect(fast, 'partial_volume_files', binarize, 'in_file')
"""
Apply inverse transform to take segmentations to functional space
"""
applyxfm = MapNode(
freesurfer.ApplyVolTransform(inverse=True, interp='nearest'),
iterfield=['target_file'],
name='inverse_transform')
register.connect(inputnode, 'subjects_dir', applyxfm, 'subjects_dir')
register.connect(bbregister, 'out_reg_file', applyxfm, 'reg_file')
register.connect(binarize, 'out_file', applyxfm, 'target_file')
register.connect(inputnode, 'mean_image', applyxfm, 'source_file')
"""
Apply inverse transform to aparc file
"""
aparcxfm = Node(
freesurfer.ApplyVolTransform(inverse=True, interp='nearest'),
name='aparc_inverse_transform')
register.connect(inputnode, 'subjects_dir', aparcxfm, 'subjects_dir')
register.connect(bbregister, 'out_reg_file', aparcxfm, 'reg_file')
register.connect(fssource, ('aparc_aseg', get_aparc_aseg), aparcxfm,
'target_file')
register.connect(inputnode, 'mean_image', aparcxfm, 'source_file')
"""
Convert the BBRegister transformation to ANTS ITK format
"""
convert2itk = Node(C3dAffineTool(), name='convert2itk')
convert2itk.inputs.fsl2ras = True
convert2itk.inputs.itk_transform = True
register.connect(bbregister, 'out_fsl_file', convert2itk, 'transform_file')
register.connect(inputnode, 'mean_image', convert2itk, 'source_file')
register.connect(stripper, 'out_file', convert2itk, 'reference_file')
"""
Compute registration between the subject's structural and MNI template
* All parameters are set using the example from:
#https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh
* This is currently set to perform a very quick registration. However,
the registration can be made significantly more accurate for cortical
structures by increasing the number of iterations.
"""
reg = Node(ants.Registration(), name='antsRegister')
reg.inputs.output_transform_prefix = "output_"
reg.inputs.transforms = ['Rigid', 'Affine', 'SyN']
reg.inputs.transform_parameters = [(0.1, ), (0.1, ), (0.2, 3.0, 0.0)]
reg.inputs.number_of_iterations = [[10000, 11110, 11110]] * 2 + [[
100, 30, 20
]]
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = True
reg.inputs.initial_moving_transform_com = True
reg.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
reg.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
reg.inputs.sampling_strategy = ['Regular'] * 2 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
reg.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
reg.inputs.convergence_window_size = [20] * 2 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ['vox'] * 3
reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 3
reg.inputs.use_histogram_matching = [False] * 2 + [True]
reg.inputs.winsorize_lower_quantile = 0.005
reg.inputs.winsorize_upper_quantile = 0.995
reg.inputs.float = True
reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
reg.inputs.num_threads = 4
reg.plugin_args = {'sbatch_args': '-c%d' % 4}
register.connect(stripper, 'out_file', reg, 'moving_image')
register.connect(inputnode, 'target_image', reg, 'fixed_image')
"""
Concatenate the affine and ants transforms into a list
"""
merge = Node(Merge(2), iterfield=['in2'], name='mergexfm')
register.connect(convert2itk, 'itk_transform', merge, 'in2')
register.connect(reg, ('composite_transform', pickfirst), merge, 'in1')
"""
Transform the mean image. First to anatomical and then to target
"""
warpmean = Node(ants.ApplyTransforms(), name='warpmean')
warpmean.inputs.input_image_type = 3
warpmean.inputs.interpolation = 'Linear'
warpmean.inputs.invert_transform_flags = [False, False]
warpmean.terminal_output = 'file'
warpmean.inputs.args = '--float'
warpmean.inputs.num_threads = 4
warpmean.plugin_args = {'sbatch_args': '-c%d' % 4}
register.connect(inputnode, 'target_image', warpmean, 'reference_image')
register.connect(inputnode, 'mean_image', warpmean, 'input_image')
register.connect(merge, 'out', warpmean, 'transforms')
"""
Assign all the output files
"""
register.connect(reg, 'warped_image', outputnode, 'anat2target')
register.connect(warpmean, 'output_image', outputnode, 'transformed_mean')
register.connect(applyxfm, 'transformed_file', outputnode,
'segmentation_files')
register.connect(aparcxfm, 'transformed_file', outputnode, 'aparc')
register.connect(bbregister, 'out_fsl_file', outputnode,
'func2anat_transform')
register.connect(bbregister, 'out_reg_file', outputnode, 'out_reg_file')
register.connect(reg, 'composite_transform', outputnode,
'anat2target_transform')
register.connect(merge, 'out', outputnode, 'transforms')
register.connect(bbregister, 'min_cost_file', outputnode, 'min_cost_file')
return register
def create_workflow(files,
target_file,
subject_id,
TR,
slice_times,
norm_threshold=1,
num_components=5,
vol_fwhm=None,
surf_fwhm=None,
lowpass_freq=-1,
highpass_freq=-1,
subjects_dir=None,
sink_directory=os.getcwd(),
target_subject=['fsaverage3', 'fsaverage4'],
name='resting'):
wf = Workflow(name=name)
# Rename files in case they are named identically
name_unique = MapNode(
Rename(format_string='rest_%(run)02d'),
iterfield=['in_file', 'run'],
name='rename')
name_unique.inputs.keep_ext = True
name_unique.inputs.run = list(range(1, len(files) + 1))
name_unique.inputs.in_file = files
realign = Node(nipy.SpaceTimeRealigner(), name="spacetime_realign")
realign.inputs.slice_times = slice_times
realign.inputs.tr = TR
realign.inputs.slice_info = 2
realign.plugin_args = {'sbatch_args': '-c%d' % 4}
# Compute TSNR on realigned data regressing polynomials up to order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(realign, "out_file", tsnr, "in_file")
# Compute the median image across runs
calc_median = Node(CalculateMedian(), name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
"""
Segment and Register
"""
registration = create_reg_workflow(name='registration')
wf.connect(calc_median, 'median_file', registration,
'inputspec.mean_image')
registration.inputs.inputspec.subject_id = subject_id
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = target_file
"""Quantify TSNR in each freesurfer ROI
"""
get_roi_tsnr = MapNode(
fs.SegStats(default_color_table=True),
iterfield=['in_file'],
name='get_aparc_tsnr')
get_roi_tsnr.inputs.avgwf_txt_file = True
wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_tsnr,
'segmentation_file')
"""Use :class:`nipype.algorithms.rapidart` to determine which of the
images in the functional series are outliers based on deviations in
intensity or movement.
"""
art = Node(interface=ArtifactDetect(), name="art")
art.inputs.use_differences = [True, True]
art.inputs.use_norm = True
art.inputs.norm_threshold = norm_threshold
art.inputs.zintensity_threshold = 9
art.inputs.mask_type = 'spm_global'
art.inputs.parameter_source = 'NiPy'
"""Here we are connecting all the nodes together. Notice that we add the merge node only if you choose
to use 4D. Also `get_vox_dims` function is passed along the input volume of normalise to set the optimal
voxel sizes.
"""
wf.connect([
(name_unique, realign, [('out_file', 'in_file')]),
(realign, art, [('out_file', 'realigned_files')]),
(realign, art, [('par_file', 'realignment_parameters')]),
])
def selectindex(files, idx):
import numpy as np
from nipype.utils.filemanip import filename_to_list, list_to_filename
return list_to_filename(
np.array(filename_to_list(files))[idx].tolist())
mask = Node(fsl.BET(), name='getmask')
mask.inputs.mask = True
wf.connect(calc_median, 'median_file', mask, 'in_file')
# get segmentation in normalized functional space
def merge_files(in1, in2):
out_files = filename_to_list(in1)
out_files.extend(filename_to_list(in2))
return out_files
# filter some noise
# Compute motion regressors
motreg = Node(
Function(
input_names=['motion_params', 'order', 'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(realign, 'par_file', motreg, 'motion_params')
# Create a filter to remove motion and art confounds
createfilter1 = Node(
Function(
input_names=[
'motion_params', 'comp_norm', 'outliers', 'detrend_poly'
],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 2
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
filter1 = MapNode(
fsl.GLM(
out_f_name='F_mcart.nii.gz',
out_pf_name='pF_mcart.nii.gz',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filtermotion')
wf.connect(realign, 'out_file', filter1, 'in_file')
wf.connect(realign, ('out_file', rename, '_filtermotart'), filter1,
'out_res_name')
wf.connect(createfilter1, 'out_files', filter1, 'design')
createfilter2 = MapNode(
ACompCor(),
iterfield=['realigned_file', 'extra_regressors'],
name='makecompcorrfilter')
createfilter2.inputs.components_file = 'noise_components.txt'
createfilter2.inputs.num_components = num_components
wf.connect(createfilter1, 'out_files', createfilter2, 'extra_regressors')
wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
wf.connect(registration,
('outputspec.segmentation_files', selectindex, [0, 2]),
createfilter2, 'mask_file')
filter2 = MapNode(
fsl.GLM(out_f_name='F.nii.gz', out_pf_name='pF.nii.gz', demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filter_noise_nosmooth')
wf.connect(filter1, 'out_res', filter2, 'in_file')
wf.connect(filter1, ('out_res', rename, '_cleaned'), filter2,
'out_res_name')
wf.connect(createfilter2, 'components_file', filter2, 'design')
wf.connect(mask, 'mask_file', filter2, 'mask')
bandpass = Node(
Function(
input_names=['files', 'lowpass_freq', 'highpass_freq', 'fs'],
output_names=['out_files'],
function=bandpass_filter,
imports=imports),
name='bandpass_unsmooth')
bandpass.inputs.fs = 1. / TR
bandpass.inputs.highpass_freq = highpass_freq
bandpass.inputs.lowpass_freq = lowpass_freq
wf.connect(filter2, 'out_res', bandpass, 'files')
"""Smooth the functional data using
:class:`nipype.interfaces.fsl.IsotropicSmooth`.
"""
smooth = MapNode(
interface=fsl.IsotropicSmooth(), name="smooth", iterfield=["in_file"])
smooth.inputs.fwhm = vol_fwhm
wf.connect(bandpass, 'out_files', smooth, 'in_file')
collector = Node(Merge(2), name='collect_streams')
wf.connect(smooth, 'out_file', collector, 'in1')
wf.connect(bandpass, 'out_files', collector, 'in2')
"""
Transform the remaining images. First to anatomical and then to target
"""
warpall = MapNode(
ants.ApplyTransforms(), iterfield=['input_image'], name='warpall')
warpall.inputs.input_image_type = 3
warpall.inputs.interpolation = 'Linear'
warpall.inputs.invert_transform_flags = [False, False]
warpall.terminal_output = 'file'
warpall.inputs.reference_image = target_file
warpall.inputs.args = '--float'
warpall.inputs.num_threads = 2
warpall.plugin_args = {'sbatch_args': '-c%d' % 2}
# transform to target
wf.connect(collector, 'out', warpall, 'input_image')
wf.connect(registration, 'outputspec.transforms', warpall, 'transforms')
mask_target = Node(fsl.ImageMaths(op_string='-bin'), name='target_mask')
wf.connect(registration, 'outputspec.anat2target', mask_target, 'in_file')
maskts = MapNode(fsl.ApplyMask(), iterfield=['in_file'], name='ts_masker')
wf.connect(warpall, 'output_image', maskts, 'in_file')
wf.connect(mask_target, 'out_file', maskts, 'mask_file')
# map to surface
# extract aparc+aseg ROIs
# extract subcortical ROIs
# extract target space ROIs
# combine subcortical and cortical rois into a single cifti file
#######
# Convert aparc to subject functional space
# Sample the average time series in aparc ROIs
sampleaparc = MapNode(
freesurfer.SegStats(default_color_table=True),
iterfield=['in_file', 'summary_file', 'avgwf_txt_file'],
name='aparc_ts')
sampleaparc.inputs.segment_id = (
[8] + list(range(10, 14)) + [17, 18, 26, 47] + list(range(49, 55)) +
[58] + list(range(1001, 1036)) + list(range(2001, 2036)))
wf.connect(registration, 'outputspec.aparc', sampleaparc,
'segmentation_file')
wf.connect(collector, 'out', sampleaparc, 'in_file')
def get_names(files, suffix):
"""Generate appropriate names for output files
"""
from nipype.utils.filemanip import (split_filename, filename_to_list,
list_to_filename)
import os
out_names = []
for filename in files:
path, name, _ = split_filename(filename)
out_names.append(os.path.join(path, name + suffix))
return list_to_filename(out_names)
wf.connect(collector, ('out', get_names, '_avgwf.txt'), sampleaparc,
'avgwf_txt_file')
wf.connect(collector, ('out', get_names, '_summary.stats'), sampleaparc,
'summary_file')
# Sample the time series onto the surface of the target surface. Performs
# sampling into left and right hemisphere
target = Node(IdentityInterface(fields=['target_subject']), name='target')
target.iterables = ('target_subject', filename_to_list(target_subject))
samplerlh = MapNode(
freesurfer.SampleToSurface(),
iterfield=['source_file'],
name='sampler_lh')
samplerlh.inputs.sampling_method = "average"
samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
samplerlh.inputs.sampling_units = "frac"
samplerlh.inputs.interp_method = "trilinear"
samplerlh.inputs.smooth_surf = surf_fwhm
# samplerlh.inputs.cortex_mask = True
samplerlh.inputs.out_type = 'niigz'
samplerlh.inputs.subjects_dir = subjects_dir
samplerrh = samplerlh.clone('sampler_rh')
samplerlh.inputs.hemi = 'lh'
wf.connect(collector, 'out', samplerlh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerlh, 'reg_file')
wf.connect(target, 'target_subject', samplerlh, 'target_subject')
samplerrh.set_input('hemi', 'rh')
wf.connect(collector, 'out', samplerrh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerrh, 'reg_file')
wf.connect(target, 'target_subject', samplerrh, 'target_subject')
# Combine left and right hemisphere to text file
combiner = MapNode(
Function(
input_names=['left', 'right'],
output_names=['out_file'],
function=combine_hemi,
imports=imports),
iterfield=['left', 'right'],
name="combiner")
wf.connect(samplerlh, 'out_file', combiner, 'left')
wf.connect(samplerrh, 'out_file', combiner, 'right')
# Sample the time series file for each subcortical roi
ts2txt = MapNode(
Function(
input_names=['timeseries_file', 'label_file', 'indices'],
output_names=['out_file'],
function=extract_subrois,
imports=imports),
iterfield=['timeseries_file'],
name='getsubcortts')
ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
list(range(49, 55)) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm_v2.nii.gz'))
wf.connect(maskts, 'out_file', ts2txt, 'timeseries_file')
######
substitutions = [
('_target_subject_', ''),
('_filtermotart_cleaned_bp_trans_masked', ''),
('_filtermotart_cleaned_bp', ''),
]
substitutions += [("_smooth%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_ts_masker%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_getsubcortts%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_combiner%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_filtermotion%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_filter_noise_nosmooth%d" % i, "")
for i in range(11)[::-1]]
substitutions += [("_makecompcorfilter%d" % i, "")
for i in range(11)[::-1]]
substitutions += [("_get_aparc_tsnr%d/" % i, "run%d_" % (i + 1))
for i in range(11)[::-1]]
substitutions += [("T1_out_brain_pve_0_maths_warped", "compcor_csf"),
("T1_out_brain_pve_1_maths_warped",
"compcor_gm"), ("T1_out_brain_pve_2_maths_warped",
"compcor_wm"),
("output_warped_image_maths",
"target_brain_mask"), ("median_brain_mask",
"native_brain_mask"), ("corr_",
"")]
regex_subs = [
('_combiner.*/sar', '/smooth/'),
('_combiner.*/ar', '/unsmooth/'),
('_aparc_ts.*/sar', '/smooth/'),
('_aparc_ts.*/ar', '/unsmooth/'),
('_getsubcortts.*/sar', '/smooth/'),
('_getsubcortts.*/ar', '/unsmooth/'),
('series/sar', 'series/smooth/'),
('series/ar', 'series/unsmooth/'),
('_inverse_transform./', ''),
]
# Save the relevant data into an output directory
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
datasink.inputs.substitutions = substitutions
datasink.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(realign, 'par_file', datasink, 'resting.qa.motion')
wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
wf.connect(registration, 'outputspec.segmentation_files', datasink,
'resting.mask_files')
wf.connect(registration, 'outputspec.anat2target', datasink,
'resting.qa.ants')
wf.connect(mask, 'mask_file', datasink, 'resting.mask_files.@brainmask')
wf.connect(mask_target, 'out_file', datasink, 'resting.mask_files.target')
wf.connect(filter1, 'out_f', datasink, 'resting.qa.compmaps.@mc_F')
wf.connect(filter1, 'out_pf', datasink, 'resting.qa.compmaps.@mc_pF')
wf.connect(filter2, 'out_f', datasink, 'resting.qa.compmaps')
wf.connect(filter2, 'out_pf', datasink, 'resting.qa.compmaps.@p')
wf.connect(registration, 'outputspec.min_cost_file', datasink,
'resting.qa.mincost')
wf.connect(tsnr, 'tsnr_file', datasink, 'resting.qa.tsnr.@map')
wf.connect([(get_roi_tsnr, datasink,
[('avgwf_txt_file', 'resting.qa.tsnr'),
('summary_file', 'resting.qa.tsnr.@summary')])])
wf.connect(bandpass, 'out_files', datasink,
'resting.timeseries.@bandpassed')
wf.connect(smooth, 'out_file', datasink, 'resting.timeseries.@smoothed')
wf.connect(createfilter1, 'out_files', datasink,
'resting.regress.@regressors')
wf.connect(createfilter2, 'components_file', datasink,
'resting.regress.@compcorr')
wf.connect(maskts, 'out_file', datasink, 'resting.timeseries.target')
wf.connect(sampleaparc, 'summary_file', datasink,
'resting.parcellations.aparc')
wf.connect(sampleaparc, 'avgwf_txt_file', datasink,
'resting.parcellations.aparc.@avgwf')
wf.connect(ts2txt, 'out_file', datasink,
'resting.parcellations.grayo.@subcortical')
datasink2 = Node(interface=DataSink(), name="datasink2")
datasink2.inputs.base_directory = sink_directory
datasink2.inputs.container = subject_id
datasink2.inputs.substitutions = substitutions
datasink2.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(combiner, 'out_file', datasink2,
'resting.parcellations.grayo.@surface')
return wf
def create_skullstrip_workflow(name="skullstrip"):
"""Remove non-brain voxels from the timeseries."""
