def create_reconall_pipeline(name='reconall'):
reconall = Workflow(name='reconall')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
recon_all = Node(
fs.ReconAll(
args='-all -hippo-subfields -no-isrunning'
), #for RSV152 took out s because of preprocessing with version 6.0
name="recon_all")
#recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
recon_all.plugin_args = {'submit_specs': 'request_memory = 9000'}
# function to replace / in subject id string with a _
def sub_id(sub_id):
return sub_id.replace('/', '_')
reconall.connect([
(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files'),
(('fs_subject_id', sub_id), 'subject_id')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
def create_workflow_allin_slices(name='motion_correction', iterfield=['in_file']):
workflow = Workflow(name=name)
inputs = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'ref_func',
'ref_func_weights',
'funcs',
'funcs_masks',
'mc_method',
]), name='in')
inputs.iterables = [
('mc_method', ['afni:3dAllinSlices'])
]
mc = MapNode(
AFNIAllinSlices(),
iterfield=iterfield,
name='mc')
workflow.connect(
[(inputs, mc,
[('funcs', 'in_file'),
('ref_func_weights', 'in_weight_file'),
('ref_func', 'ref_file'),
])])
return workflow
def freesurfer_nifti():
'''
Simple method to convert freesurfer mgz files to nifti format
'''
#start with a useful function to grab data
#define workflow
flow = Workflow(name='freesurfer_nifti')
inputnode = Node(
util.IdentityInterface(fields=['mgz_image', 'anatomical']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['aparc_aseg_nifti']),
name='outputnode')
#define nodes
convert_aparc_aseg = Node(interface=freesurfer.MRIConvert(),
name='aparc_aseg_nifti')
convert_aparc_aseg.inputs.out_type = 'nii'
anatomical = Node(interface=freesurfer.MRIConvert(),
name='anatomical_ready')
anatomical.inputs.out_type = 'nii'
#connect nodes
return flow
def func2mni_wf():
mni_skull_2mm = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz'
mni_brain_2mm = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
flow = Workflow('func2mni_nonlinear')
inputnode = Node(util.IdentityInterface(fields=['func_image',
'reference_image',
'func2anat_affine',
'anat2mni_warp']),name = 'inputnode')
outputnode = Node(util.IdentityInterface(fields=['func2mni_2mm',
'func2mni_4mm']),name = 'outputnode')
applywarp = Node(fsl.ApplyWarp(), name = 'apply_warp',)
applywarp.inputs.ref_file = mni_brain_2mm
flirt4mm = Node(fsl.FLIRT(), name = 'resample_4mm')
flirt4mm.inputs.reference = mni_brain_2mm
flirt4mm.inputs.apply_isoxfm = 4.0
flow.connect(inputnode, 'func_image' , applywarp, 'in_file')
flow.connect(inputnode, 'anat2mni_warp' , applywarp, 'field_file')
flow.connect(inputnode, 'func2anat_affine' , applywarp, 'premat')
flow.connect(applywarp, 'out_file' , flirt4mm, 'in_file')
flow.connect(applywarp, 'out_file' , outputnode, 'func2mni_2mm')
flow.connect(flirt4mm, 'out_file' , outputnode, 'func2mni_4mm')
return flow
def create_ants_registration_pipeline(name='ants_registration'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
ants_registration = Workflow(name='ants_registration')
# inputnode
inputnode = Node(util.IdentityInterface(
fields=['corr_Z', 'ants_affine', 'ants_warp', 'ref']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'ants_reg_corr_Z',
]),
name='outputnode')
#also transform to mni space
collect_transforms = Node(interface=util.Merge(2),
name='collect_transforms')
ants_reg = MapNode(ants.ApplyTransforms(input_image_type=3,
dimension=3,
interpolation='Linear'),
name='ants_reg',
iterfield='input_image')
ants_registration.connect([
(inputnode, ants_reg, [('corr_Z', 'input_image')]),
(inputnode, ants_reg, [('ref', 'reference_image')]),
(inputnode, collect_transforms, [('ants_affine', 'in1')]),
(inputnode, collect_transforms, [('ants_warp', 'in2')]),
(collect_transforms, ants_reg, [('out', 'transforms')]),
(ants_reg, outputnode, [('output_image', 'ants_reg_corr_Z')])
])
return ants_registration
def test_nipype_srtm_zhou2003_roi(self):
from temporalimage import Quantity
from temporalimage.t4d import _csvwrite_frameTiming
import pandas as pd
from .generate_test_data import generate_fakeTAC_SRTM
self.t, self.dt, self.TAC, self.refTAC = generate_fakeTAC_SRTM(BP=0.5, R1=0.7)
frameStart = self.t - self.dt/2
frameEnd = self.t + self.dt/2
csvfilename = os.path.join(self.tmpdirname,'srtm_roi_timing.csv')
_csvwrite_frameTiming(frameStart, frameEnd, csvfilename, time_unit='min')
roiTACcsvfile = os.path.join(self.tmpdirname,'roi_tacs.csv')
roiTACs = pd.DataFrame({'target': self.TAC,
'ref': self.refTAC})
roiTACs.T.to_csv(roiTACcsvfile, index_label='ROI')
infosource = Node(IdentityInterface(fields=['in_file']),
name="infosource")
infosource.iterables = ('in_file', [roiTACcsvfile])
km = Node(KineticModelROI(model='SRTM_Zhou2003',
#roiTACcsvFile=roiTACcsvfile,
frameTimingFile=csvfilename,
refRegion='ref',
startActivity=self.startActivity,
weights=self.weights), name="km")
km_workflow = Workflow(name="km_workflow", base_dir=self.tmpdirname)
km_workflow.connect([
(infosource, km, [('in_file', 'roiTACcsvFile')])
])
km_workflow.run()
def create_workflow_hrfpattern_spm():
# GLM
design = Node(interface=spm_design(), name='design_glm')
design.inputs.timing_units = 'secs'
design.inputs.interscan_interval = .85