# Define the workflow inputs
inputnode = Node(
IdentityInterface(["subject_id", "timeseries", "reg_file"]), "inputs")
# Mean the timeseries across the fourth dimension
origmean = MapNode(fsl.MeanImage(), "in_file", "origmean")
# Grab the Freesurfer aparc+aseg file as an anatomical brain mask
getaseg = Node(
io.SelectFiles({"aseg": "{subject_id}/mri/aparc+aseg.mgz"},
base_directory=os.environ["SUBJECTS_DIR"]), "getaseg")
# Threshold the aseg volume to get a boolean mask
makemask = Node(fs.Binarize(dilate=4, min=0.5), "makemask")
# Transform the brain mask into functional space
transform = MapNode(fs.ApplyVolTransform(inverse=True, interp="nearest"),
["reg_file", "source_file"], "transform")
# Convert the mask to nifti and rename
convertmask = MapNode(fs.MRIConvert(out_file="functional_mask.nii.gz"),
"in_file", "convertmask")
# Use the mask to skullstrip the timeseries
stripts = MapNode(fs.ApplyMask(), ["in_file", "mask_file"], "stripts")
# Use the mask to skullstrip the mean image
stripmean = MapNode(fs.ApplyMask(), ["in_file", "mask_file"], "stripmean")
# Generate images summarizing the skullstrip and resulting data
reportmask = MapNode(MaskReport(), ["mask_file", "orig_file", "mean_file"],
"reportmask")
# Define the workflow outputs
outputnode = Node(
IdentityInterface(["timeseries", "mean_file", "mask_file", "report"]),
"outputs")
# Define and connect the workflow
skullstrip = Workflow(name)
skullstrip.connect([
(inputnode, origmean, [("timeseries", "in_file")]),
(inputnode, getaseg, [("subject_id", "subject_id")]),
(origmean, transform, [("out_file", "source_file")]),
(getaseg, makemask, [("aseg", "in_file")]),
(makemask, transform, [("binary_file", "target_file")]),
(inputnode, transform, [("reg_file", "reg_file")]),
(transform, stripts, [("transformed_file", "mask_file")]),
(transform, stripmean, [("transformed_file", "mask_file")]),
(inputnode, stripts, [("timeseries", "in_file")]),
(origmean, stripmean, [("out_file", "in_file")]),
(stripmean, reportmask, [("out_file", "mean_file")]),
(origmean, reportmask, [("out_file", "orig_file")]),
(transform, reportmask, [("transformed_file", "mask_file")]),
(transform, convertmask, [("transformed_file", "in_file")]),
(stripts, outputnode, [("out_file", "timeseries")]),
(stripmean, outputnode, [("out_file", "mean_file")]),
(convertmask, outputnode, [("out_file", "mask_file")]),
(reportmask, outputnode, [("out_files", "report")]),
])
return skullstrip
def create_preprocessing_workflow(name="preproc", exp_info=None):
"""Return a Nipype workflow for fMRI preprocessing.
This mostly follows the preprocessing in FSL, although some
of the processing has been moved into pure Python.
Parameters
----------
name : string
workflow object name
exp_info : dict
dictionary with experimental information
"""
preproc = Workflow(name)
if exp_info is None:
exp_info = lyman.default_experiment_parameters()
# Define the inputs for the preprocessing workflow
in_fields = ["timeseries", "subject_id"]
if exp_info["whole_brain_template"]:
in_fields.append("whole_brain")
if exp_info["fieldmap_template"]:
in_fields.append("fieldmap")
inputnode = Node(IdentityInterface(in_fields), "inputs")
# Remove equilibrium frames and convert to float
prepare = MapNode(PrepTimeseries(), "in_file", "prep_timeseries")
prepare.inputs.frames_to_toss = exp_info["frames_to_toss"]
# Unwarp using fieldmap images
if exp_info["fieldmap_template"]:
unwarp = create_unwarp_workflow(fieldmap_pe=exp_info["fieldmap_pe"])
# Motion and slice time correct
realign = create_realignment_workflow(
temporal_interp=exp_info["temporal_interp"],
TR=exp_info["TR"],
slice_order=exp_info["slice_order"],
interleaved=exp_info["interleaved"])
# Estimate a registration from funtional to anatomical space
coregister = create_bbregister_workflow(partial_brain=bool(
exp_info["whole_brain_template"]),
init_with=exp_info["coreg_init"])
# Skullstrip the brain using the Freesurfer segmentation
skullstrip = create_skullstrip_workflow()
# Smooth intelligently in the volume
susan = create_susan_smooth()
susan.inputs.inputnode.fwhm = exp_info["smooth_fwhm"]
# Scale and filter the timeseries
filter_smooth = create_filtering_workflow("filter_smooth",
exp_info["hpf_cutoff"],
exp_info["TR"],
"smoothed_timeseries")
filter_rough = create_filtering_workflow("filter_rough",
exp_info["hpf_cutoff"],
exp_info["TR"],
"unsmoothed_timeseries")
# Automatically detect motion and intensity outliers
artifacts = MapNode(ArtifactDetection(),
["timeseries", "mask_file", "motion_file"],
"artifacts")
artifacts.inputs.intensity_thresh = exp_info["intensity_threshold"]
artifacts.inputs.motion_thresh = exp_info["motion_threshold"]
artifacts.inputs.spike_thresh = exp_info["spike_threshold"]
# Extract nuisance variables from anatomical sources
confounds = create_confound_extraction_workflow("confounds",
exp_info["wm_components"])
# Save the experiment info for this run
saveparams = MapNode(SaveParameters(exp_info=exp_info), "in_file",
"saveparams")
preproc.connect([
(inputnode, prepare, [("timeseries", "in_file")]),
(realign, artifacts, [("outputs.motion_file", "motion_file")]),
(realign, coregister, [("outputs.timeseries", "inputs.timeseries")]),
(inputnode, coregister, [("subject_id", "inputs.subject_id")]),
(realign, skullstrip, [("outputs.timeseries", "inputs.timeseries")]),
(inputnode, skullstrip, [("subject_id", "inputs.subject_id")]),
(coregister, skullstrip, [("outputs.tkreg_mat", "inputs.reg_file")]),
(skullstrip, artifacts, [("outputs.mask_file", "mask_file")]),
(skullstrip, susan, [("outputs.mask_file", "inputnode.mask_file"),
("outputs.timeseries", "inputnode.in_files")]),
(susan, filter_smooth, [("outputnode.smoothed_files",
"inputs.timeseries")]),
(skullstrip, filter_smooth, [("outputs.mask_file", "inputs.mask_file")
]),
(skullstrip, filter_rough, [("outputs.timeseries", "inputs.timeseries")
]),
(skullstrip, filter_rough, [("outputs.mask_file", "inputs.mask_file")
]),
(filter_rough, artifacts, [("outputs.timeseries", "timeseries")]),
(filter_rough, confounds, [("outputs.timeseries", "inputs.timeseries")
]),
(inputnode, confounds, [("subject_id", "inputs.subject_id")]),
(skullstrip, confounds, [("outputs.mask_file", "inputs.brain_mask")]),
(coregister, confounds, [("outputs.tkreg_mat", "inputs.reg_file")]),
(inputnode, saveparams, [("timeseries", "in_file")]),
])
# Optionally add a connection for unwarping
if bool(exp_info["fieldmap_template"]):
preproc.connect([
(inputnode, unwarp, [("fieldmap", "inputs.fieldmap")]),
(prepare, unwarp, [("out_file", "inputs.timeseries")]),
(unwarp, realign, [("outputs.timeseries", "inputs.timeseries")])
])
else:
preproc.connect([
(prepare, realign, [("out_file", "inputs.timeseries")]),
])
# Optionally connect the whole brain template
if bool(exp_info["whole_brain_template"]):
preproc.connect([(inputnode, coregister, [
("whole_brain_template", "inputs.whole_brain_template")
])])
# Define the outputs of the top-level workflow
output_fields = [
"smoothed_timeseries", "unsmoothed_timeseries", "example_func",
"mean_func", "functional_mask", "realign_report", "mask_report",
"artifact_report", "confound_file", "flirt_affine", "tkreg_affine",
"coreg_report", "json_file"
]
if bool(exp_info["fieldmap_template"]):
output_fields.append("unwarp_report")
outputnode = Node(IdentityInterface(output_fields), "outputs")
preproc.connect([
(realign, outputnode, [("outputs.example_func", "example_func"),
("outputs.report", "realign_report")]),
(skullstrip, outputnode, [("outputs.mask_file", "functional_mask"),
("outputs.report", "mask_report")]),
(artifacts, outputnode, [("out_files", "artifact_report")]),
(coregister, outputnode, [("outputs.tkreg_mat", "tkreg_affine"),
("outputs.flirt_mat", "flirt_affine"),
("outputs.report", "coreg_report")]),
(filter_smooth, outputnode, [("outputs.timeseries",
"smoothed_timeseries")]),
(filter_rough, outputnode, [("outputs.timeseries",
"unsmoothed_timeseries"),
("outputs.mean_file", "mean_func")]),
(confounds, outputnode, [("outputs.confound_file", "confound_file")]),
(saveparams, outputnode, [("json_file", "json_file")]),
])
if bool(exp_info["fieldmap_template"]):
preproc.connect([
(unwarp, outputnode, [("outputs.report", "unwarp_report")]),
])
return preproc, inputnode, outputnode
def create_realignment_workflow(name="realignment",
temporal_interp=True,
TR=2,
slice_order="up",
interleaved=True):
"""Motion and slice-time correct the timeseries and summarize."""
inputnode = Node(IdentityInterface(["timeseries"]), "inputs")
# Get the middle volume of each run for motion correction
extractref = MapNode(ExtractRealignmentTarget(), "in_file", "extractref")
# Motion correct to middle volume of each run
mcflirt = MapNode(
fsl.MCFLIRT(cost="normcorr",
interpolation="spline",
save_mats=True,
save_rms=True,
save_plots=True), ["in_file", "ref_file"], "mcflirt")
# Optionally emoporally interpolate to correct for slice time differences
if temporal_interp:
slicetime = MapNode(fsl.SliceTimer(time_repetition=TR), "in_file",
"slicetime")
if slice_order == "down":
slicetime.inputs.index_dir = True
elif slice_order != "up":
raise ValueError("slice_order must be 'up' or 'down'")
if interleaved:
slicetime.inputs.interleaved = True
# Generate a report on the motion correction
mcreport = MapNode(RealignmentReport(),
["target_file", "realign_params", "displace_params"],
"mcreport")
# Define the outputs
outputnode = Node(
IdentityInterface(
["timeseries", "example_func", "report", "motion_file"]),
"outputs")
# Define and connect the sub workflow
realignment = Workflow(name)
realignment.connect([
(inputnode, extractref, [("timeseries", "in_file")]),
(inputnode, mcflirt, [("timeseries", "in_file")]),
(extractref, mcflirt, [("out_file", "ref_file")]),
(extractref, mcreport, [("out_file", "target_file")]),
(mcflirt, mcreport, [("par_file", "realign_params"),
("rms_files", "displace_params")]),
(extractref, outputnode, [("out_file", "example_func")]),
(mcreport, outputnode, [("realign_report", "report"),
("motion_file", "motion_file")]),
])
if temporal_interp:
realignment.connect([(mcflirt, slicetime, [("out_file", "in_file")]),
(slicetime, outputnode,
[("slice_time_corrected_file", "timeseries")])])
else:
realignment.connect([(mcflirt, outputnode, [("out_file", "timeseries")
])])
return realignment
def create_workflow(files,
target_file,
subject_id,
TR,
slice_times,
norm_threshold=1,
num_components=5,
vol_fwhm=None,
surf_fwhm=None,
lowpass_freq=-1,
highpass_freq=-1,
subjects_dir=None,
sink_directory=os.getcwd(),
target_subject=['fsaverage3', 'fsaverage4'],
name='resting'):
wf = Workflow(name=name)
# Rename files in case they are named identically
name_unique = MapNode(Rename(format_string='rest_%(run)02d'),
iterfield=['in_file', 'run'],
name='rename')
name_unique.inputs.keep_ext = True
name_unique.inputs.run = list(range(1, len(files) + 1))
name_unique.inputs.in_file = files
realign = Node(nipy.SpaceTimeRealigner(), name="spacetime_realign")
realign.inputs.slice_times = slice_times
realign.inputs.tr = TR
realign.inputs.slice_info = 2
realign.plugin_args = {'sbatch_args': '-c%d' % 4}
# Compute TSNR on realigned data regressing polynomials up to order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(realign, "out_file", tsnr, "in_file")
# Compute the median image across runs
calc_median = Node(Function(input_names=['in_files'],
output_names=['median_file'],
function=median,
imports=imports),
name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
"""Segment and Register
"""
registration = create_reg_workflow(name='registration')
wf.connect(calc_median, 'median_file', registration, 'inputspec.mean_image')
registration.inputs.inputspec.subject_id = subject_id
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = target_file
"""Quantify TSNR in each freesurfer ROI
"""
get_roi_tsnr = MapNode(fs.SegStats(default_color_table=True),
iterfield=['in_file'], name='get_aparc_tsnr')
get_roi_tsnr.inputs.avgwf_txt_file = True
wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_tsnr, 'segmentation_file')
"""Use :class:`nipype.algorithms.rapidart` to determine which of the
images in the functional series are outliers based on deviations in
intensity or movement.