design.inputs.bases = {'hrf': {'derivs': [0, 0]}}
estimate = Node(interface=EstimateModel(), name="estimate")
estimate.inputs.estimation_method = {'Classical': 1}
contrastestimate = Node(interface=EstimateContrast(), name="contrast")
contrastestimate.inputs.contrasts = [('Visual', 'T', [
'1',
], [
1,
])]
w = Workflow(name='hrfpattern_spm')
w.connect(input_node, 'bold', model, 'functional_runs')
w.connect(input_node, 'events', model, 'bids_event_file')
w.connect(model, 'session_info', design, 'session_info')
w.connect(design, 'spm_mat_file', estimate, 'spm_mat_file')
w.connect(estimate, 'spm_mat_file', contrastestimate, 'spm_mat_file')
w.connect(estimate, 'beta_images', contrastestimate, 'beta_images')
w.connect(estimate, 'residual_image', contrastestimate, 'residual_image')
w.connect(contrastestimate, 'spmT_images', output_node, 'T_image')
return w
def ica_aroma_workflow():
flow = Workflow('denoise_ica_aroma')
inputnode = Node(util.IdentityInterface(fields=[
'fslDir', 'inFile', 'mask', 'dim', 'TR', 'mc', 'denType', 'affmat',
'warp'
]),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['denoised']),
name='outputnode')
aroma = Node(util.Function(input_names=[
'fslDir', 'inFile', 'mask', 'dim', 'TR', 'mc', 'denType', 'affmat',
'warp'
],
output_names=['denoised'],
function=ica_aroma_denoise),
name='ICA_AROMA')
flow.connect(inputnode, 'fslDir', aroma, 'fslDir')
flow.connect(inputnode, 'inFile', aroma, 'inFile')
flow.connect(inputnode, 'mask', aroma, 'mask')
flow.connect(inputnode, 'dim', aroma, 'dim')
flow.connect(inputnode, 'TR', aroma, 'TR')
flow.connect(inputnode, 'mc', aroma, 'mc')
flow.connect(inputnode, 'denType', aroma, 'denType')
flow.connect(inputnode, 'affmat', aroma, 'affmat')
flow.connect(inputnode, 'warp', aroma, 'warp')
flow.connect(aroma, 'denoised', outputnode, 'denoised')
return flow
def create_normalize_pipeline(name='normalize'):
# workflow
normalize = Workflow(name='normalize')
# Define nodes
inputnode = Node(interface=util.IdentityInterface(fields=['epi_coreg',
'tr']),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(fields=[
'normalized_file']),
name='outputnode')
# time-normalize scans
normalize_time = Node(util.Function(input_names=['in_file', 'tr'],
output_names=['out_file'],
function=time_normalizer),
name='normalize_time')
normalize_time.plugin_args = {'submit_specs': 'request_memory = 17000'}
normalize.connect([(inputnode, normalize_time, [('tr', 'tr')]),
(inputnode, normalize_time, [('epi_coreg', 'in_file')]),
(normalize_time, outputnode, [('out_file', 'normalized_file')])
])
# time-normalize scans
return normalize
def create_reconall_pipeline(name='reconall_wf'):
reconall_wf = Workflow(name='reconall_wf')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
reconall = Node(
fs.ReconAll(args='-all -no-isrunning',
openmp=8), #subfield segmentation after recon-all
name="reconall")
#recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
reconall_wf.plugin_args = {'submit_specs': 'request_memory = 9000'}
reconall_wf.connect([
(inputnode, reconall, [('fs_subject_id', 'subject_id')]),
(inputnode, reconall, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files')]),
(reconall, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall_wf
def make_workflow():
flairs = [os.path.abspath(i) for i in glob.glob(args.flair)]
weights = [os.path.abspath(i) for i in glob.glob(args.weights)]
weights_source = Node(interface=IdentityInterface(fields=['weights']),
name='weights_source')
weights_source.inputs.weights = weights
data_source = Node(IdentityInterface(fields=['flairs']),
name='data_source')
data_source.iterables = ('flairs', flairs)
sink = Node(interface=DataSink(), name='sink')
sink.inputs.base_directory = wmh_dir
sink.inputs.substitutions = [
('_flairs_', ''),
('_FLAIR.nii.gz/', '/'),
]
sink.inputs.regexp_substitutions = [
('\.\..*\.\.', ''),
]
test_wf = ibbmTum_wf.get_test_wf(row_st=192, cols_st=192, thres_mask=10)
wmh = Workflow(name='wmh', base_dir=wf_temp)
wmh.connect(weights_source, 'weights', test_wf, 'inputspec.weights')
wmh.connect(data_source, 'flairs', test_wf, 'inputspec.flair')
wmh.connect(test_wf, 'outputspec.wmh_mask', sink, '@pred')
return wmh
def create_reconall_pipeline(name='reconall'):
reconall = Workflow(name='reconall')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
recon_all = Node(fs.ReconAll(args='-nuiterations 7 -no-isrunning'),
name="recon_all")
recon_all.plugin_args = {'submit_specs': 'request_memory = 9000'}
# function to replace / in subject id string with a _
def sub_id(sub_id):
return sub_id.replace('/', '_')
reconall.connect([
(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files'),
(('fs_subject_id', sub_id), 'subject_id')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
def create_converter_structural_pipeline(working_dir, ds_dir, name="converter_struct"):
# initiate workflow
converter_wf = Workflow(name=name)
converter_wf.base_dir = os.path.join(working_dir, "LeiCA_resting")
# set fsl output
fsl.FSLCommand.set_default_output_type("NIFTI_GZ")
# inputnode
inputnode = Node(util.IdentityInterface(fields=["t1w_dicom"]), name="inputnode")
outputnode = Node(util.IdentityInterface(fields=["t1w"]), name="outputnode")
niftisink = Node(nio.DataSink(), name="niftisink")
niftisink.inputs.base_directory = os.path.join(ds_dir, "raw_niftis")
# convert to nifti
# todo check if geometry bugs attac. use dcm2nii?
converter_t1w = Node(DcmStack(embed_meta=True), name="converter_t1w")
converter_t1w.plugin_args = {"submit_specs": "request_memory = 2000"}
converter_t1w.inputs.out_format = "t1w"
converter_wf.connect(inputnode, "t1w_dicom", converter_t1w, "dicom_files")
# reorient to standard orientation
reor_2_std = Node(fsl.Reorient2Std(), name="reor_2_std")
converter_wf.connect(converter_t1w, "out_file", reor_2_std, "in_file")
converter_wf.connect(reor_2_std, "out_file", outputnode, "t1w")
# save original niftis
converter_wf.connect(reor_2_std, "out_file", niftisink, "sMRI")
converter_wf.write_graph(dotfilename="converter_struct", graph2use="flat", format="pdf")
return converter_wf
def preprocess(input_file,
output_dir,
conform=True,
bias_correct=True,
skullstrip=True):
preprocess_flow = Workflow(name='preprocess', base_dir=output_dir)
conform = Node(MRIConvert(conform=True,
out_type='niigz',
out_file='conformed.nii.gz'),
name='conform')
n4 = Node(N4BiasFieldCorrection(dimension=3,
bspline_fitting_distance=300,
shrink_factor=3,
n_iterations=[50, 50, 30, 20],
output_image='n4.nii.gz'),
name='n4')
robex = Node(ROBEX(seed=1729, stripped_image='brain.nii.gz'), name='robex')
preprocess_flow.connect([(conform, n4, [('out_file', 'input_image')]),
(n4, robex, [('output_image', 'input_image')])])
preprocess_flow.write_graph(graph2use='orig')
conform.inputs.in_file = input_file
preprocess_flow.run('MultiProc', plugin_args={'n_procs': 5})
def create_ants_registration_pipeline(name='ants_registration'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
ants_registration = Workflow(name='ants_registration')
# inputnode
inputnode = Node(util.IdentityInterface(
fields=['denoised_ts', 'composite_transform', 'ref']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'ants_reg_ts',
]),
name='outputnode')
ants_reg = Node(ants.ApplyTransforms(input_image_type=3,
dimension=3,
interpolation='Linear'),
name='ants_reg')
ants_registration.connect([
(inputnode, ants_reg, [('denoised_ts', 'input_image')]),
(inputnode, ants_reg, [('ref', 'reference_image')]),
(inputnode, ants_reg, [('composite_transform', 'transforms')]),
(ants_reg, outputnode, [('output_image', 'ants_reg_ts')])
])
return ants_registration
def create_smoothing_pipeline(name='smoothing'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI')
# initiate workflow
smoothing = Workflow(name='smoothing')
# inputnode
inputnode=Node(util.IdentityInterface(fields=['ts_transformed',
'fwhm'
]),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['ts_smoothed'
]),
name='outputnode')
#apply smoothing
smooth = MapNode(fsl.Smooth(),name = 'smooth', iterfield='in_file')
smoothing.connect([
(inputnode, smooth, [
('ts_transformed', 'in_file'),
('fwhm', 'fwhm')]
),
(smooth, outputnode, [('smoothed_file', 'ts_smoothed')]
)
])
return smoothing
def create(self): #, **kwargs):
""" Create the nodes and connections for the workflow """
# Preamble
csvReader = CSVReader()
csvReader.inputs.in_file = self.csv_file.default_value
csvReader.inputs.header = self.hasHeader.default_value
csvOut = csvReader.run()
print("=" * 80)
print(csvOut.outputs.__dict__)
print("=" * 80)
iters = {}
label = list(csvOut.outputs.__dict__.keys())[0]
result = eval("csvOut.outputs.{0}".format(label))
iters['tests'], iters['trains'] = subsample_crossValidationSet(
result, self.sample_size.default_value)
# Main event
out_fields = ['T1', 'T2', 'Label', 'trainindex', 'testindex']
inputsND = Node(interface=IdentityInterface(fields=out_fields),
run_without_submitting=True,
name='inputs')
inputsND.iterables = [('trainindex', iters['trains']),
('testindex', iters['tests'])]
if not self.hasHeader.default_value:
inputsND.inputs.T1 = csvOut.outputs.column_0
inputsND.inputs.Label = csvOut.outputs.column_1
inputsND.inputs.T2 = csvOut.outputs.column_2
else:
inputsND.inputs.T1 = csvOut.outputs.__dict__['t1']
inputsND.inputs.Label = csvOut.outputs.__dict__['label']
inputsND.inputs.T2 = csvOut.outputs.__dict__['t2']
pass #TODO
metaflow = Workflow(name='metaflow')
metaflow.config['execution'] = {
'plugin': 'Linear',
'stop_on_first_crash': 'false',
'stop_on_first_rerun':
'false', # This stops at first attempt to rerun, before running, and before deleting previous results.
'hash_method': 'timestamp',
'single_thread_matlab':
'true', # Multi-core 2011a multi-core for matrix multiplication.
'remove_unnecessary_outputs': 'true',
'use_relative_paths':
'false', # relative paths should be on, require hash update when changed.
'remove_node_directories': 'false', # Experimental
'local_hash_check': 'false'
}
metaflow.add_nodes([inputsND])
"""import pdb; pdb.set_trace()"""
fusionflow = FusionLabelWorkflow()
self.connect([
(metaflow, fusionflow, [('inputs.trainindex', 'trainT1s.index'),
('inputs.T1', 'trainT1s.inlist')]),
(metaflow, fusionflow, [('inputs.trainindex', 'trainLabels.index'),
('inputs.Label', 'trainLabels.inlist')]),
(metaflow, fusionflow, [('inputs.testindex', 'testT1s.index'),
('inputs.T1', 'testT1s.inlist')])
])
def create_dcmconvert_pipeline(name='dcmconvert'):
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
from nipype.interfaces.dcmstack import DcmStack
# workflow
dcmconvert = Workflow(name='dcmconvert')
#inputnode
inputnode = Node(util.IdentityInterface(fields=['dicoms', 'filename']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=['nifti']),
name='outputnode')
# conversion node
converter = Node(DcmStack(embed_meta=True), name='converter')
# connections
dcmconvert.connect([(inputnode, converter, [('dicoms', 'dicom_files'),
('filename', 'out_format')]),
(converter, outputnode, [('out_file', 'nifti')])])
return dcmconvert