"""
art = Node(interface=ArtifactDetect(), name="art")
art.inputs.use_differences = [True, True]
art.inputs.use_norm = True
art.inputs.norm_threshold = norm_threshold
art.inputs.zintensity_threshold = 9
art.inputs.mask_type = 'spm_global'
art.inputs.parameter_source = 'NiPy'
"""Here we are connecting all the nodes together. Notice that we add the merge node only if you choose
to use 4D. Also `get_vox_dims` function is passed along the input volume of normalise to set the optimal
voxel sizes.
"""
wf.connect([(name_unique, realign, [('out_file', 'in_file')]),
(realign, art, [('out_file', 'realigned_files')]),
(realign, art, [('par_file', 'realignment_parameters')]),
])
def selectindex(files, idx):
import numpy as np
from nipype.utils.filemanip import filename_to_list, list_to_filename
return list_to_filename(np.array(filename_to_list(files))[idx].tolist())
mask = Node(fsl.BET(), name='getmask')
mask.inputs.mask = True
wf.connect(calc_median, 'median_file', mask, 'in_file')
# get segmentation in normalized functional space
def merge_files(in1, in2):
out_files = filename_to_list(in1)
out_files.extend(filename_to_list(in2))
return out_files
# filter some noise
# Compute motion regressors
motreg = Node(Function(input_names=['motion_params', 'order',
'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(realign, 'par_file', motreg, 'motion_params')
# Create a filter to remove motion and art confounds
createfilter1 = Node(Function(input_names=['motion_params', 'comp_norm',
'outliers', 'detrend_poly'],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 2
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
filter1 = MapNode(fsl.GLM(out_f_name='F_mcart.nii.gz',
out_pf_name='pF_mcart.nii.gz',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filtermotion')
wf.connect(realign, 'out_file', filter1, 'in_file')
wf.connect(realign, ('out_file', rename, '_filtermotart'),
filter1, 'out_res_name')
wf.connect(createfilter1, 'out_files', filter1, 'design')
createfilter2 = MapNode(ACompCor(),
iterfield=['realigned_file', 'extra_regressors'],
name='makecompcorrfilter')
createfilter2.inputs.components_file = 'noise_components.txt'
createfilter2.inputs.num_components = num_components
wf.connect(createfilter1, 'out_files', createfilter2, 'extra_regressors')
wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
wf.connect(registration, ('outputspec.segmentation_files', selectindex, [0, 2]),
createfilter2, 'mask_file')
filter2 = MapNode(fsl.GLM(out_f_name='F.nii.gz',
out_pf_name='pF.nii.gz',
demean=True),
iterfield=['in_file', 'design', 'out_res_name'],
name='filter_noise_nosmooth')
wf.connect(filter1, 'out_res', filter2, 'in_file')
wf.connect(filter1, ('out_res', rename, '_cleaned'),
filter2, 'out_res_name')
wf.connect(createfilter2, 'components_file', filter2, 'design')
wf.connect(mask, 'mask_file', filter2, 'mask')
bandpass = Node(Function(input_names=['files', 'lowpass_freq',
'highpass_freq', 'fs'],
output_names=['out_files'],
function=bandpass_filter,
imports=imports),
name='bandpass_unsmooth')
bandpass.inputs.fs = 1. / TR
bandpass.inputs.highpass_freq = highpass_freq
bandpass.inputs.lowpass_freq = lowpass_freq
wf.connect(filter2, 'out_res', bandpass, 'files')
"""Smooth the functional data using
:class:`nipype.interfaces.fsl.IsotropicSmooth`.
"""
smooth = MapNode(interface=fsl.IsotropicSmooth(), name="smooth", iterfield=["in_file"])
smooth.inputs.fwhm = vol_fwhm
wf.connect(bandpass, 'out_files', smooth, 'in_file')
collector = Node(Merge(2), name='collect_streams')
wf.connect(smooth, 'out_file', collector, 'in1')
wf.connect(bandpass, 'out_files', collector, 'in2')
"""
Transform the remaining images. First to anatomical and then to target
"""
warpall = MapNode(ants.ApplyTransforms(), iterfield=['input_image'],
name='warpall')
warpall.inputs.input_image_type = 3
warpall.inputs.interpolation = 'Linear'
warpall.inputs.invert_transform_flags = [False, False]
warpall.inputs.terminal_output = 'file'
warpall.inputs.reference_image = target_file
warpall.inputs.args = '--float'
warpall.inputs.num_threads = 2
warpall.plugin_args = {'sbatch_args': '-c%d' % 2}
# transform to target
wf.connect(collector, 'out', warpall, 'input_image')
wf.connect(registration, 'outputspec.transforms', warpall, 'transforms')
mask_target = Node(fsl.ImageMaths(op_string='-bin'), name='target_mask')
wf.connect(registration, 'outputspec.anat2target', mask_target, 'in_file')
maskts = MapNode(fsl.ApplyMask(), iterfield=['in_file'], name='ts_masker')
wf.connect(warpall, 'output_image', maskts, 'in_file')
wf.connect(mask_target, 'out_file', maskts, 'mask_file')
# map to surface
# extract aparc+aseg ROIs
# extract subcortical ROIs
# extract target space ROIs
# combine subcortical and cortical rois into a single cifti file
#######
# Convert aparc to subject functional space
# Sample the average time series in aparc ROIs
sampleaparc = MapNode(freesurfer.SegStats(default_color_table=True),
iterfield=['in_file', 'summary_file',
'avgwf_txt_file'],
name='aparc_ts')
sampleaparc.inputs.segment_id = ([8] + list(range(10, 14)) + [17, 18, 26, 47] +
list(range(49, 55)) + [58] + list(range(1001, 1036)) +
list(range(2001, 2036)))
wf.connect(registration, 'outputspec.aparc',
sampleaparc, 'segmentation_file')
wf.connect(collector, 'out', sampleaparc, 'in_file')
def get_names(files, suffix):
"""Generate appropriate names for output files
"""
from nipype.utils.filemanip import (split_filename, filename_to_list,
list_to_filename)
import os
out_names = []
for filename in files:
path, name, _ = split_filename(filename)
out_names.append(os.path.join(path, name + suffix))
return list_to_filename(out_names)
wf.connect(collector, ('out', get_names, '_avgwf.txt'),
sampleaparc, 'avgwf_txt_file')
wf.connect(collector, ('out', get_names, '_summary.stats'),
sampleaparc, 'summary_file')
# Sample the time series onto the surface of the target surface. Performs
# sampling into left and right hemisphere
target = Node(IdentityInterface(fields=['target_subject']), name='target')
target.iterables = ('target_subject', filename_to_list(target_subject))
samplerlh = MapNode(freesurfer.SampleToSurface(),
iterfield=['source_file'],
name='sampler_lh')
samplerlh.inputs.sampling_method = "average"
samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
samplerlh.inputs.sampling_units = "frac"
samplerlh.inputs.interp_method = "trilinear"
samplerlh.inputs.smooth_surf = surf_fwhm
# samplerlh.inputs.cortex_mask = True
samplerlh.inputs.out_type = 'niigz'
samplerlh.inputs.subjects_dir = subjects_dir
samplerrh = samplerlh.clone('sampler_rh')
samplerlh.inputs.hemi = 'lh'
wf.connect(collector, 'out', samplerlh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerlh, 'reg_file')
wf.connect(target, 'target_subject', samplerlh, 'target_subject')
samplerrh.set_input('hemi', 'rh')
wf.connect(collector, 'out', samplerrh, 'source_file')
wf.connect(registration, 'outputspec.out_reg_file', samplerrh, 'reg_file')
wf.connect(target, 'target_subject', samplerrh, 'target_subject')
# Combine left and right hemisphere to text file
combiner = MapNode(Function(input_names=['left', 'right'],
output_names=['out_file'],
function=combine_hemi,
imports=imports),
iterfield=['left', 'right'],
name="combiner")
wf.connect(samplerlh, 'out_file', combiner, 'left')
wf.connect(samplerrh, 'out_file', combiner, 'right')
# Sample the time series file for each subcortical roi
ts2txt = MapNode(Function(input_names=['timeseries_file', 'label_file',
'indices'],
output_names=['out_file'],
function=extract_subrois,
imports=imports),
iterfield=['timeseries_file'],
name='getsubcortts')
ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
list(range(49, 55)) + [58]
ts2txt.inputs.label_file = \
os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
'2mm_v2.nii.gz'))
wf.connect(maskts, 'out_file', ts2txt, 'timeseries_file')
######
substitutions = [('_target_subject_', ''),
('_filtermotart_cleaned_bp_trans_masked', ''),
('_filtermotart_cleaned_bp', ''),
]
substitutions += [("_smooth%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_ts_masker%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_getsubcortts%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_combiner%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_filtermotion%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_filter_noise_nosmooth%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_makecompcorfilter%d" % i, "") for i in range(11)[::-1]]
substitutions += [("_get_aparc_tsnr%d/" % i, "run%d_" % (i + 1)) for i in range(11)[::-1]]
substitutions += [("T1_out_brain_pve_0_maths_warped", "compcor_csf"),
("T1_out_brain_pve_1_maths_warped", "compcor_gm"),
("T1_out_brain_pve_2_maths_warped", "compcor_wm"),
("output_warped_image_maths", "target_brain_mask"),
("median_brain_mask", "native_brain_mask"),
("corr_", "")]
regex_subs = [('_combiner.*/sar', '/smooth/'),
('_combiner.*/ar', '/unsmooth/'),
('_aparc_ts.*/sar', '/smooth/'),
('_aparc_ts.*/ar', '/unsmooth/'),
('_getsubcortts.*/sar', '/smooth/'),
('_getsubcortts.*/ar', '/unsmooth/'),
('series/sar', 'series/smooth/'),
('series/ar', 'series/unsmooth/'),
('_inverse_transform./', ''),
]
# Save the relevant data into an output directory
datasink = Node(interface=DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
datasink.inputs.substitutions = substitutions
datasink.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(realign, 'par_file', datasink, 'resting.qa.motion')
wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
wf.connect(registration, 'outputspec.segmentation_files', datasink, 'resting.mask_files')
wf.connect(registration, 'outputspec.anat2target', datasink, 'resting.qa.ants')
wf.connect(mask, 'mask_file', datasink, 'resting.mask_files.@brainmask')
wf.connect(mask_target, 'out_file', datasink, 'resting.mask_files.target')
wf.connect(filter1, 'out_f', datasink, 'resting.qa.compmaps.@mc_F')
wf.connect(filter1, 'out_pf', datasink, 'resting.qa.compmaps.@mc_pF')
wf.connect(filter2, 'out_f', datasink, 'resting.qa.compmaps')
wf.connect(filter2, 'out_pf', datasink, 'resting.qa.compmaps.@p')
wf.connect(registration, 'outputspec.min_cost_file', datasink, 'resting.qa.mincost')
wf.connect(tsnr, 'tsnr_file', datasink, 'resting.qa.tsnr.@map')
wf.connect([(get_roi_tsnr, datasink, [('avgwf_txt_file', 'resting.qa.tsnr'),
('summary_file', 'resting.qa.tsnr.@summary')])])
wf.connect(bandpass, 'out_files', datasink, 'resting.timeseries.@bandpassed')
wf.connect(smooth, 'out_file', datasink, 'resting.timeseries.@smoothed')
wf.connect(createfilter1, 'out_files',
datasink, 'resting.regress.@regressors')
wf.connect(createfilter2, 'components_file',
datasink, 'resting.regress.@compcorr')
wf.connect(maskts, 'out_file', datasink, 'resting.timeseries.target')
wf.connect(sampleaparc, 'summary_file',
datasink, 'resting.parcellations.aparc')
wf.connect(sampleaparc, 'avgwf_txt_file',
datasink, 'resting.parcellations.aparc.@avgwf')
wf.connect(ts2txt, 'out_file',
datasink, 'resting.parcellations.grayo.@subcortical')
datasink2 = Node(interface=DataSink(), name="datasink2")
datasink2.inputs.base_directory = sink_directory
datasink2.inputs.container = subject_id
datasink2.inputs.substitutions = substitutions
datasink2.inputs.regexp_substitutions = regex_subs # (r'(/_.*(\d+/))', r'/run\2')
wf.connect(combiner, 'out_file',
datasink2, 'resting.parcellations.grayo.@surface')
return wf
from nipype import Node, Workflow
from nipype.interfaces import fsl
from nipype.interfaces.fsl import BET
from pathlib import Path
import os
ROOT_DIR = Path(os.path.dirname(os.path.abspath(__file__))).parent
in_file = os.path.join(ROOT_DIR, 'data', '031768_t1w_deface_stx.nii.gz')
# workflow
skullstrip = Node(fsl.BET(in_file=in_file, mask=True), name="skullstrip")
smooth = Node(fsl.IsotropicSmooth(in_file=in_file, fwhm=4), name="smooth")
mask = Node(fsl.ApplyMask(), name="mask")
wf = Workflow(name="smoothflow",
base_dir=os.path.join(ROOT_DIR, 'nipy_pipeline'))
# First the "simple", but more restricted method
wf.connect(skullstrip, "mask_file", mask, "mask_file")
# Now the more complicated method
wf.connect([(smooth, mask, [("out_file", "in_file")])])
wf.run()
def test_mapnode_json(tmpdir):
"""Tests that mapnodes don't generate excess jsons"""
tmpdir.chdir()
wd = os.getcwd()
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1 + 1
n1 = MapNode(
Function(input_names=["in1"], output_names=["out"], function=func1),
iterfield=["in1"],
name="n1",
)
n1.inputs.in1 = [1]
w1 = Workflow(name="test")
w1.base_dir = wd
w1.config["execution"]["crashdump_dir"] = wd
w1.add_nodes([n1])
w1.run()
n1.inputs.in1 = [2]
w1.run()
# should rerun
n1.inputs.in1 = [1]
eg = w1.run()
node = list(eg.nodes())[0]
outjson = glob(os.path.join(node.output_dir(), "_0x*.json"))
assert len(outjson) == 1
# check that multiple json's don't trigger rerun
with open(os.path.join(node.output_dir(), "test.json"), "wt") as fp:
fp.write("dummy file")
w1.config["execution"].update(**{"stop_on_first_rerun": True})
w1.run()
import glob
from nipype import Node, Workflow, MapNode
from nipype.algorithms.misc import Gunzip
img_files = glob.glob('/home/or/kpe_conn/fsl/maths/hippRight_ses2-1_*.nii.gz')
gunzip = MapNode(Gunzip(), name='gunzip',
iterfield=['in_file'])
gunzip.inputs.in_file = img_files
# use if comparing same session:
onesamplettestdes = Node(spm.OneSampleTTestDesign(),
name="onesampttestdes")
tTest= Workflow(name='oneSampleTtest_total')
tTest.base_dir = ('/media/Data/work/amg_coordsseedBased')
# EstimateModel - estimates the model
level2estimate = Node(spm.EstimateModel(estimation_method={'Classical': 1}),
name="level2estimate")
# EstimateContrast - estimates group contrast
level2conestimate = Node(spm.EstimateContrast(group_contrast=True),
name="level2conestimate")
cont1 = ['Group', 'T', ['mean'], [1]]
level2conestimate.inputs.contrasts = [cont1]
# Threshold - thresholds contrasts
level2thresh = Node(spm.Threshold(contrast_index=1,
use_topo_fdr=True,
def run(base_dir, TR):
template = d.tpm
matlab_cmd = '/home/cpulido/Documentos/programas/spm/spm12/run_spm12.sh /opt/mcr/v95/ script'
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
print('SPM version: ' + str(spm.SPMCommand().version))
#base_dir = '/home/colciencias/test/base/'
structural_dir = opj(base_dir, 'struc')
experiment_dir = opj(base_dir, 'output/')
output_dir = 'datasink'
working_dir = 'workingdir'
subject_list = ['1']
# list of subject identifiers
fwhm = 8 # Smoothing widths to apply (Gaussian kernel size)
#TR = 3 # Repetition time
init_volume = 5 # Firts volumen identification which will use in the pipeline
iso_size = 2 # Isometric resample of functional images to voxel size (in mm)
# ExtractROI - skip dummy scans
extract = Node(ExtractROI(t_min=init_volume,
t_size=-1,
output_type='NIFTI'),
name="extract")
# MCFLIRT - motion correction
mcflirt = Node(MCFLIRT(mean_vol=True, save_plots=True,
output_type='NIFTI'),
name="motion_correction")
# SliceTimer - correct for slice wise acquisition
slicetimer = Node(SliceTimer(index_dir=False,
interleaved=True,
output_type='NIFTI',
time_repetition=TR),
name="slice_timing_correction")
# Smooth - image smoothing
smooth = Node(spm.Smooth(fwhm=fwhm), name="smooth")
n4bias = Node(N4Bias(out_file='t1_n4bias.nii.gz'), name='n4bias')
descomposition = Node(Descomposition(n_components=20,
low_pass=0.1,
high_pass=0.01,
tr=TR),
name='descomposition')
# Artifact Detection - determines outliers in functional images
art = Node(ArtifactDetect(norm_threshold=2,
zintensity_threshold=3,
mask_type='spm_global',
parameter_source='FSL',
use_differences=[True, False],
plot_type='svg'),
name="artifact_detection")
extract_confounds_ws_csf = Node(
ExtractConfounds(out_file='ev_without_gs.csv'),
name='extract_confounds_ws_csf')
extract_confounds_gs = Node(ExtractConfounds(out_file='ev_with_gs.csv',
delimiter=','),
name='extract_confounds_global_signal')
signal_extraction = Node(SignalExtraction(
time_series_out_file='time_series.csv',
correlation_matrix_out_file='correlation_matrix.png',
atlas_identifier='cort-maxprob-thr25-2mm',
tr=TR,
plot=True),
name='signal_extraction')
art_remotion = Node(ArtifacRemotion(out_file='fmri_art_removed.nii'),
name='artifact_remotion')
# BET - Skullstrip anatomical anf funtional images
bet_t1 = Node(BET(frac=0.5, robust=True, mask=True,
output_type='NIFTI_GZ'),
name="bet_t1")
# bet_fmri = Node(BET(frac=0.6, functional = True, output_type='NIFTI_GZ'), name="bet_fmri")
# FAST - Image Segmentation
segmentation = Node(FAST(output_type='NIFTI'), name="segmentation")
# Normalize - normalizes functional and structural images to the MNI template
normalize_fmri = Node(Normalize12(jobtype='estwrite',
tpm=template,
write_voxel_sizes=[2, 2, 2],
write_bounding_box=[[-90, -126, -72],
[90, 90, 108]]),
name="normalize_fmri")
gunzip = Node(Gunzip(), name="gunzip")
normalize_t1 = Node(Normalize12(
jobtype='estwrite',
tpm=template,
write_voxel_sizes=[iso_size, iso_size, iso_size],
write_bounding_box=[[-90, -126, -72], [90, 90, 108]]),
name="normalize_t1")
normalize_masks = Node(Normalize12(
jobtype='estwrite',
tpm=template,
write_voxel_sizes=[iso_size, iso_size, iso_size],
write_bounding_box=[[-90, -126, -72], [90, 90, 108]]),
name="normalize_masks")
# Threshold - Threshold WM probability image
threshold = Node(Threshold(thresh=0.5, args='-bin',
output_type='NIFTI_GZ'),
name="wm_mask_threshold")
# FLIRT - pre-alignment of functional images to anatomical images
coreg_pre = Node(FLIRT(dof=6, output_type='NIFTI_GZ'),
name="linear_warp_estimation")
# FLIRT - coregistration of functional images to anatomical images with BBR
coreg_bbr = Node(FLIRT(dof=6,
cost='bbr',
schedule=opj(os.getenv('FSLDIR'),
'etc/flirtsch/bbr.sch'),
output_type='NIFTI_GZ'),
name="nonlinear_warp_estimation")
# Apply coregistration warp to functional images
applywarp = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI'),
name="registration_fmri")
# Apply coregistration warp to mean file
applywarp_mean = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI_GZ'),
name="registration_mean_fmri")
# Infosource - a function free node to iterate over the list of subject names
infosource = Node(IdentityInterface(fields=['subject_id']),
name="infosource")
infosource.iterables = [('subject_id', subject_list)]
# SelectFiles - to grab the data (alternativ to DataGrabber)
anat_file = opj(structural_dir, '{subject_id}', 't1.nii')
func_file = opj('{subject_id}', 'fmri.nii')
templates = {'anat': anat_file, 'func': func_file}
selectfiles = Node(SelectFiles(templates, base_directory=base_dir),
name="selectfiles")
# Datasink - creates output folder for important outputs
datasink = Node(DataSink(base_directory=experiment_dir,
container=output_dir),
name="datasink")
# Create a coregistration workflow
coregwf = Workflow(name='coreg_fmri_to_t1')
coregwf.base_dir = opj(experiment_dir, working_dir)
# Create a preprocessing workflow
preproc = Workflow(name='preproc')
preproc.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the coregistration workflow
coregwf.connect([
(bet_t1, n4bias, [('out_file', 'in_file')]),
(n4bias, segmentation, [('out_file', 'in_files')]),
(segmentation, threshold, [(('partial_volume_files', get_latest),
'in_file')]),
(n4bias, coreg_pre, [('out_file', 'reference')]),
(threshold, coreg_bbr, [('out_file', 'wm_seg')]),
(coreg_pre, coreg_bbr, [('out_matrix_file', 'in_matrix_file')]),
(coreg_bbr, applywarp, [('out_matrix_file', 'in_matrix_file')]),
(n4bias, applywarp, [('out_file', 'reference')]),
(coreg_bbr, applywarp_mean, [('out_matrix_file', 'in_matrix_file')]),
(n4bias, applywarp_mean, [('out_file', 'reference')]),
])
## Use the following DataSink output substitutions
substitutions = [('_subject_id_', 'sub-')]
# ('_fwhm_', 'fwhm-'),
# ('_roi', ''),
# ('_mcf', ''),
# ('_st', ''),
# ('_flirt', ''),
# ('.nii_mean_reg', '_mean'),
# ('.nii.par', '.par'),
# ]
#subjFolders = [('fwhm-%s/' % f, 'fwhm-%s_' % f) for f in fwhm]
#substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions
# Connect all components of the preprocessing workflow
preproc.connect([
(infosource, selectfiles, [('subject_id', 'subject_id')]),
(selectfiles, extract, [('func', 'in_file')]),
(extract, mcflirt, [('roi_file', 'in_file')]),
(mcflirt, slicetimer, [('out_file', 'in_file')]),
(selectfiles, coregwf, [('anat', 'bet_t1.in_file'),
('anat', 'nonlinear_warp_estimation.reference')
]),
(mcflirt, coregwf, [('mean_img', 'linear_warp_estimation.in_file'),
('mean_img', 'nonlinear_warp_estimation.in_file'),
('mean_img', 'registration_mean_fmri.in_file')]),
(slicetimer, coregwf, [('slice_time_corrected_file',
'registration_fmri.in_file')]),
(coregwf, art, [('registration_fmri.out_file', 'realigned_files')]),
(mcflirt, art, [('par_file', 'realignment_parameters')]),
(art, art_remotion, [('outlier_files', 'outlier_files')]),
(coregwf, art_remotion, [('registration_fmri.out_file', 'in_file')]),
(coregwf, gunzip, [('n4bias.out_file', 'in_file')]),
(selectfiles, normalize_fmri, [('anat', 'image_to_align')]),
(art_remotion, normalize_fmri, [('out_file', 'apply_to_files')]),
(selectfiles, normalize_t1, [('anat', 'image_to_align')]),
(gunzip, normalize_t1, [('out_file', 'apply_to_files')]),
(selectfiles, normalize_masks, [('anat', 'image_to_align')]),
(coregwf, normalize_masks, [(('segmentation.partial_volume_files',
get_wm_csf), 'apply_to_files')]),
(normalize_fmri, smooth, [('normalized_files', 'in_files')]),
(smooth, extract_confounds_ws_csf, [('smoothed_files', 'in_file')]),
(normalize_masks, extract_confounds_ws_csf, [('normalized_files',
'list_mask')]),
(mcflirt, extract_confounds_ws_csf, [('par_file', 'file_concat')]),
(smooth, extract_confounds_gs, [('smoothed_files', 'in_file')]),
(normalize_t1, extract_confounds_gs,
[(('normalized_files', change_to_list), 'list_mask')]),
(extract_confounds_ws_csf, extract_confounds_gs, [('out_file',
'file_concat')]),
(smooth, signal_extraction, [('smoothed_files', 'in_file')]),
(extract_confounds_gs, signal_extraction, [('out_file',
'confounds_file')]),
#(extract_confounds_ws_csf, signal_extraction, [('out_file', 'confounds_file')]),
(smooth, descomposition, [('smoothed_files', 'in_file')]),
(extract_confounds_ws_csf, descomposition, [('out_file',
'confounds_file')]),
(extract_confounds_gs, datasink,
[('out_file', 'preprocessing.@confounds_with_gs')]),
(extract_confounds_ws_csf, datasink,
[('out_file', 'preprocessing.@confounds_without_gs')]),
(smooth, datasink, [('smoothed_files', 'preprocessing.@smoothed')]),
(normalize_fmri, datasink, [('normalized_files',
'preprocessing.@fmri_normalized')]),
(normalize_t1, datasink, [('normalized_files',
'preprocessing.@t1_normalized')]),
(normalize_masks, datasink, [('normalized_files',
'preprocessing.@masks_normalized')]),
(signal_extraction, datasink, [('time_series_out_file',
'preprocessing.@time_serie')]),
(signal_extraction, datasink, [('correlation_matrix_out_file',
'preprocessing.@correlation_matrix')]),
(descomposition, datasink, [('out_file',
'preprocessing.@descomposition')]),
(descomposition, datasink,
[('plot_files', 'preprocessing.@descomposition_plot_files')]),
(descomposition, datasink,
[('time_series', 'preprocessing.@descomposition_time_series')])
])
#preproc.write_graph(graph2use='colored', format='png', simple_form=True)
preproc.run()
os.system('rm -rf %s' % opj(base_dir, 'output/') + working_dir)
def get_nuisance_regressors_wf(outdir, timepoints, subject_id, global_signal=False, order=0, derivatives=1, comp=3):
"""Creates nipype workflow for nuisance correction composed by:
Intercept + Drift (cosine transform) + Motion Correction + WhiteMatter&CSF Nuisance Regressors (CompCor)
Parameters
----------
outdir:
subject_id:
global_signal:
timepoints:
order:
derivatives:
comp:
Returns
-------
wf_reg:
"""
from nipype.algorithms import confounds
from nipype import Workflow, Node
from nipype.interfaces import utility, fsl
import os
if global_signal:
gb='_GB'
else:
gb=''
wf_reg=Workflow(name=subject_id+gb,base_dir=outdir);
print ("Setting INPUT node...");
node_input = Node(utility.IdentityInterface(fields=[
"realign_movpar_txt",
'rfmri_unwarped_imgs',
'mask_wm',
'mask_csf',
'global_mask_img',
'bold_img'
]),
name='input_node'
)
#Merging wm and csf masks
node_merge_wm_csf = Node(utility.base.Merge(2),name='Merge_wm_csf')
#AcompCor
node_ACompCor=Node(confounds.ACompCor(
num_components=3,
#save_pre_filter='high_pass_filter.txt',
pre_filter=False,
# high_pass_cutoff=128,
repetition_time=0.8,
merge_method='none',
#use_regress_poly=False,
#realigned_file= fMRI_BOLD_unwarped,
# mask_files='/institut/processed_data/BBHI_func/output2/sub-41064/GetMasksInT1Space/binarize_mask/MNI152_WM_09_warp_thresh.nii.gz',
),
name="AcompCor_mask")
#node_ACompCor.inputs.save_pre_filter=os.path.join(os.path.join(os.path.join(wf_reg.base_dir,wf_reg.name),node_ACompCor.name), 'high_pass_filter.txt')
#cosine_filter
node_cosine_filter_reg=Node(utility.Function(input_names=["timepoints", "timestep","period_cut","output_dir"],
output_names=["cosine_filter_txt"],
function=cosine_filter_txt),
name="cosine_filter")
node_cosine_filter_reg.inputs.output_dir=os.path.join(os.path.join(os.path.join(wf_reg.base_dir,wf_reg.name)),node_cosine_filter_reg.name)
node_cosine_filter_reg.inputs.timepoints=timepoints
node_cosine_filter_reg.inputs.timestep=0.8
#node_cosine_filter_reg.overwrite=True
#global_signal