def create_reconall_pipeline(name='reconall'):
reconall = Workflow(name='reconall')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['anat',
'fs_subjects_dir',
'fs_subject_id'
]),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['fs_subjects_dir',
'fs_subject_id']),
name='outputnode')
# run reconall
recon_all = Node(fs.ReconAll(args='-autorecon2 -nuiterations 7 -no-isrunning -hippo-subfields'),
name="recon_all")
# recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
recon_all.plugin_args = {'submit_specs': 'request_memory = 9000'}
# function to replace / in subject id string with a _
def sub_id(sub_id):
return sub_id.replace('/', '_')
reconall.connect([(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files'),
(('fs_subject_id', sub_id), 'subject_id')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
def make_w_coreg_3T_afni():
n_in = Node(IdentityInterface(fields=[
'mean',
'T1w',
]), name='input')
n_out = Node(IdentityInterface(fields=[
'mat_func2struct',
]),
name='output')
n_allineate = Node(interface=Allineate(), name='allineate')
n_allineate.inputs.one_pass = True
n_allineate.inputs.args = '-master BASE'
n_allineate.inputs.warp_type = 'shift_rotate'
n_allineate.inputs.cost = 'nmi'
n_allineate.inputs.outputtype = 'NIFTI'
n_allineate.inputs.out_file = 'afni_realigned.nii.gz'
n_allineate.inputs.out_matrix = 'afni_realigned.aff12.1D'
w = Workflow('coreg_afni')
w.connect(n_in, 'mean', n_allineate, 'in_file')
w.connect(n_in, 'T1w', n_allineate, 'reference')
w.connect(n_allineate, 'out_matrix', n_out, 'mat_func2struct')
return w
def __call__(self, **kwargs):
kwargs = modify_paths(kwargs, relative=False)
interface = self.interface()
# Set the inputs early to get some argument checking
interface.inputs.set(**kwargs)
# Make a name for our node
inputs = interface.inputs.get_hashval()
hasher = hashlib.new('md5')
hasher.update(pickle.dumps(inputs))
dir_name = '%s-%s' % (interface.__class__.__module__.replace('.', '-'),
interface.__class__.__name__)
job_name = hasher.hexdigest()
node = Node(interface, name=job_name)
node.base_dir = os.path.join(self.base_dir, dir_name)
cwd = os.getcwd()
try:
out = node.run()
finally:
# node.run() changes to the node directory - if something goes wrong
# before it cds back you would end up in strange places
os.chdir(cwd)
if self.callback is not None:
self.callback(dir_name, job_name)
return out
def make_segment(self):
# Ref: http://nipype.readthedocs.io/en/0.12.1/interfaces/generated/nipype.interfaces.fsl.utils.html#reorient2std
ro = Node(interface=fsl.Reorient2Std(), name='ro')
# Ref: http://nipype.readthedocs.io/en/latest/interfaces/generated/interfaces.spm/preprocess.html#segment
seg = Node(interface=spm.NewSegment(channel_info=(0.0001, 60, (True,
True))),
name="seg")
spm_tissues_split = Node(Function(['in_list'], ['gm', 'wm', 'csf'],
self.spm_tissues),
name='spm_tissues_split')
gzip = Node(Function(['in_list'], ['out_list'], self.gzip_spm),
name='gzip')
segment = Workflow(name='Segment', base_dir=self.temp_dir)
gunzip = Node(interface=Gunzip(), name='gunzip')
# for new segment
segment.connect(ro, 'out_file', gunzip, 'in_file')
segment.connect(gunzip, 'out_file', seg, 'channel_files')
segment.connect(seg, 'native_class_images', spm_tissues_split,
'in_list')
return segment
def __call__(self, **kwargs):
kwargs = modify_paths(kwargs, relative=False)
interface = self.interface()
# Set the inputs early to get some argument checking
interface.inputs.set(**kwargs)
# Make a name for our node
inputs = interface.inputs.get_hashval()
hasher = hashlib.new('md5')
hasher.update(pickle.dumps(inputs))
dir_name = '%s-%s' % (interface.__class__.__module__.replace(
'.', '-'), interface.__class__.__name__)
job_name = hasher.hexdigest()
node = Node(interface, name=job_name)
node.base_dir = os.path.join(self.base_dir, dir_name)
cwd = os.getcwd()
try:
out = node.run()
finally:
# node.run() changes to the node directory - if something goes wrong
# before it cds back you would end up in strange places
os.chdir(cwd)
if self.callback is not None:
self.callback(dir_name, job_name)
return out
def create_normalize_pipeline(name='normalize'):
# workflow
normalize = Workflow(name='normalize')
# Define nodes
inputnode = Node(interface=util.IdentityInterface(fields=['epi_coreg',
'tr']),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(fields=[
'normalized_file']),
name='outputnode')
# time-normalize scans
normalize_time=Node(util.Function(input_names=['in_file','tr'],
output_names=['out_file'],
function=time_normalizer),
name='normalize_time')
normalize_time.plugin_args={'submit_specs': 'request_memory = 17000'}
normalize.connect([(inputnode, normalize_time, [('tr', 'tr')]),
(inputnode, normalize_time, [('epi_coreg', 'in_file')]),
(normalize_time, outputnode, [('out_file', 'normalized_file')])
])
# time-normalize scans
return normalize
def create_reconall_pipeline(name='reconall'):
reconall = Workflow(name='reconall')
#inputnode
inputnode = Node(util.IdentityInterface(
fields=['anat', 'fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
outputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='outputnode')
# run reconall
recon_all = create_skullstripped_recon_flow()
# function to replace / in subject id string with a _
def sub_id(sub_id):
return sub_id.replace('/', '_')
reconall.connect([(inputnode, recon_all,
[('fs_subjects_dir', 'inputspec.subjects_dir'),
('anat', 'inputspec.T1_files'),
(('fs_subject_id', sub_id), 'inputspec.subject_id')]),
(recon_all, outputnode,
[('outputspec.subject_id', 'fs_subject_id'),
('outputspec.subjects_dir', 'fs_subjects_dir')])])
return reconall
def make_full_workflow(session='7TGE', n_fmap=10):