# if global_signal :
# node_global_signal=Node(utility.Function(input_names=["timeseries_file", "label_file", "filename"],
# output_names=["global_signal_txt"],
# function=extract_subrois),
# name="global_signal")
# node_global_signal.inputs.filename=os.path.join(os.path.join(os.path.join(os.path.join(wf_reg.base_dir,wf_reg.name)),node_global_signal.name),'global_signal.txt')
# #node_global_signal.overwrite=True
#motion regressors
motion_regressors_interface = utility.Function(input_names=["realign_movpar_txt", "output_dir","order","derivatives"],
output_names=["motion_reg_txt"],
function=motion_regressors)
node_motion_regressors=Node(motion_regressors_interface, name="motion_regressors_txt")
node_motion_regressors.inputs.output_dir=os.path.join(os.path.join(os.path.join(wf_reg.base_dir,wf_reg.name)),node_motion_regressors.name)
#node_motion_regressors.overwrite=True
#merges all regressors
node_merge_txts = Node(utility.base.Merge(4),name='Merge_txt_inputs')
node_merge_regressors = Node(utility.Function(input_names=["nuisance_txts", "output_dir"],
output_names=["nuisance_txt"],
function=merge_nuisance_regressors),
name="merge_nuisance_txt")
node_merge_regressors.inputs.output_dir=os.path.join(os.path.join(wf_reg.base_dir,wf_reg.name),node_merge_regressors.name)
node_filter_regressor = Node(fsl.FilterRegressor(
#design_file (-d) nuissance_txt
filter_all=True,
#in_file (-i) bold after SPM coregistration to T1
#out_file
),
name="filter_regressors_bold")
node_output = Node(utility.IdentityInterface(fields=[
'nuisance_txt',
'bold_nuisance_filtered'
]),
name='output_node')
wf_reg.connect([ (node_input, node_merge_wm_csf, [('mask_wm','in1'),
('mask_csf', 'in2')]),
(node_input, node_ACompCor,[('rfmri_unwarped_imgs', 'realigned_file')]),
(node_merge_wm_csf, node_ACompCor, [('out', 'mask_files')]),
(node_input, node_motion_regressors,[('realign_movpar_txt', 'realign_movpar_txt')]),
(node_motion_regressors,node_merge_txts, [('motion_reg_txt', 'in1')]),
(node_ACompCor,node_merge_txts, [('components_file', 'in2')]),
(node_cosine_filter_reg,node_merge_txts, [('cosine_filter_txt', 'in3')]),
(node_merge_txts, node_merge_regressors, [('out', 'nuisance_txts')]),
])
# if global_signal:
# wf_reg.connect([
# (node_input, node_global_signal,[('rfmri_unwarped_imgs', 'timeseries_file'),
# ('global_mask_img', 'label_file')]),
# (node_global_signal, node_merge_txts, [('global_signal_txt', 'in4')])
# ])
wf_reg.connect([ (node_merge_regressors, node_filter_regressor, [('nuisance_txt','design_file')]),
(node_input, node_filter_regressor, [('bold_img','in_file')]),
(node_filter_regressor, node_output, [('out_file','bold_nuisance_filtered')]),
(node_merge_regressors, node_output,[('nuisance_txt', 'nuisance_txt')])
])
return wf_reg
# FINDING CLUSTERS IN THE ANALYSIS RESULTS
# cluster node
cluster = Node(fsl.Cluster(in_file=imgZStat,
threshold=zThresh,
out_index_file=True,
out_threshold_file=True,
out_localmax_txt_file=True),
name='cluster')
# data sink node
datasink = Node(DataSink(base_directory=statsDir),
name='datasink')
# workflow connecting clustering to the datasink
clusterWF = Workflow(name="clusterWF", base_dir=outDir)
clusterWF.connect(cluster, 'index_file', datasink, 'index_file')
clusterWF.connect(cluster, 'threshold_file', datasink, 'threshold_file')
clusterWF.connect(cluster, 'localmax_txt_file', datasink, 'localmax_txt_file')
clusterWF.run()
# LOADING CLUSTER MAXIMA TABLE
fMaxTable = os.path.join(statsDir,'localmax_txt_file/zstat1_localmax.txt')
maxData = pd.read_csv(fMaxTable, sep='\t') # reading the maxima file as a dataframe
maxData.dropna(how='all', axis=1, inplace=True) # removing empty columns
print(maxData)
# CALCULATING CLUSTER SIZES
fClusInd = os.path.join(statsDir,'index_file/zstat1_index.nii.gz')
def init_single_ses_anat_preproc_wf(subject,
session,
bids_dir,
smriprep_dir,
out_dir,
omp_nthreads=1,
name='anat_preproc_wf',
smriprep06=False):
wf = Workflow(name=name)
if smriprep06:
def subject_info_fnc(bids_dir, smriprep_dir, subject, session):
from pathlib import Path
tpl_t1w = str(
Path(
smriprep_dir,
f"sub-{subject}/anat/sub-{subject}_desc-preproc_T1w.nii.gz"
))
tpl_brainmask = str(
Path(
smriprep_dir,
f"sub-{subject}/anat/sub-{subject}_desc-brain_mask.nii.gz")
)
t1ws = list(
Path(bids_dir).glob(
f"sub-{subject}/ses-{session}/anat/*_T1w.nii.gz"))
assert len(
t1ws) > 0, f"Expected at least one file, but found {t1ws}"
t1ws.sort()
xfms = list(
Path(smriprep_dir).glob(
f"sub-{subject}/ses-{session}/anat/*_run-*_T1w_space-orig_target-T1w_affine.txt"
))
xfms.sort()
for f in t1ws:
if not f.is_file():
raise FileNotFoundError(f)
t1ws = [str(o) for o in t1ws] # as Path is not taken everywhere
xfms = [str(o) for o in xfms]
return tpl_t1w, tpl_brainmask, t1ws, xfms
else:
def subject_info_fnc(bids_dir, smriprep_dir, subject, session):
from pathlib import Path
tpl_t1w = str(
Path(smriprep_dir,
f"sub-{subject}/anat/sub-{subject}_T1w_preproc.nii.gz"))
tpl_brainmask = str(
Path(smriprep_dir,
f"sub-{subject}/anat/sub-{subject}_T1w_brainmask.nii.gz"))
if not Path(tpl_t1w).is_file():
tpl_t1w = str(
list(
Path(smriprep_dir).glob(
f"sub-{subject}/ses*/anat/sub-{subject}*_T1w_preproc.nii.gz"
))[0])
tpl_brainmask = str(
list(
Path(smriprep_dir).glob(
f"sub-{subject}/ses*/anat/sub-{subject}*_T1w_brainmask.nii.gz"
))[0])
if not Path(tpl_t1w).is_file():
raise FileNotFoundError(tpl_t1w)
t1ws = list(
Path(bids_dir).glob(
f"sub-{subject}/ses-{session}/anat/*_T1w.nii.gz"))
assert len(
t1ws) > 0, f"Expected at least one file, but found {t1ws}"
t1ws.sort()
xfms = list(
Path(smriprep_dir).glob(
f"sub-{subject}/ses-{session}/anat/*_run-*_T1w_space-orig_target-T1w_affine.txt"
))
xfms.sort()
for f in t1ws + xfms:
if not f.is_file():
raise FileNotFoundError(f)
t1ws = [str(o) for o in t1ws] # as Path is not taken everywhere
xfms = [str(o) for o in xfms]
return tpl_t1w, tpl_brainmask, t1ws, xfms
grabber = pe.Node(niu.Function(
input_names=["bids_dir", "smriprep_dir", "subject", "session"],
output_names=["tpl_t1w", "tpl_brainmask", "t1ws", "xfms"],
function=subject_info_fnc),
name="grabber")
grabber.inputs.bids_dir = bids_dir
grabber.inputs.smriprep_dir = smriprep_dir
grabber.inputs.subject = subject
grabber.inputs.session = session
t1w_biascorr = pe.MapNode(ants.N4BiasFieldCorrection(
save_bias=False, num_threads=omp_nthreads),
iterfield=["input_image"],
name="t1w_biascorr")
wf.connect(grabber, "t1ws", t1w_biascorr, "input_image")
t1w_tpl_space = pe.MapNode(fsl.FLIRT(dof=6),
iterfield=["in_file"],
name="t1w_tpl_space")
wf.connect(grabber, "tpl_t1w", t1w_tpl_space, "reference")
wf.connect(t1w_biascorr, "output_image", t1w_tpl_space, "in_file")
merge_t1w = pe.Node(fsl.Merge(dimension="t"), name='merge_t1w')
wf.connect(t1w_tpl_space, "out_file", merge_t1w, "in_files")
mean_t1w = pe.Node(fsl.MeanImage(), name='mean_t1w')
wf.connect(merge_t1w, "merged_file", mean_t1w, "in_file")
t1w_brain_tpl_space = pe.Node(fsl.ApplyMask(), name="t1w_brain_tpl_space")
wf.connect(mean_t1w, "out_file", t1w_brain_tpl_space, "in_file")
wf.connect(grabber, "tpl_brainmask", t1w_brain_tpl_space, "mask_file")
ds = init_t1w_derivatives_wf(bids_dir, out_dir)
ds.inputs.inputnode.subject = subject
ds.inputs.inputnode.session = session
wf.connect(mean_t1w, "out_file", ds, "inputnode.t1w_template_space")
wf.connect(t1w_brain_tpl_space, "out_file", ds,
"inputnode.t1w_brain_template_space")
return wf
def group_multregress_openfmri(dataset_dir, model_id=None, task_id=None, l1output_dir=None, out_dir=None,
no_reversal=False, plugin=None, plugin_args=None, flamemodel='flame1',
nonparametric=False, use_spm=False):
meta_workflow = Workflow(name='mult_regress')
meta_workflow.base_dir = work_dir
for task in task_id:
task_name = get_taskname(dataset_dir, task)
cope_ids = l1_contrasts_num(model_id, task_name, dataset_dir)
regressors_needed, contrasts, groups, subj_list = get_sub_vars(dataset_dir, task_name, model_id)
for idx, contrast in enumerate(contrasts):
wk = Workflow(name='model_%03d_task_%03d_contrast_%s' % (model_id, task, contrast[0][0]))
info = Node(util.IdentityInterface(fields=['model_id', 'task_id', 'dataset_dir', 'subj_list']),
name='infosource')
info.inputs.model_id = model_id
info.inputs.task_id = task
info.inputs.dataset_dir = dataset_dir
dg = Node(DataGrabber(infields=['model_id', 'task_id', 'cope_id'],
outfields=['copes', 'varcopes']), name='grabber')
dg.inputs.template = os.path.join(l1output_dir,
'model%03d/task%03d/%s/%scopes/%smni/%scope%02d.nii%s')
if use_spm:
dg.inputs.template_args['copes'] = [['model_id', 'task_id', subj_list, '', 'spm/',
'', 'cope_id', '']]
dg.inputs.template_args['varcopes'] = [['model_id', 'task_id', subj_list, 'var', 'spm/',
'var', 'cope_id', '.gz']]
else:
dg.inputs.template_args['copes'] = [['model_id', 'task_id', subj_list, '', '', '',
'cope_id', '.gz']]
dg.inputs.template_args['varcopes'] = [['model_id', 'task_id', subj_list, 'var', '',
'var', 'cope_id', '.gz']]
dg.iterables=('cope_id', cope_ids)
dg.inputs.sort_filelist = False
wk.connect(info, 'model_id', dg, 'model_id')
wk.connect(info, 'task_id', dg, 'task_id')
model = Node(MultipleRegressDesign(), name='l2model')
model.inputs.groups = groups
model.inputs.contrasts = contrasts[idx]
model.inputs.regressors = regressors_needed[idx]
mergecopes = Node(Merge(dimension='t'), name='merge_copes')
wk.connect(dg, 'copes', mergecopes, 'in_files')
if flamemodel != 'ols':
mergevarcopes = Node(Merge(dimension='t'), name='merge_varcopes')
wk.connect(dg, 'varcopes', mergevarcopes, 'in_files')
mask_file = fsl.Info.standard_image('MNI152_T1_2mm_brain_mask.nii.gz')
flame = Node(FLAMEO(), name='flameo')
flame.inputs.mask_file = mask_file
flame.inputs.run_mode = flamemodel
#flame.inputs.infer_outliers = True
wk.connect(model, 'design_mat', flame, 'design_file')
wk.connect(model, 'design_con', flame, 't_con_file')
wk.connect(mergecopes, 'merged_file', flame, 'cope_file')
if flamemodel != 'ols':
wk.connect(mergevarcopes, 'merged_file', flame, 'var_cope_file')
wk.connect(model, 'design_grp', flame, 'cov_split_file')
if nonparametric:
palm = Node(Function(input_names=['cope_file', 'design_file', 'contrast_file',
'group_file', 'mask_file', 'cluster_threshold'],
output_names=['palm_outputs'],
function=run_palm),
name='palm')
palm.inputs.cluster_threshold = 3.09
palm.inputs.mask_file = mask_file
palm.plugin_args = {'sbatch_args': '-p om_all_nodes -N1 -c2 --mem=10G', 'overwrite': True}
wk.connect(model, 'design_mat', palm, 'design_file')
wk.connect(model, 'design_con', palm, 'contrast_file')
wk.connect(mergecopes, 'merged_file', palm, 'cope_file')
wk.connect(model, 'design_grp', palm, 'group_file')
smoothest = Node(SmoothEstimate(), name='smooth_estimate')
wk.connect(flame, 'zstats', smoothest, 'zstat_file')
smoothest.inputs.mask_file = mask_file
cluster = Node(Cluster(), name='cluster')
wk.connect(smoothest,'dlh', cluster, 'dlh')
wk.connect(smoothest, 'volume', cluster, 'volume')
cluster.inputs.connectivity = 26
cluster.inputs.threshold = 2.3
cluster.inputs.pthreshold = 0.05
cluster.inputs.out_threshold_file = True
cluster.inputs.out_index_file = True
cluster.inputs.out_localmax_txt_file = True
wk.connect(flame, 'zstats', cluster, 'in_file')
ztopval = Node(ImageMaths(op_string='-ztop', suffix='_pval'),
name='z2pval')
wk.connect(flame, 'zstats', ztopval,'in_file')
sinker = Node(DataSink(), name='sinker')
sinker.inputs.base_directory = os.path.join(out_dir, 'task%03d' % task, contrast[0][0])
sinker.inputs.substitutions = [('_cope_id', 'contrast'),
('_maths_', '_reversed_')]
wk.connect(flame, 'zstats', sinker, 'stats')
wk.connect(cluster, 'threshold_file', sinker, 'stats.@thr')
wk.connect(cluster, 'index_file', sinker, 'stats.@index')
wk.connect(cluster, 'localmax_txt_file', sinker, 'stats.@localmax')
if nonparametric:
wk.connect(palm, 'palm_outputs', sinker, 'stats.palm')
if not no_reversal:
zstats_reverse = Node( BinaryMaths() , name='zstats_reverse')
zstats_reverse.inputs.operation = 'mul'
zstats_reverse.inputs.operand_value = -1
wk.connect(flame, 'zstats', zstats_reverse, 'in_file')
cluster2=cluster.clone(name='cluster2')
wk.connect(smoothest, 'dlh', cluster2, 'dlh')
wk.connect(smoothest, 'volume', cluster2, 'volume')
wk.connect(zstats_reverse, 'out_file', cluster2, 'in_file')
ztopval2 = ztopval.clone(name='ztopval2')
wk.connect(zstats_reverse, 'out_file', ztopval2, 'in_file')
wk.connect(zstats_reverse, 'out_file', sinker, 'stats.@neg')
wk.connect(cluster2, 'threshold_file', sinker, 'stats.@neg_thr')
wk.connect(cluster2, 'index_file',sinker, 'stats.@neg_index')
wk.connect(cluster2, 'localmax_txt_file', sinker, 'stats.@neg_localmax')
meta_workflow.add_nodes([wk])
return meta_workflow
segstatPost = Node(Function(input_names = ['aparc_stats'],
output_names = ['clearedFileName'],
function = segstat_shaping),
name = 'segstat_Postprocesser')