n_in = Node(IdentityInterface(fields=[
'T1w',
'func',
'fmap',
'subject',
]),
name='input')
n_out = Node(IdentityInterface(fields=[
'func1',
'func2',
'filtered1',
'filtered2',
'mat_func2struct',
]),
name='output')
n_merge = Node(interface=Merge(), name='merge')
n_merge.inputs.dimension = 't'
w_preproc = make_workflow(n_fmap)
w_smooth1 = make_w_smooth('1')
w_smooth2 = make_w_smooth('2')
w = Workflow(session)
w.connect(n_in, 'func', n_merge, 'in_files')
w.connect(n_merge, 'merged_file', w_preproc, 'input.func')
w.connect(n_in, 'fmap', w_preproc, 'input.fmap')
w.connect(w_preproc, 'output.func1', n_out, 'func1')
w.connect(w_preproc, 'output.func2', n_out, 'func2')
w.connect(w_preproc, 'output.func1', w_smooth1, 'input.func')
w.connect(w_preproc, 'output.func2', w_smooth2, 'input.func')
w.connect(w_smooth1, 'output.func', n_out, 'filtered1')
w.connect(w_smooth2, 'output.func', n_out, 'filtered2')
if session.startswith('7T'):
w_coreg_7T = make_w_coreg_7T()
w.connect(n_in, 'T1w', w_coreg_7T, 'input.T1w')
w.connect(w_preproc, 'output.mean', w_coreg_7T, 'input.mean')
w.connect(w_coreg_7T, 'output.mat_ants', n_out, 'mat_func2struct')
else:
w_coreg = make_w_freesurfer2func()
w_coreg_3T = make_w_coreg_3T_ants()
"""
w.connect(n_in, 'T1w', w_coreg, 'input.T1w')
w.connect(n_in, 'subject', w_coreg, 'input.subject')
w.connect(w_preproc, 'output.mean', w_coreg, 'input.mean')
"""
w.connect(n_in, 'T1w', w_coreg_3T, 'input.T1w')
w.connect(w_preproc, 'output.mean', w_coreg_3T, 'input.mean')
w.connect(w_coreg_3T, 'output.mat_func2struct', n_out,
'mat_func2struct')
return w
def stub_node_factory(*args, **kwargs):
if 'name' not in kwargs.keys():
raise Exception()
name = kwargs['name']
if name == 'compcor':
return Node(*args, **kwargs)
else: # replace with an IdentityInterface
return Node(IdentityInterface(fields=ALL_FIELDS), name=name)
def stub_wf(*args, **kwargs):
wflow = Workflow(name='realigner')
inputnode = Node(IdentityInterface(fields=['func']), name='inputspec')
outputnode = Node(
interface=IdentityInterface(fields=['realigned_file']),
name='outputspec')
wflow.connect(inputnode, 'func', outputnode, 'realigned_file')
return wflow
def make_infosource(self):
# Infosource: Iterate through subject names
infosource = Node(interface=IdentityInterface(fields=['subject_id']),
name="infosource")
infosource.iterables = ('subject_id', self.subject_list)
return infosource
def node_result_file(u: pe.Node) -> Path:
u._output_dir = None # reset this just in case
output_dir = u.output_dir()
assert isinstance(output_dir, str)
result_file = Path(output_dir) / f"result_{u.name}.pklz"
return result_file
def create_converter_diffusion_pipeline(working_dir,
ds_dir,
name='converter_diffusion'):
# initiate workflow
converter_wf = Workflow(name=name)
converter_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['dMRI_dicom']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['dMRI']),
name='outputnode')
niftisink = Node(nio.DataSink(), name='niftisink')
niftisink.inputs.base_directory = os.path.join(ds_dir, 'raw_niftis')
#######
converter_dMRI = Node(Dcm2nii(), name="converter_dMRI")
converter_dMRI.inputs.gzip_output = True
converter_dMRI.inputs.nii_output = True
converter_dMRI.inputs.anonymize = False
converter_dMRI.plugin_args = {'submit_specs': 'request_memory = 2000'}
converter_wf.connect(inputnode, 'dMRI_dicom', converter_dMRI,
'source_names')
dMRI_rename = Node(util.Rename(format_string='DTI_mx_137.nii.gz'),
name='dMRI_rename')
converter_wf.connect(converter_dMRI, 'converted_files', dMRI_rename,
'in_file')
bvecs_rename = Node(util.Rename(format_string='DTI_mx_137.bvecs'),
name='bvecs_rename')
converter_wf.connect(converter_dMRI, 'bvecs', bvecs_rename, 'in_file')
bvals_rename = Node(util.Rename(format_string='DTI_mx_137.bvals'),
name='bvals_rename')
converter_wf.connect(converter_dMRI, "bvals", bvals_rename, 'in_file')
# reorient to standard orientation
reor_2_std = Node(fsl.Reorient2Std(), name='reor_2_std')
converter_wf.connect(dMRI_rename, 'out_file', reor_2_std, 'in_file')
converter_wf.connect(reor_2_std, 'out_file', outputnode, 'dMRI')
# save original niftis
converter_wf.connect(reor_2_std, 'out_file', niftisink, 'dMRI.@dwi')
converter_wf.connect(bvals_rename, 'out_file', niftisink, 'dMRI.@bvals')
converter_wf.connect(bvecs_rename, 'out_file', niftisink, 'dMRI.@bvecs')
converter_wf.write_graph(dotfilename='converter_struct',
graph2use='flat',
format='pdf')
return converter_wf
def create_quick_registration(name='quickreg'):
# workflow
quickreg = Workflow(name='quickreg')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['anat', 'standard']),
name='inputnode')
#MapNode(util.IdentityInterface(fields=['anat', 'standard']), name='inputnode', iterfield=['anat'])
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'anat2std_transforms', 'composite', 'anat2std', 'std2anat_transforms',
'std2anat', 'inverse_composite'
]),
name='outputnode')
antsreg = Node(
ants.Registration(
dimension=3,
transforms=['SyN'],
metric=['CC'],
metric_weight=[1],
number_of_iterations=[[70, 50, 30]],
convergence_threshold=[1e-6],
convergence_window_size=[10],
shrink_factors=[[8, 4, 2]],
smoothing_sigmas=[[3, 2, 1]],
sigma_units=['vox'],
initial_moving_transform_com=1,
transform_parameters=[(0.1, 3.0, 0.0)],
sampling_strategy=['None'],
sampling_percentage=[1],
radius_or_number_of_bins=[4],
num_threads=1,
interpolation='Linear',
winsorize_lower_quantile=0.005,
winsorize_upper_quantile=0.995,
collapse_output_transforms=True,
output_warped_image=True,
write_composite_transform=True,
#output_inverse_warped_image=True,
#output_warped_image=True,
use_histogram_matching=True,
),
name='antsreg')
# connections
quickreg.connect([(inputnode, antsreg, [('anat', 'moving_image'),
('standard', 'fixed_image')]),
(antsreg, outputnode,
[('forward_transforms', 'anat2std_transforms'),
('reverse_transforms', 'std2anat_transforms'),
('inverse_composite_transform', 'inverse_composite'),
('warped_image', 'anat2std'),
('composite_transform', 'composite'),
('inverse_warped_image', 'std2anat')])])
return quickreg
def anatomical_preprocessing():
'''
Inputs:
MP2RAGE Skull stripped image using Spectre-2010
Workflow:
1. reorient to RPI
2. create a brain mask
Returns:
brain
brain_mask
'''
# define workflow
flow = Workflow('anat_preprocess')
inputnode = Node(util.IdentityInterface(
fields=['anat', 'anat_gm', 'anat_wm', 'anat_csf', 'anat_first']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=[
'brain',
'brain_gm',
'brain_wm',
'brain_csf',
'brain_first',
'brain_mask',
]),
name='outputnode')
reorient = Node(interface=preprocess.Resample(), name='anat_reorient')
reorient.inputs.orientation = 'RPI'
reorient.inputs.outputtype = 'NIFTI'
erode = Node(interface=fsl.ErodeImage(), name='anat_preproc')
reorient_gm = reorient.clone('anat_preproc_gm')
reorient_wm = reorient.clone('anat_preproc_wm')
reorient_cm = reorient.clone('anat_preproc_csf')
reorient_first = reorient.clone('anat_preproc_first')
make_mask = Node(interface=fsl.UnaryMaths(), name='anat_preproc_mask')
make_mask.inputs.operation = 'bin'
# connect workflow nodes
flow.connect(inputnode, 'anat', reorient, 'in_file')
flow.connect(inputnode, 'anat_gm', reorient_gm, 'in_file')
flow.connect(inputnode, 'anat_wm', reorient_wm, 'in_file')
flow.connect(inputnode, 'anat_csf', reorient_cm, 'in_file')
flow.connect(inputnode, 'anat_first', reorient_first, 'in_file')
flow.connect(reorient, 'out_file', erode, 'in_file')
flow.connect(erode, 'out_file', make_mask, 'in_file')
flow.connect(make_mask, 'out_file', outputnode, 'brain_mask')
flow.connect(erode, 'out_file', outputnode, 'brain')
flow.connect(reorient_gm, 'out_file', outputnode, 'brain_gm')
flow.connect(reorient_wm, 'out_file', outputnode, 'brain_wm')
flow.connect(reorient_cm, 'out_file', outputnode, 'brain_csf')
flow.connect(reorient_first, 'out_file', outputnode, 'brain_first')
return flow
def make_workflow_roi(region):
"""
Benson_ROI_Names = {'V1', 'V2', 'V3', 'hV4', 'VO1', 'VO2', 'LO1', 'LO2', 'TO1', 'TO2', 'V3B', 'V3A'};
Wang_ROI_Names = [
'V1v', 'V1d', 'V2v', 'V2d', 'V3v', 'V3d', 'hV4', 'VO1', 'VO2', 'PHC1', 'PHC2',
'TO2', 'TO1', 'LO2', 'LO1', 'V3B', 'V3A', 'IPS0', 'IPS1', 'IPS2', 'IPS3', 'IPS4' ,
'IPS5', 'SPL1', 'FEF'];
"""
w = Workflow(f'roi_{region}')
n_in = Node(IdentityInterface(fields=[
'atlas',
'func_to_struct',
'struct_to_freesurfer',
'ref',
]),
name='input')
n_out = Node(IdentityInterface(fields=[
'mask_file',
]), name='output')
n_m = Node(Merge(2), 'merge')
n_v = Node(MathsCommand(), region)
n_v.inputs.out_file = 'roi.nii.gz'
n_v.inputs.nan2zeros = True
if region == 'V1':
n_v.inputs.args = '-uthr 1 -bin'
elif region == 'V2':
n_v.inputs.args = '-thr 2 -uthr 3 -bin'
elif region == 'V3':
n_v.inputs.args = '-thr 4 -uthr 5 -bin'
else:
raise ValueError(f'Unknown region {region}. It should be V1, V2, V3')
at = Node(ApplyTransforms(), 'applytransform')
at.inputs.dimension = 3
at.inputs.output_image = 'roi_func.nii.gz'
at.inputs.interpolation = 'Linear'
at.inputs.default_value = 0
at.inputs.invert_transform_flags = [True, True]
w.connect(n_in, 'atlas', n_v, 'in_file')
w.connect(n_v, 'out_file', at, 'input_image')
w.connect(n_in, 'ref', at, 'reference_image')
w.connect(n_in, 'struct_to_freesurfer', n_m, 'in1')
w.connect(n_in, 'func_to_struct', n_m, 'in2')
w.connect(n_m, 'out', at, 'transforms')
w.connect(at, 'output_image', n_out, 'mask_file')
return w
def _merge_nii(file_list, out_filename):
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.fsl as fsl
merge = Node(fsl.Merge(dimension='t'), name='merge')
merge.base_dir = os.getcwd()
merge.inputs.in_files = file_list
merge.inputs.merged_file = out_filename
result = merge.run()
return result.outputs.merged_file
def create(self): # , **kwargs):
""" Create the nodes and connections for the workflow """
# Preamble
csvReader = CSVReader()
csvReader.inputs.in_file = self.csv_file.default_value
csvReader.inputs.header = self.hasHeader.default_value
csvOut = csvReader.run()
print(("=" * 80))
print((csvOut.outputs.__dict__))
print(("=" * 80))
iters = OrderedDict()
label = list(csvOut.outputs.__dict__.keys())[0]
result = eval("csvOut.outputs.{0}".format(label))
iters['tests'], iters['trains'] = subsample_crossValidationSet(result, self.sample_size.default_value)
# Main event
out_fields = ['T1', 'T2', 'Label', 'trainindex', 'testindex']
inputsND = Node(interface=IdentityInterface(fields=out_fields),
run_without_submitting=True, name='inputs')
inputsND.iterables = [('trainindex', iters['trains']),
('testindex', iters['tests'])]
if not self.hasHeader.default_value:
inputsND.inputs.T1 = csvOut.outputs.column_0
inputsND.inputs.Label = csvOut.outputs.column_1
inputsND.inputs.T2 = csvOut.outputs.column_2
else:
inputsND.inputs.T1 = csvOut.outputs.__dict__['t1']
inputsND.inputs.Label = csvOut.outputs.__dict__['label']
inputsND.inputs.T2 = csvOut.outputs.__dict__['t2']
pass # TODO
metaflow = Workflow(name='metaflow')
metaflow.config['execution'] = {
'plugin': 'Linear',
'stop_on_first_crash': 'false',
'stop_on_first_rerun': 'false',
# This stops at first attempt to rerun, before running, and before deleting previous results.
'hash_method': 'timestamp',
'single_thread_matlab': 'true', # Multi-core 2011a multi-core for matrix multiplication.
'remove_unnecessary_outputs': 'true',
'use_relative_paths': 'false', # relative paths should be on, require hash update when changed.