# ### Compute the FC
compFCNode = Node(Function(input_names = ['path', 'subName', 'avgwf_txt_file', 'summary_file_cleared'],
output_names = ['matfile_name'],
function = compute_functional_connectivity),
name = 'compute_FC')
# ## Define the Workflow
wf = Workflow('fMRI_Processing')
# wf.connect([(inputNode, rawFinderNode, [('raw_files', 'root_paths')])])
wf.connect([(inputNode, folderMaker, [('subject_folder', 'path_name')])])
# wf.connect([(rawFinderNode, convertNode, [(('out_paths', selectFromList, 0), 'in_file')]),
wf.connect([(inputNode, convertNode, [(('raw_files', selectFromList, 0), 'in_file')]),
(folderMaker, convertNode, [(('folder_path', fileNameBuilder, fileNames['bold_file']), 'out_file')])])
wf.connect([(convertNode, featNode, [('out_file', 'bold_file')]),
(folderMaker, featNode, [('folder_path', 'bold_folder')]),
(inputNode, featNode, [('brainmask', 'brainmask_file')])])
wf.connect([(featNode, exfunc2anat, [(('feat_dir', featFileNameBuilder, 'mean_func.nii.gz'), 'in_file')]),
def test_mapnode_json(tmpdir):
"""Tests that mapnodes don't generate excess jsons
"""
wd = str(tmpdir)
os.chdir(wd)
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
w1.add_nodes([n1])
w1.run()
n1.inputs.in1 = [2]
w1.run()
# should rerun
n1.inputs.in1 = [1]
eg = w1.run()
node = eg.nodes()[0]
outjson = glob(os.path.join(node.output_dir(), '_0x*.json'))
assert len(outjson) == 1
# check that multiple json's don't trigger rerun
with open(os.path.join(node.output_dir(), 'test.json'), 'wt') as fp:
fp.write('dummy file')
w1.config['execution'].update(**{'stop_on_first_rerun': True})
w1.run()
t_min=4, # first 4 volumes are deleted
t_size=-1),
name="extract")
# creating motion correction node
mcflirt = Node(
fsl.MCFLIRT(save_rms=True,
save_plots=True), # saving displacement parameters
name="mcflirt")
# creating datasink to collect outputs
datasink = Node(DataSink(base_directory=os.path.join(outDir, 'Results')),
name='datasink')
# creating a workflow
moCor = Workflow(name="MoCor", base_dir=outDir)
# connecting the nodes
moCor.connect(extract, 'roi_file', mcflirt, 'in_file')
# output to datasink
moCor.connect(mcflirt, 'out_file', datasink, 'out_file') # corrected fMRI
moCor.connect(mcflirt, 'par_file', datasink, 'par_file') # motion parameter
moCor.connect(mcflirt, 'rms_files', datasink, 'rms_files') # relative motion
# writing out graph
moCor.write_graph(graph2use='orig', dotfilename='graph_orig.dot')
# showing the graph
plt.figure(figsize=[4, 4])
img = mpimg.imread(os.path.join(outDir, "moCor", "graph_orig.png"))
def create_volume_mixedfx_workflow(name="volume_group",
subject_list=None,
regressors=None,
contrasts=None,
exp_info=None):
# Handle default arguments
if subject_list is None:
subject_list = []
if regressors is None:
regressors = dict(group_mean=[])
if contrasts is None:
contrasts = [["group_mean", "T", ["group_mean"], [1]]]
if exp_info is None:
exp_info = lyman.default_experiment_parameters()
# Define workflow inputs
inputnode = Node(IdentityInterface(["l1_contrast",
"copes",
"varcopes",
"dofs"]),
"inputnode")
# Merge the fixed effect summary images into one 4D image
merge = Node(MergeAcrossSubjects(), "merge")
# Make a simple design
design = Node(fsl.MultipleRegressDesign(regressors=regressors,
contrasts=contrasts),
"design")
# Fit the mixed effects model
flameo = Node(fsl.FLAMEO(run_mode=exp_info["flame_mode"]), "flameo")
# Estimate the smoothness of the data
smoothest = Node(fsl.SmoothEstimate(), "smoothest")
# Correct for multiple comparisons
cluster = Node(fsl.Cluster(threshold=exp_info["cluster_zthresh"],
pthreshold=exp_info["grf_pthresh"],
out_threshold_file=True,
out_index_file=True,
out_localmax_txt_file=True,
peak_distance=exp_info["peak_distance"],
use_mm=True),
"cluster")
# Project the mask and thresholded zstat onto the surface
surfproj = create_surface_projection_workflow(exp_info=exp_info)
# Segment the z stat image with a watershed algorithm
watershed = Node(Watershed(), "watershed")
# Make static report images in the volume
report = Node(MFXReport(), "report")
report.inputs.subjects = subject_list
# Save the experiment info
saveparams = Node(SaveParameters(exp_info=exp_info), "saveparams")
# Define the workflow outputs
outputnode = Node(IdentityInterface(["copes",
"varcopes",
"mask_file",
"flameo_stats",
"thresh_zstat",
"surf_zstat",
"surf_mask",
"cluster_image",
"seg_file",
"peak_file",
"lut_file",
"report",
"json_file"]),
"outputnode")
# Define and connect up the workflow
group = Workflow(name)
group.connect([
(inputnode, merge,
[("copes", "cope_files"),
("varcopes", "varcope_files"),
("dofs", "dof_files")]),
(inputnode, saveparams,
[("copes", "in_file")]),
(merge, flameo,
[("cope_file", "cope_file"),
("varcope_file", "var_cope_file"),
("dof_file", "dof_var_cope_file"),
("mask_file", "mask_file")]),
(design, flameo,
[("design_con", "t_con_file"),
("design_grp", "cov_split_file"),
("design_mat", "design_file")]),
(flameo, smoothest,
[("zstats", "zstat_file")]),
(merge, smoothest,
[("mask_file", "mask_file")]),
(smoothest, cluster,
[("dlh", "dlh"),
("volume", "volume")]),
(flameo, cluster,
[("zstats", "in_file")]),
(cluster, watershed,
[("threshold_file", "zstat_file"),
("localmax_txt_file", "localmax_file")]),
(merge, report,
[("mask_file", "mask_file"),
("cope_file", "cope_file")]),
(flameo, report,
[("zstats", "zstat_file")]),
(cluster, report,
[("threshold_file", "zstat_thresh_file"),
("localmax_txt_file", "localmax_file")]),
(watershed, report,
[("seg_file", "seg_file")]),
(merge, surfproj,
[("mask_file", "inputs.mask_file")]),
(cluster, surfproj,
[("threshold_file", "inputs.zstat_file")]),
(merge, outputnode,
[("cope_file", "copes"),
("varcope_file", "varcopes"),
("mask_file", "mask_file")]),
(flameo, outputnode,
[("stats_dir", "flameo_stats")]),
(cluster, outputnode,
[("threshold_file", "thresh_zstat"),
("index_file", "cluster_image")]),
(watershed, outputnode,
[("seg_file", "seg_file"),
("peak_file", "peak_file"),
("lut_file", "lut_file")]),
(surfproj, outputnode,
[("outputs.surf_zstat", "surf_zstat"),
("outputs.surf_mask", "surf_mask")]),
(report, outputnode,
[("out_files", "report")]),
(saveparams, outputnode,
[("json_file", "json_file")]),
])
return group, inputnode, outputnode
def COMPOSER(verbose=False, is_bruker=False):
inputnode = Node(IdentityInterface(fields=['in_file', 'ref_file']),
name='input')
outputnode = Node(IdentityInterface(fields=['out_file']), name='output')
wf = Workflow(name='COMPOSER')
in_mag = Node(Complex(magnitude_out_file='in_mag.nii.gz', verbose=verbose),
name='in_magnitude')
ref_mag = Node(Complex(magnitude_out_file='ref_mag.nii.gz',
verbose=verbose),
name='ref_magnitude')
if is_bruker:
wf.connect([(inputnode, in_mag, [('in_file', 'realimag')])])
wf.connect([(inputnode, ref_mag, [('ref_file', 'realimag')])])
else:
wf.connect([(inputnode, in_mag, [('in_file', 'complex')])])
wf.connect([(inputnode, ref_mag, [('ref_file', 'complex')])])
in_mean = Node(maths.MeanImage(), name='in_mean')
ref_mean = Node(maths.MeanImage(), name='ref_mean')
wf.connect([(in_mag, in_mean, [('magnitude_out_file', 'in_file')]),
(ref_mag, ref_mean, [('magnitude_out_file', 'in_file')])])
register = Node(Registration(dimension=3,
initial_moving_transform_com=1,
transforms=['Rigid'],
metric=['Mattes'],
metric_weight=[1],
transform_parameters=[(0.1, )],
number_of_iterations=[[1000, 500, 250]],
collapse_output_transforms=False,
initialize_transforms_per_stage=False,
radius_or_number_of_bins=[32],
sampling_strategy=['Regular', None],
sampling_percentage=[0.25, None],
convergence_threshold=[1.e-6],
smoothing_sigmas=[[4, 2, 1]],
shrink_factors=[[8, 4, 2]],
sigma_units=['vox'],
output_warped_image=True,
verbose=True),
name='register')
wf.connect([(in_mean, register, [('out_file', 'moving_image')]),
(ref_mean, register, [('out_file', 'fixed_image')])])
if is_bruker:
resample = Node(ApplyTransforms(dimension=3, input_image_type=3),
name='resample_reference')
in_x = Node(Complex(complex_out_file='in_x.nii.gz', verbose=verbose),
name='in_x')
ref_x = Node(Complex(complex_out_file='ref_x.nii.gz', verbose=verbose),
name='ref_x')
cc = Node(CoilCombine(), name='cc')
wf.connect([(inputnode, resample, [('ref_file', 'input_image')]),
(in_mean, resample, [('out_file', 'reference_image')]),
(register, resample, [('reverse_transforms', 'transforms')
]),
(inputnode, in_x, [('in_file', 'realimag')]),
(resample, ref_x, [('output_image', 'realimag')]),
(in_x, cc, [('complex_out_file', 'in_file')]),
(ref_x, cc, [('complex_out_file', 'composer_file')]),
(cc, outputnode, [('out_file', 'out_file')])])
else:
raise ('Not Yet Supported')
return wf
def define_template_workflow(info, subjects, qc=True):
# --- Workflow parameterization
subject_source = Node(IdentityInterface(["subject"]),
name="subject_source",
iterables=("subject", subjects))
# Data input
template_input = Node(TemplateInput(data_dir=info.data_dir),
"template_input")
# --- Definition of functional template space
crop_image = Node(fs.ApplyMask(args="-bb 4"), "crop_image")
zoom_image = Node(fs.MRIConvert(resample_type="cubic",
out_type="niigz",
vox_size=info.voxel_size,
),
"zoom_image")
reorient_image = Node(fsl.Reorient2Std(out_file="anat.nii.gz"),
"reorient_image")
generate_reg = Node(fs.Tkregister2(fsl_out="anat2func.mat",
reg_file="anat2func.dat",
reg_header=True),
"generate_reg")
invert_reg = Node(fs.Tkregister2(reg_file="func2anat.dat",
reg_header=True),
"invert_reg")
# --- Identification of surface vertices
hemi_source = Node(IdentityInterface(["hemi"]), "hemi_source",
iterables=("hemi", ["lh", "rh"]))
tag_surf = Node(fs.Surface2VolTransform(surf_name="graymid",
transformed_file="ribbon.nii.gz",
vertexvol_file="vertices.nii.gz",
mkmask=True),
"tag_surf")
mask_cortex = Node(MaskWithLabel(fill_value=-1), "mask_cortex")
combine_hemis = JoinNode(fsl.Merge(dimension="t",
merged_file="surf.nii.gz"),
name="combine_hemis",
joinsource="hemi_source",
joinfield="in_files")
make_ribbon = Node(MakeRibbon(), "make_ribbon")
# --- Segementation of anatomical tissue in functional space
transform_wmparc = Node(fs.ApplyVolTransform(inverse=True,
interp="nearest",
args="--keep-precision"),
"transform_wmparc")
anat_segment = Node(AnatomicalSegmentation(), "anat_segment")
# --- Template QC
template_qc = Node(TemplateReport(), "template_qc")
# --- Workflow ouptut
save_info = Node(SaveInfo(info_dict=info.trait_get()), "save_info")
template_output = Node(DataSink(base_directory=info.proc_dir,
parameterization=False),
"template_output")
# === Assemble pipeline
workflow = Workflow(name="template", base_dir=info.cache_dir)
processing_edges = [
(subject_source, template_input,
[("subject", "subject")]),
(template_input, crop_image,
[("norm_file", "in_file"),
("wmparc_file", "mask_file")]),
(crop_image, zoom_image,
[("out_file", "in_file")]),
(zoom_image, reorient_image,
[("out_file", "in_file")]),
(subject_source, generate_reg,
[("subject", "subject_id")]),
(template_input, generate_reg,
[("norm_file", "moving_image")]),
(reorient_image, generate_reg,
[("out_file", "target_image")]),
(subject_source, invert_reg,
[("subject", "subject_id")]),
(template_input, invert_reg,
[("norm_file", "target_image")]),
(reorient_image, invert_reg,
[("out_file", "moving_image")]),
(hemi_source, tag_surf,
[("hemi", "hemi")]),
(invert_reg, tag_surf,
[("reg_file", "reg_file")]),
(reorient_image, tag_surf,
[("out_file", "template_file")]),
(template_input, mask_cortex,
[("label_files", "label_files")]),
(hemi_source, mask_cortex,
[("hemi", "hemi")]),
(tag_surf, mask_cortex,
[("vertexvol_file", "in_file")]),
(mask_cortex, combine_hemis,
[("out_file", "in_files")]),
(combine_hemis, make_ribbon,
[("merged_file", "in_file")]),
(reorient_image, transform_wmparc,
[("out_file", "source_file")]),
(template_input, transform_wmparc,
[("wmparc_file", "target_file")]),
(invert_reg, transform_wmparc,
[("reg_file", "reg_file")]),
(reorient_image, anat_segment,
[("out_file", "anat_file")]),
(transform_wmparc, anat_segment,
[("transformed_file", "wmparc_file")]),
(combine_hemis, anat_segment,
[("merged_file", "surf_file")]),
(template_input, template_output,
[("output_path", "container")]),
(reorient_image, template_output,
[("out_file", "@anat")]),
(generate_reg, template_output,
[("fsl_file", "@anat2func")]),
(anat_segment, template_output,
[("seg_file", "@seg"),
("lut_file", "@lut"),
("edge_file", "@edge"),
("mask_file", "@mask")]),
(combine_hemis, template_output,
[("merged_file", "@surf")]),
(make_ribbon, template_output,
[("out_file", "@ribon")]),
]
workflow.connect(processing_edges)
# Optionally connect QC nodes
qc_edges = [
(reorient_image, template_qc,
[("out_file", "anat_file")]),
(combine_hemis, template_qc,
[("merged_file", "surf_file")]),
(anat_segment, template_qc,