'remove_node_directories': 'false', # Experimental
'local_hash_check': 'false'
}
metaflow.add_nodes([inputsND])
"""import pdb; pdb.set_trace()"""
fusionflow = FusionLabelWorkflow()
self.connect(
[(metaflow, fusionflow, [('inputs.trainindex', 'trainT1s.index'), ('inputs.T1', 'trainT1s.inlist')]),
(metaflow, fusionflow,
[('inputs.trainindex', 'trainLabels.index'), ('inputs.Label', 'trainLabels.inlist')]),
(metaflow, fusionflow, [('inputs.testindex', 'testT1s.index'), ('inputs.T1', 'testT1s.inlist')])
])
def func_preprocess(name = 'func_preproc'):
'''
Method to preprocess functional data after warping to anatomical space.
Accomplished after one step Distortion Correction, Motion Correction and Boundary based linear registration to
anatomical space.
Precodure includes:
# 1- skull strip
# 2- Normalize the image intensity values.
# 3- Calculate Mean of Skull stripped image
# 4- Create brain mask from Normalized data.
'''
# Define Workflow
flow = Workflow(name=name)
inputnode = Node(util.IdentityInterface(fields=['func_in']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['func_preproc',
'func_preproc_mean',
'func_preproc_mask']),
name = 'outputnode')
# 2- Normalize the image intensity values.
norm = Node(interface = fsl.ImageMaths(), name = 'func_normalized')
norm.inputs.op_string = '-ing 1000'
norm.out_data_type = 'float'
norm.output_type = 'NIFTI'
# 4- Create brain mask from Normalized data.
mask = Node(interface = fsl.BET(), name = 'func_preprocessed')
mask.inputs.functional = True
mask.inputs.mask = True
mask.inputs.frac = 0.5
mask.inputs.vertical_gradient = 0
mask.inputs.threshold = True
# 3- Calculate Mean of Skull stripped image
mean = Node(interface = preprocess.TStat(), name = 'func_preprocessed_mean')
mean.inputs.options = '-mean'
mean.inputs.outputtype = 'NIFTI'
flow.connect( inputnode , 'func_in' , norm, 'in_file' )
flow.connect( norm , 'out_file' , mask, 'in_file' )
flow.connect( norm , 'out_file' , mean, 'in_file' )
flow.connect( mask , 'out_file' , outputnode, 'func_preproc')
flow.connect( mask , 'mask_file' , outputnode, 'func_preproc_mask')
flow.connect( mean , 'out_file' , outputnode, 'func_preproc_mean')
return flow
def create_conversion(
name, subject, scans, working_dir, out_dir, folder, xnat_server, xnat_user, xnat_pass, project_id, exp_id
):
convert = Workflow(name=name)
convert.base_dir = working_dir
convert.config["execution"]["crashdump_dir"] = convert.base_dir + "/crash_files"
# infosource to iterate over scans
scan_infosource = Node(util.IdentityInterface(fields=["scan_key", "scan_val"]), name="scan_infosource")
scan_infosource.iterables = [("scan_key", scans.keys()), ("scan_val", scans.values())]
scan_infosource.synchronize = True
# xnat source
xnatsource = Node(
nio.XNATSource(
infields=["project_id", "subject_id", "exp_id", "scan_id"],
outfields=["dicom"],
server=xnat_server,
user=xnat_user,
pwd=xnat_pass,
cache_dir=working_dir,
),
name="xnatsource",
)
xnatsource.inputs.query_template = (
"/projects/%s/subjects/%s/experiments/%s/scans/%d/resources/DICOM/files"
) # files')
xnatsource.inputs.query_template_args["dicom"] = [["project_id", "subject_id", "exp_id", "scan_id"]]
xnatsource.inputs.project_id = project_id
xnatsource.inputs.subject_id = subject
xnatsource.inputs.exp_id = exp_id
convert.connect([(scan_infosource, xnatsource, [("scan_val", "scan_id")])])
# workflow to convert dicoms
dcmconvert = create_dcmconvert_pipeline()
convert.connect(
[
(scan_infosource, dcmconvert, [("scan_key", "inputnode.filename")]),
(xnatsource, dcmconvert, [("dicom", "inputnode.dicoms")]),
]
)
# xnat sink
sink = Node(nio.DataSink(base_directory=out_dir, parameterization=False), name="sink")
convert.connect([(dcmconvert, sink, [("outputnode.nifti", folder)])])
convert.run()
def anatomical_preprocessing():
'''
Inputs:
MP2RAGE Skull stripped image using Spectre-2010
Workflow:
1. reorient to RPI
2. create a brain mask
Returns:
brain
brain_mask
'''
# define workflow
flow = Workflow('anat_preprocess')
inputnode = Node(util.IdentityInterface(fields=['anat', 'anat_gm', 'anat_wm', 'anat_csf', 'anat_first']), name = 'inputnode')
outputnode = Node(util.IdentityInterface(fields=['brain','brain_gm', 'brain_wm', 'brain_csf', 'brain_first', 'brain_mask',]), name = 'outputnode')
reorient = Node(interface=preprocess.Resample(), name = 'anat_reorient')
reorient.inputs.orientation = 'RPI'
reorient.inputs.outputtype = 'NIFTI'
erode = Node(interface=fsl.ErodeImage(), name = 'anat_preproc')
reorient_gm = reorient.clone('anat_preproc_gm')
reorient_wm = reorient.clone('anat_preproc_wm')
reorient_cm = reorient.clone('anat_preproc_csf')
reorient_first = reorient.clone('anat_preproc_first')
make_mask = Node(interface=fsl.UnaryMaths(), name = 'anat_preproc_mask')
make_mask.inputs.operation = 'bin'
# connect workflow nodes
flow.connect(inputnode, 'anat' , reorient, 'in_file' )
flow.connect(inputnode, 'anat_gm' , reorient_gm, 'in_file' )
flow.connect(inputnode, 'anat_wm' , reorient_wm, 'in_file' )
flow.connect(inputnode, 'anat_csf' , reorient_cm, 'in_file' )
flow.connect(inputnode, 'anat_first' , reorient_first,'in_file' )
flow.connect(reorient, 'out_file' , erode, 'in_file' )
flow.connect(erode, 'out_file' , make_mask, 'in_file' )
flow.connect(make_mask, 'out_file' , outputnode, 'brain_mask' )
flow.connect(erode, 'out_file' , outputnode, 'brain' )
flow.connect(reorient_gm, 'out_file' , outputnode, 'brain_gm' )