[("lut_file", "lut_file"),
("seg_file", "seg_file"),
("edge_file", "edge_file"),
("mask_file", "mask_file")]),
(subject_source, save_info,
[("subject", "parameterization")]),
(save_info, template_output,
[("info_file", "qc.@info_json")]),
(template_qc, template_output,
[("seg_plot", "qc.@seg_plot"),
("mask_plot", "qc.@mask_plot"),
("edge_plot", "qc.@edge_plot"),
("surf_plot", "qc.@surf_plot"),
("anat_plot", "qc.@anat_plot")]),
]
if qc:
workflow.connect(qc_edges)
return workflow
# creating datasink to collect outputs
datasink = Node(DataSink(base_directory=outDir), name='datasink')
## Use the following DataSink output substitutions
substitutions = [('_subject_id_', '/sub-')]
datasink.inputs.substitutions = substitutions
###########
#
# SETTING UP THE WORKFLOW NODES
#
###########
# creating the workflow
firstLevel = Workflow(name="Level1", base_dir=outDir)
# connecting nodes
firstLevel.connect(sf, 'func', susan, 'in_file')
firstLevel.connect(sf, 'mask', applymask, 'mask_file')
firstLevel.connect(sf, 'events', taskevents, 'fileEvent')
firstLevel.connect(susan, 'smoothed_file', applymask, 'in_file')
firstLevel.connect(applymask, 'out_file', modelspec, 'functional_runs')
firstLevel.connect(taskevents, 'subject_info', modelspec, 'subject_info')
firstLevel.connect(modelspec, 'session_info', level1design, 'session_info')
firstLevel.connect(taskevents, 'contrast_list', level1design, 'contrasts')
firstLevel.connect(level1design, 'fsf_files', modelgen, 'fsf_file')
firstLevel.connect(level1design, 'ev_files', modelgen, 'ev_files')
firstLevel.connect(level1design, 'fsf_files', feat, 'fsf_file')
firstLevel.connect(feat, 'feat_dir', datasink, 'feat_dir')
firstLevel.connect(applymask, 'out_file', datasink, 'preproc_out_file')
def group_onesample_openfmri(dataset_dir,model_id=None,task_id=None,l1output_dir=None,out_dir=None, no_reversal=False):
wk = Workflow(name='one_sample')
wk.base_dir = os.path.abspath(work_dir)
info = Node(util.IdentityInterface(fields=['model_id','task_id','dataset_dir']),
name='infosource')
info.inputs.model_id=model_id
info.inputs.task_id=task_id
info.inputs.dataset_dir=dataset_dir
num_copes=contrasts_num(model_id,task_id,dataset_dir)
dg = Node(DataGrabber(infields=['model_id','task_id','cope_id'],
outfields=['copes', 'varcopes']),name='grabber')
dg.inputs.template = os.path.join(l1output_dir,'model%03d/task%03d/*/%scopes/mni/%scope%02d.nii.gz')
dg.inputs.template_args['copes'] = [['model_id','task_id','', '', 'cope_id']]
dg.inputs.template_args['varcopes'] = [['model_id','task_id','var', 'var', 'cope_id']]
dg.iterables=('cope_id',num_copes)
dg.inputs.sort_filelist = True
wk.connect(info,'model_id',dg,'model_id')
wk.connect(info,'task_id',dg,'task_id')
model = Node(L2Model(), name='l2model')
wk.connect(dg, ('copes', get_len), model, 'num_copes')
mergecopes = Node(Merge(dimension='t'), name='merge_copes')
wk.connect(dg, 'copes', mergecopes, 'in_files')
mergevarcopes = Node(Merge(dimension='t'), name='merge_varcopes')
wk.connect(dg, 'varcopes', mergevarcopes, 'in_files')
mask_file = fsl.Info.standard_image('MNI152_T1_2mm_brain_mask.nii.gz')
flame = Node(FLAMEO(), name='flameo')
flame.inputs.mask_file = mask_file
flame.inputs.run_mode = 'flame1'
wk.connect(model, 'design_mat', flame, 'design_file')
wk.connect(model, 'design_con', flame, 't_con_file')
wk.connect(mergecopes, 'merged_file', flame, 'cope_file')
wk.connect(mergevarcopes, 'merged_file', flame, 'var_cope_file')
wk.connect(model, 'design_grp', flame, 'cov_split_file')
smoothest = Node(SmoothEstimate(), name='smooth_estimate')
wk.connect(flame, 'zstats', smoothest, 'zstat_file')
smoothest.inputs.mask_file = mask_file
cluster = Node(Cluster(), name='cluster')
wk.connect(smoothest,'dlh', cluster, 'dlh')
wk.connect(smoothest, 'volume', cluster, 'volume')
cluster.inputs.connectivity = 26
cluster.inputs.threshold=2.3
cluster.inputs.pthreshold = 0.05
cluster.inputs.out_threshold_file = True
cluster.inputs.out_index_file = True
cluster.inputs.out_localmax_txt_file = True
wk.connect(flame, 'zstats', cluster, 'in_file')
ztopval = Node(ImageMaths(op_string='-ztop', suffix='_pval'),
name='z2pval')
wk.connect(flame, 'zstats', ztopval,'in_file')
sinker = Node(DataSink(), name='sinker')
sinker.inputs.base_directory = os.path.abspath(out_dir)
sinker.inputs.substitutions = [('_cope_id', 'contrast'),
('_maths__', '_reversed_')]
wk.connect(flame, 'zstats', sinker, 'stats')
wk.connect(cluster, 'threshold_file', sinker, 'stats.@thr')
wk.connect(cluster, 'index_file', sinker, 'stats.@index')
wk.connect(cluster, 'localmax_txt_file', sinker, 'stats.@localmax')
if no_reversal == False:
zstats_reverse = Node( BinaryMaths() , name='zstats_reverse')
zstats_reverse.inputs.operation = 'mul'
zstats_reverse.inputs.operand_value= -1
wk.connect(flame, 'zstats', zstats_reverse, 'in_file')
cluster2=cluster.clone(name='cluster2')
wk.connect(smoothest,'dlh',cluster2,'dlh')
wk.connect(smoothest,'volume',cluster2,'volume')
wk.connect(zstats_reverse,'out_file',cluster2,'in_file')
ztopval2 = ztopval.clone(name='ztopval2')
wk.connect(zstats_reverse,'out_file',ztopval2,'in_file')
wk.connect(zstats_reverse,'out_file',sinker,'stats.@neg')
wk.connect(cluster2,'threshold_file',sinker,'stats.@neg_thr')
wk.connect(cluster2,'index_file',sinker,'stats.@neg_index')
wk.connect(cluster2,'localmax_txt_file',sinker,'stats.@neg_localmax')
return wk
subject_directory = os.path.dirname(tissue_classify_directory)
hncma_atlas = os.path.join(subject_directory, "WarpedAtlas2Subject",
"hncma_atlas.nii.gz")
direction_files = dict()
for name in ["rho", "phi", "theta"]:
direction_files[name] = os.path.join(subject_directory,
"WarpedAtlas2Subject",
"{0}.nii.gz".format(name))
lh_white_surface_file = os.path.join(subject_directory, "FreeSurfer",
"surf", "lh.white")
rh_white_surface_file = os.path.join(subject_directory, "FreeSurfer",
"surf", "rh.white")
logb_wf = create_logismosb_machine_learning_workflow()
wf = Workflow("MachineLearning_Baseline_{0}".format(session_id))
datasink = Node(DataSink(), name="DataSink")
datasink.inputs.base_directory = os.path.join(results_dir, session_id)
for hemisphere in ("lh", "rh"):
for matter in ("gm", "wm"):
wf.connect(
logb_wf,
"output_spec.{0}_{1}surface_file".format(hemisphere, matter),
datasink, "EdgePrediction.@{0}_{1}".format(hemisphere, matter))
logb_wf.inputs.input_spec.t1_file = t1_file
logb_wf.inputs.input_spec.orig_t1 = t1_file
logb_wf.inputs.input_spec.t2_file = t2_file
logb_wf.inputs.input_spec.posteriors = posterior_files
logb_wf.inputs.input_spec.hncma_file = hncma_atlas
logb_wf.inputs.input_spec.abc_file = abc_file
def init_t1w_derivatives_wf(bids_root, output_dir, name='t1w_derivatives_wf'):
"""Set up a battery of datasinks to store derivatives in the right location."""
base_directory = str(output_dir.parent)
out_path_base = str(output_dir.name)
wf = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=[
'subject', 'session', 't1w_template_space', 't1w_brain_template_space'
]),
name='inputnode')
def generic_bids_file_fct(bids_root, subject, session):
from pathlib import Path
return Path(
bids_root
) / f"sub-{subject}/ses-{session}/anat/sub-{subject}_ses-{session}_T1w.nii.gz"
generic_bids_file = pe.Node(niu.Function(
input_names=["bids_root", "subject", "session"],
output_names=["out_file"],
function=generic_bids_file_fct),
name='generic_bids_file')
generic_bids_file.inputs.bids_root = bids_root
wf.connect(inputnode, "subject", generic_bids_file, "subject")
wf.connect(inputnode, "session", generic_bids_file, "session")
ds_t1w_preproc = pe.Node(DerivativesDataSink(base_directory=base_directory,
out_path_base=out_path_base,
keep_dtype=True,
compress=True,
space="tpl"),
name='ds_t1w_preproc',
run_without_submitting=True)
wf.connect(generic_bids_file, "out_file", ds_t1w_preproc, "source_file")
wf.connect(inputnode, "t1w_template_space", ds_t1w_preproc, "in_file")
ds_t1w_brain = pe.Node(DerivativesDataSink(base_directory=base_directory,
out_path_base=out_path_base,
keep_dtype=True,
compress=True,
space="tpl",
desc="brain"),
name='ds_t1w_brain',
run_without_submitting=True)
wf.connect(generic_bids_file, "out_file", ds_t1w_brain, "source_file")
wf.connect(inputnode, "t1w_brain_template_space", ds_t1w_brain, "in_file")
return wf
def create_distortion_correct():
# fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
distor_correct = Workflow(name='distor_correct')
# input node
inputnode = Node(util.IdentityInterface(
fields=['dwi', 'dwi_ap', 'dwi_pa', 'bvals', 'bvecs']),
name='inputnode')
# output node
outputnode = Node(util.IdentityInterface(fields=[
'bo_brain', "bo_brainmask", 'noise', 'dwi_denoised', "dwi_unringed",
"dwi_appa", "topup_bo", "topup_corr", "topup_field", "topup_fieldcoef",
"eddy_corr", "rotated_bvecs", "total_movement_rms", "outlier_report",
"cnr_maps", "residuals", "shell_params", "eddy_params"
]),
name='outputnode')
# to define the path in the current directory
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
''
# noise reduction on all images
''
denoise = Node(DWIdenoise(noise='noise.nii.gz'), name="denoise")
''
# artefact removal
''
# run unring: remove the ringing artefacts
unring = Node(MRdegibbs(), name="unring")
''
# topup and eddy
''
# merge AP PA files together
b0_comb = Node(util.Merge(2), name='b0_comb')
merger = Node(fsl.Merge(), name='merger')
merger.inputs.dimension = 't'
merger.inputs.merged_file = 'dwi_appa.nii.gz'
distor_correct.connect([(inputnode, b0_comb, [('dwi_ap', 'in1')]),
(inputnode, b0_comb, [('dwi_pa', 'in2')]),
(b0_comb, merger, [('out', 'in_files')])])
# topup
config = os.path.join(__location__, 'b02b0.cnf')
acqparams = os.path.join(__location__, 'acqparams_dwi.txt')
topup = Node(fsl.TOPUP(), name='topup')
topup.inputs.config = config #use optimised parameters
topup.inputs.encoding_file = acqparams
# topup.inputs.out_base = 'diff_topup'
# skullstrip process using bet
# mean of all b0 unwarped images
maths = Node(fsl.ImageMaths(op_string='-Tmean'), name="maths")
# create a brain mask from the b0 unwarped
bet = Node(interface=fsl.BET(), name='bet')
bet.inputs.mask = True
bet.inputs.frac = 0.2
bet.inputs.robust = True
# eddy motion correction
indx = os.path.join(__location__, 'index.txt')
eddy = Node(fsl.epi.Eddy(), name="eddy")
eddy.inputs.num_threads = 8 ## total number of CPUs to use
#eddy.inputs.args = '--cnr_maps --residuals'
eddy.inputs.repol = True
eddy.inputs.in_acqp = acqparams
eddy.inputs.in_index = indx
eddy.inputs.cnr_maps = True
eddy.inputs.residuals = True
''
# connect the nodes
''
distor_correct.connect([
(merger, topup, [("merged_file", "in_file")]),
(topup, outputnode, [('out_corrected', 'topup_bo')]),
(topup, outputnode, [('out_fieldcoef', 'topup_fieldcoef')]),
(topup, outputnode, [('out_field', 'topup_field')]),
(topup, maths, [('out_corrected', 'in_file')]),
(maths, outputnode, [('out_file', 'dwi_appa')]),
(maths, bet, [("out_file", "in_file")]),
(bet, outputnode, [("mask_file", "bo_brainmask")]),
(bet, outputnode, [("out_file", "bo_brain")]),
(bet, eddy, [("mask_file", "in_mask")]),
(inputnode, eddy, [("bvecs", "in_bvec")]),
(inputnode, eddy, [("bvals", "in_bval")]),
(topup, eddy, [("out_fieldcoef", "in_topup_fieldcoef")]),
(topup, eddy, [("out_movpar", "in_topup_movpar")]),
(inputnode, denoise, [('dwi', 'in_file')]),
(denoise, outputnode, [('out_file', 'dwi_denoised')]),
(denoise, unring, [('out_file', 'in_file')]),
(unring, outputnode, [('out_file', 'dwi_unringed')]),
(unring, eddy, [("out_file", "in_file")]),
(eddy, outputnode, [("out_corrected", "eddy_corr")]),
(eddy, outputnode, [("out_parameter", "eddy_params")]),
(eddy, outputnode, [("out_rotated_bvecs", "rotated_bvecs")]),
(eddy, outputnode, [("out_movement_rms", "total_movement_rms")]),
(eddy, outputnode, [("out_shell_alignment_parameters", "shell_params")
]),
(eddy, outputnode, [("out_outlier_report", "outlier_report")]),
(eddy, outputnode, [("out_cnr_maps", "cnr_maps")]),
(eddy, outputnode, [("out_residuals", "residuals")])
])
return distor_correct
def test_mapnode_json():
"""Tests that mapnodes don't generate excess jsons
"""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
w1.add_nodes([n1])
w1.run()
n1.inputs.in1 = [2]
w1.run()
# should rerun
n1.inputs.in1 = [1]
eg = w1.run()
node = eg.nodes()[0]
outjson = glob(os.path.join(node.output_dir(), '_0x*.json'))
yield assert_equal, len(outjson), 1
# check that multiple json's don't trigger rerun
with open(os.path.join(node.output_dir(), 'test.json'), 'wt') as fp:
fp.write('dummy file')
w1.config['execution'].update(**{'stop_on_first_rerun': True})
error_raised = False
try:
w1.run()
except:
error_raised = True
yield assert_false, error_raised
os.chdir(cwd)
rmtree(wd)
def define_model_results_workflow(info, subjects, qc=True):
# TODO I am copying a lot from above ...
# --- Workflow parameterization and data input
# We just need two levels of iterables here: one subject-level and
# one "flat" run-level iterable (i.e. all runs collapsing over
# sessions). Unlike in the model fit workflow, we always want to process
# all sessions.
scan_info = info.scan_info
experiment = info.experiment_name
model = info.model_name
iterables = generate_iterables(scan_info, experiment, subjects)
subject_iterables, run_iterables = iterables
subject_source = Node(IdentityInterface(["subject"]),
name="subject_source",
iterables=("subject", subject_iterables))
run_source = Node(IdentityInterface(["subject", "run"]),
name="run_source",
itersource=("subject_source", "subject"),
iterables=("run", run_iterables))
data_input = Node(ModelResultsInput(experiment=experiment,
model=model,
proc_dir=info.proc_dir),
"data_input")
# --- Run-level contrast estimation
estimate_contrasts = Node(EstimateContrasts(info=info.trait_get()),
"estimate_contrasts")
# --- Subject-level contrast estimation
model_results = JoinNode(ModelResults(info=info.trait_get()),
name="model_results",
joinsource="run_source",
joinfield=["contrast_files",
"variance_files",
"name_files"])
# --- Data output
save_info = Node(SaveInfo(info_dict=info.trait_get()), "save_info")
run_output = Node(DataSink(base_directory=info.proc_dir,
parameterization=False),
"run_output")
results_path = Node(ModelResultsPath(proc_dir=info.proc_dir,
experiment=experiment,
model=model),
"results_path")
subject_output = Node(DataSink(base_directory=info.proc_dir,
parameterization=False),
"subject_output")
# === Assemble pipeline
cache_base = op.join(info.cache_dir, experiment)
workflow = Workflow(name="model_results", base_dir=cache_base)
# Connect processing nodes
processing_edges = [
(subject_source, run_source,
[("subject", "subject")]),
(subject_source, data_input,
[("subject", "subject")]),
(run_source, data_input,
[("run", "run_tuple")]),
(data_input, estimate_contrasts,
[("mask_file", "mask_file"),
("beta_file", "beta_file"),
("error_file", "error_file"),
("ols_file", "ols_file"),
("model_file", "model_file")]),
(subject_source, model_results,
[("subject", "subject")]),
(data_input, model_results,
[("anat_file", "anat_file")]),
(estimate_contrasts, model_results,
[("contrast_file", "contrast_files"),
("variance_file", "variance_files"),
("name_file", "name_files")]),
(run_source, save_info,
[("run", "parameterization")]),
(save_info, run_output,
[("info_file", "qc.@info_json")]),
(data_input, run_output,
[("output_path", "container")]),
(estimate_contrasts, run_output,
[("contrast_file", "@contrast"),
("variance_file", "@variance"),
("tstat_file", "@tstat"),
("name_file", "@names")]),
(subject_source, results_path,
[("subject", "subject")]),
(results_path, subject_output,
[("output_path", "container")]),
(model_results, subject_output,
[("result_directories", "@results")]),
]
workflow.connect(processing_edges)
return workflow
cleanFaNode = mrmultNode.clone('multiplyFA_Mask')
thresholdFANode = Node(mrtrix.Threshold(), name = 'threshold_FA')
thresholdFANode.inputs.absolute_threshold_value = absolute_threshold_value
# Response function coefficient
estResponseNode = Node(mrtrix.EstimateResponseForSH(), name = 'estimate_deconv_response')
# CSD computation
csdNode = Node(mrtrix.ConstrainedSphericalDeconvolution(), name = 'compute_CSD')
# ### Connect the Nodes in the workflow
wf = Workflow(name = 'MRTrix_preproc')
wf.connect([
(inputNode, fsl2mrtrixNode, [('bval_file', 'bval_file'),
('bvec_file', 'bvec_file'),
(('tracking_dir', fileNameBuilder, fileNames['gradFile']), 'out_encoding_file')]),
(inputNode, dwi2tensorNode, [('dwi_file', 'in_file'),
(('tracking_dir', fileNameBuilder, fileNames['dtFile']), 'out_filename')]),
(fsl2mrtrixNode, dwi2tensorNode, [('encoding_file', 'encoding_file')]),
(dwi2tensorNode, tensor2faNode, [('tensor', 'in_file')]),
(inputNode, tensor2faNode, [(('tracking_dir', fileNameBuilder, fileNames['faFile']), 'out_filename')]),
(tensor2faNode, mrmultNode, [('FA', 'in1')]),
(inputNode, mrmultNode, [('wmmask', 'in2')]),
(inputNode, mrmultNode, [(('tracking_dir', fileNameBuilder, fileNames['faFile']), 'out_file')]),
(dwi2tensorNode, tensor2vectorNode, [('tensor', 'in_file')]),
(inputNode, tensor2vectorNode, [(('tracking_dir', fileNameBuilder, fileNames['evFile']), 'out_filename')]),
from nipype.interfaces.io import FreeSurferSource
connection = sqlite3.connect(
"/Shared/johnsonhj/HDNI/20151001_AtrophySimulation/results.db")
cursor = connection.cursor()
num_threads = 12
base_dir = "/Shared/sinapse/CACHE/20161010_AtrophySimulation_Baseline_CACHE"
for row in cursor.execute(
"SELECT t1_image_file, t2_image_file, session_id FROM input"):
session_id = str(row[2])
t1_file = str(row[0])
t2_file = str(row[1])
wf = Workflow(name="FreeSurfer_{0}".format(session_id))
subject_directory = os.path.dirname(os.path.dirname(t1_file))
recon_all = Node(ReconAll(), "ReconAll")
recon_all.inputs.T1_files = [t1_file]
recon_all.inputs.T2_file = t2_file
recon_all.inputs.openmp = num_threads
recon_all.inputs.subject_id = "FreeSurfer"
recon_all.inputs.flags = "-no-isrunning"
recon_all.inputs.subjects_dir = os.path.join(
"/Shared/sinapse/CACHE/20161010_AtrophySimulation_Baseline",
session_id)
recon_all.plugin_args = plugin_args = {
"qsub_args": "-q HJ,UI,all.q,COE -pe smp {0}".format(num_threads),
"overwrite": True,
def create_reg_workflow(name='registration'):
"""Create a FEAT preprocessing workflow together with freesurfer
Parameters
----------
name : name of workflow (default: 'registration')
Inputs::
inputspec.source_files : files (filename or list of filenames to register)
inputspec.mean_image : reference image to use
inputspec.anatomical_image : anatomical image to coregister to
inputspec.target_image : registration target
Outputs::
outputspec.func2anat_transform : FLIRT transform
outputspec.anat2target_transform : FLIRT+FNIRT transform
outputspec.transformed_files : transformed files in target space
outputspec.transformed_mean : mean image in target space
"""
register = Workflow(name=name)
inputnode = Node(interface=IdentityInterface(fields=['source_files',
'mean_image',
'subject_id',
'subjects_dir',
'target_image']),
name='inputspec')
outputnode = Node(interface=IdentityInterface(fields=['func2anat_transform',
'out_reg_file',
'anat2target_transform',
'transforms',
'transformed_mean',
'segmentation_files',
'anat2target',
'aparc',
'min_cost_file'
]),
name='outputspec')
# Get the subject's freesurfer source directory
fssource = Node(FreeSurferSource(),
name='fssource')
fssource.run_without_submitting = True
register.connect(inputnode, 'subject_id', fssource, 'subject_id')
register.connect(inputnode, 'subjects_dir', fssource, 'subjects_dir')
convert = Node(freesurfer.MRIConvert(out_type='nii'),
name="convert")
register.connect(fssource, 'T1', convert, 'in_file')
# Coregister the median to the surface
bbregister = Node(freesurfer.BBRegister(),
name='bbregister')
bbregister.inputs.init = 'fsl'
bbregister.inputs.contrast_type = 't2'
bbregister.inputs.out_fsl_file = True
bbregister.inputs.epi_mask = True
register.connect(inputnode, 'subject_id', bbregister, 'subject_id')
register.connect(inputnode, 'mean_image', bbregister, 'source_file')
register.connect(inputnode, 'subjects_dir', bbregister, 'subjects_dir')
"""
Estimate the tissue classes from the anatomical image. But use aparc+aseg's brain mask
"""
binarize = Node(fs.Binarize(min=0.5, out_type="nii.gz", dilate=1), name="binarize_aparc")
register.connect(fssource, ("aparc_aseg", get_aparc_aseg), binarize, "in_file")
stripper = Node(fsl.ApplyMask(), name='stripper')
register.connect(binarize, "binary_file", stripper, "mask_file")
register.connect(convert, 'out_file', stripper, 'in_file')
fast = Node(fsl.FAST(), name='fast')
register.connect(stripper, 'out_file', fast, 'in_files')
"""
Binarize the segmentation
"""
binarize = MapNode(fsl.ImageMaths(op_string='-nan -thr 0.9 -ero -bin'),
iterfield=['in_file'],
name='binarize')
register.connect(fast, 'partial_volume_files', binarize, 'in_file')
"""
Apply inverse transform to take segmentations to functional space
"""
applyxfm = MapNode(freesurfer.ApplyVolTransform(inverse=True,
interp='nearest'),
iterfield=['target_file'],
name='inverse_transform')
register.connect(inputnode, 'subjects_dir', applyxfm, 'subjects_dir')
register.connect(bbregister, 'out_reg_file', applyxfm, 'reg_file')
register.connect(binarize, 'out_file', applyxfm, 'target_file')
register.connect(inputnode, 'mean_image', applyxfm, 'source_file')
"""
Apply inverse transform to aparc file
"""
aparcxfm = Node(freesurfer.ApplyVolTransform(inverse=True,
interp='nearest'),
name='aparc_inverse_transform')
register.connect(inputnode, 'subjects_dir', aparcxfm, 'subjects_dir')
register.connect(bbregister, 'out_reg_file', aparcxfm, 'reg_file')
register.connect(fssource, ('aparc_aseg', get_aparc_aseg),
aparcxfm, 'target_file')
register.connect(inputnode, 'mean_image', aparcxfm, 'source_file')
"""
Convert the BBRegister transformation to ANTS ITK format
"""
convert2itk = Node(C3dAffineTool(), name='convert2itk')
convert2itk.inputs.fsl2ras = True
convert2itk.inputs.itk_transform = True
register.connect(bbregister, 'out_fsl_file', convert2itk, 'transform_file')
register.connect(inputnode, 'mean_image', convert2itk, 'source_file')
register.connect(stripper, 'out_file', convert2itk, 'reference_file')
"""
Compute registration between the subject's structural and MNI template
This is currently set to perform a very quick registration. However, the
registration can be made significantly more accurate for cortical
structures by increasing the number of iterations
All parameters are set using the example from:
#https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh
"""
reg = Node(ants.Registration(), name='antsRegister')
reg.inputs.output_transform_prefix = "output_"
reg.inputs.transforms = ['Rigid', 'Affine', 'SyN']
reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.2, 3.0, 0.0)]
reg.inputs.number_of_iterations = [[10000, 11110, 11110]] * 2 + [[100, 30, 20]]
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = True
reg.inputs.initial_moving_transform_com = True
reg.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
reg.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
reg.inputs.sampling_strategy = ['Regular'] * 2 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
reg.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
reg.inputs.convergence_window_size = [20] * 2 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ['vox'] * 3
reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 3
reg.inputs.use_histogram_matching = [False] * 2 + [True]
reg.inputs.winsorize_lower_quantile = 0.005
reg.inputs.winsorize_upper_quantile = 0.995
reg.inputs.float = True
reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
reg.inputs.num_threads = 4
reg.plugin_args = {'sbatch_args': '-c%d' % 4}
register.connect(stripper, 'out_file', reg, 'moving_image')
register.connect(inputnode, 'target_image', reg, 'fixed_image')
"""
Concatenate the affine and ants transforms into a list
"""
merge = Node(Merge(2), iterfield=['in2'], name='mergexfm')
register.connect(convert2itk, 'itk_transform', merge, 'in2')
register.connect(reg, 'composite_transform', merge, 'in1')
"""
Transform the mean image. First to anatomical and then to target
"""
warpmean = Node(ants.ApplyTransforms(), name='warpmean')
warpmean.inputs.input_image_type = 3
warpmean.inputs.interpolation = 'Linear'
warpmean.inputs.invert_transform_flags = [False, False]
warpmean.inputs.terminal_output = 'file'
warpmean.inputs.args = '--float'
warpmean.inputs.num_threads = 4
warpmean.plugin_args = {'sbatch_args': '-c%d' % 4}
register.connect(inputnode, 'target_image', warpmean, 'reference_image')
register.connect(inputnode, 'mean_image', warpmean, 'input_image')
register.connect(merge, 'out', warpmean, 'transforms')
"""
Assign all the output files
"""
register.connect(reg, 'warped_image', outputnode, 'anat2target')
register.connect(warpmean, 'output_image', outputnode, 'transformed_mean')
register.connect(applyxfm, 'transformed_file',
outputnode, 'segmentation_files')
register.connect(aparcxfm, 'transformed_file',
outputnode, 'aparc')
register.connect(bbregister, 'out_fsl_file',
outputnode, 'func2anat_transform')
register.connect(bbregister, 'out_reg_file',
outputnode, 'out_reg_file')
register.connect(reg, 'composite_transform',
outputnode, 'anat2target_transform')
register.connect(merge, 'out', outputnode, 'transforms')
register.connect(bbregister, 'min_cost_file',
outputnode, 'min_cost_file')
return register
def test_mapnode_json():
"""Tests that mapnodes don't generate excess jsons
"""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
w1.add_nodes([n1])
w1.run()
n1.inputs.in1 = [2]
w1.run()
# should rerun
n1.inputs.in1 = [1]
eg = w1.run()
node = eg.nodes()[0]
outjson = glob(os.path.join(node.output_dir(), '_0x*.json'))
yield assert_equal, len(outjson), 1
# check that multiple json's don't trigger rerun
with open(os.path.join(node.output_dir(), 'test.json'), 'wt') as fp:
fp.write('dummy file')
w1.config['execution'].update(**{'stop_on_first_rerun': True})
error_raised = False
try:
w1.run()
except:
error_raised = True
yield assert_false, error_raised
os.chdir(cwd)
rmtree(wd)
'{contrast_id}.nii')
}
selectfiles = MapNode(SelectFiles(
templates,
base_directory='/home/rj299/scratch60/mdm_analysis/work/',
sort_filelist=True),
name="selectfiles",
iterfield=['subject_id'])
datasink = Node(nio.DataSink(
base_directory=
'/home/rj299/scratch60/mdm_analysis/output/imaging/Sink_resp_sv/'),
name="datasink")
l2analysis = Workflow(name='l2spm_sv_glm_heightp05')
l2analysis.base_dir = '/home/rj299/scratch60/mdm_analysis/work/'
l2analysis.connect([
(infosource, selectfiles, [('contrast_id', 'contrast_id'),
('subject_id', 'subject_id')]),
(selectfiles, onesamplettestdes, [('cons', 'in_files')]),
(onesamplettestdes, level2estimate, [('spm_mat_file', 'spm_mat_file')]),
(level2estimate, level2conestimate, [('spm_mat_file', 'spm_mat_file'),
('beta_images', 'beta_images'),
('residual_image', 'residual_image')
]),
(level2conestimate, level2thresh, [
('spm_mat_file', 'spm_mat_file'),
('spmT_images', 'stat_image'),
def define_model_fit_workflow(info, subjects, sessions, qc=True):
# --- Workflow parameterization and data input
# We just need two levels of iterables here: one subject-level and
# one "flat" run-level iterable (i.e. all runs collapsing over
# sessions). But we want to be able to specify sessions to process.
scan_info = info.scan_info
experiment = info.experiment_name
model = info.model_name
iterables = generate_iterables(scan_info, experiment, subjects, sessions)
subject_iterables, run_iterables = iterables
subject_source = Node(IdentityInterface(["subject"]),
name="subject_source",
iterables=("subject", subject_iterables))
run_source = Node(IdentityInterface(["subject", "run"]),
name="run_source",
itersource=("subject_source", "subject"),
iterables=("run", run_iterables))
data_input = Node(ModelFitInput(experiment=experiment,
model=model,
proc_dir=info.proc_dir),
"data_input")
# --- Data filtering and model fitting
fit_model = Node(ModelFit(data_dir=info.data_dir,
info=info.trait_get()),
"fit_model")
# --- Data output
save_info = Node(SaveInfo(info_dict=info.trait_get()), "save_info")
data_output = Node(DataSink(base_directory=info.proc_dir,
parameterization=False),
"data_output")
# === Assemble pipeline
cache_base = op.join(info.cache_dir, experiment)
workflow = Workflow(name="model_fit", base_dir=cache_base)
# Connect processing nodes
processing_edges = [
(subject_source, run_source,
[("subject", "subject")]),
(subject_source, data_input,
[("subject", "subject")]),
(run_source, data_input,
[("run", "run_tuple")]),
(data_input, fit_model,
[("subject", "subject"),
("session", "session"),
("run", "run"),
("seg_file", "seg_file"),
("surf_file", "surf_file"),
("edge_file", "edge_file"),
("mask_file", "mask_file"),
("ts_file", "ts_file"),
("noise_file", "noise_file"),
("mc_file", "mc_file")]),
(data_input, data_output,
[("output_path", "container")]),
(fit_model, data_output,
[("mask_file", "@mask"),
("beta_file", "@beta"),
("error_file", "@error"),
("ols_file", "@ols"),
("resid_file", "@resid"),
("model_file", "@model")]),
]
workflow.connect(processing_edges)
qc_edges = [
(run_source, save_info,
[("run", "parameterization")]),
(save_info, data_output,
[("info_file", "qc.@info_json")]),
(fit_model, data_output,
[("model_plot", "qc.@model_plot"),
("nuisance_plot", "qc.@nuisance_plot"),
("resid_plot", "qc.@resid_plot"),
("error_plot", "qc.@error_plot")]),
]
if qc:
workflow.connect(qc_edges)
return workflow