flow.connect(reorient_wm, 'out_file' , outputnode, 'brain_wm' )
flow.connect(reorient_cm, 'out_file' , outputnode, 'brain_csf' )
flow.connect(reorient_first, 'out_file' , outputnode, 'brain_first' )
return flow
def create_converter_diffusion_pipeline(working_dir, ds_dir, name="converter_diffusion"):
# initiate workflow
converter_wf = Workflow(name=name)
converter_wf.base_dir = os.path.join(working_dir, "LeiCA_resting")
# set fsl output
fsl.FSLCommand.set_default_output_type("NIFTI_GZ")
# inputnode
inputnode = Node(util.IdentityInterface(fields=["dMRI_dicom"]), name="inputnode")
outputnode = Node(util.IdentityInterface(fields=["dMRI"]), name="outputnode")
niftisink = Node(nio.DataSink(), name="niftisink")
niftisink.inputs.base_directory = os.path.join(ds_dir, "raw_niftis")
#######
converter_dMRI = Node(Dcm2nii(), name="converter_dMRI")
converter_dMRI.inputs.gzip_output = True
converter_dMRI.inputs.nii_output = True
converter_dMRI.inputs.anonymize = False
converter_dMRI.plugin_args = {"submit_specs": "request_memory = 2000"}
converter_wf.connect(inputnode, "dMRI_dicom", converter_dMRI, "source_names")
dMRI_rename = Node(util.Rename(format_string="DTI_mx_137.nii.gz"), name="dMRI_rename")
converter_wf.connect(converter_dMRI, "converted_files", dMRI_rename, "in_file")
bvecs_rename = Node(util.Rename(format_string="DTI_mx_137.bvecs"), name="bvecs_rename")
converter_wf.connect(converter_dMRI, "bvecs", bvecs_rename, "in_file")
bvals_rename = Node(util.Rename(format_string="DTI_mx_137.bvals"), name="bvals_rename")
converter_wf.connect(converter_dMRI, "bvals", bvals_rename, "in_file")
# reorient to standard orientation
reor_2_std = Node(fsl.Reorient2Std(), name="reor_2_std")
converter_wf.connect(dMRI_rename, "out_file", reor_2_std, "in_file")
converter_wf.connect(reor_2_std, "out_file", outputnode, "dMRI")
# save original niftis
converter_wf.connect(reor_2_std, "out_file", niftisink, "dMRI.@dwi")
converter_wf.connect(bvals_rename, "out_file", niftisink, "dMRI.@bvals")
converter_wf.connect(bvecs_rename, "out_file", niftisink, "dMRI.@bvecs")
converter_wf.write_graph(dotfilename="converter_struct", graph2use="flat", format="pdf")
return converter_wf
def __call__(self, **kwargs):
kwargs = modify_paths(kwargs, relative=False)
interface = self.interface()
# Set the inputs early to get some argument checking
interface.inputs.set(**kwargs)
# Make a name for our node
inputs = interface.inputs.get_hashval()
hasher = hashlib.new('md5')
hasher.update(pickle.dumps(inputs))
dir_name = '%s-%s' % (interface.__class__.__module__.replace('.', '-'),
interface.__class__.__name__)
job_name = hasher.hexdigest()
node = Node(interface, name=job_name)
node.base_dir = os.path.join(self.base_dir, dir_name)
out = node.run()
if self.callback is not None:
self.callback(dir_name, job_name)
return out
def smooth_data(name = 'func_smoothed'):
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
flow = Workflow(name)
inputnode = Node(util.IdentityInterface(fields=['func_data']),
name = 'inputnode')
outputnode = Node(util.IdentityInterface(fields=['func_smoothed']),
name = 'outputnode')
smooth = Node(interface=fsl.Smooth(), name='func_smooth_fwhm_4')
smooth.inputs.fwhm = 4.0
smooth.terminal_output = 'file'
flow.connect(inputnode, 'func_data' , smooth , 'in_file' )
flow.connect(smooth, 'smoothed_file' , outputnode , 'func_smoothed' )
return flow
#### running directly ############################################################################################################
fmapepi.base_dir='/scr/kansas1/huntenburg/lemon_missing/working_dir/'
#fmapepi.config['execution']={'remove_unnecessary_outputs': 'False'}
data_dir = '/scr/jessica2/Schaare/LEMON/'
fs_subjects_dir='/scr/jessica2/Schaare/LEMON/freesurfer/'
out_dir = '/scr/jessica2/Schaare/LEMON/preprocessed/'
#subjects=['LEMON001']
subjects=[]
f = open('/scr/jessica2/Schaare/LEMON/missing_subjects.txt','r')
for line in f:
subjects.append(line.strip())
# create inforsource to iterate over subjects
infosource = Node(util.IdentityInterface(fields=['subject_id','fs_subjects_dir']),
name='infosource')
infosource.inputs.fs_subjects_dir=fs_subjects_dir
infosource.iterables=('subject_id', subjects)
# define templates and select files
templates={'epi_mean':'preprocessed/{subject_id}/motion_correction/rest_moco_mean.nii.gz',
'mag': 'raw/{subject_id}/rest/fmap_mag_1.nii.gz',
'phase': 'raw/{subject_id}/rest/fmap_phase.nii.gz',
'anat_head': 'preprocessed/{subject_id}/freesurfer_anatomy/T1_out.nii.gz',
'anat_brain': 'preprocessed/{subject_id}/freesurfer_anatomy/brain_out.nii.gz',
'wmseg':'preprocessed/{subject_id}/freesurfer_anatomy/brain_out_wmseg.nii.gz'}
selectfiles = Node(nio.SelectFiles(templates,
base_directory=data_dir),
name="selectfiles")
# directories
working_dir = '/scr/ilz3/myelinconnect/working_dir/'
data_dir= '/scr/ilz3/myelinconnect/'
out_dir = '/scr/ilz3/myelinconnect/final_struct_space/rest1_1_trans'
# set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# main workflow
smooth = Workflow(name='smooth')
smooth.base_dir = working_dir
smooth.config['execution']['crashdump_dir'] = smooth.base_dir + "/crash_files"
# iterate over subjects
subject_infosource = Node(util.IdentityInterface(fields=['subject']),
name='subject_infosource')
subject_infosource.iterables=[('subject', subjects_db)]
# iterate over sessions
session_infosource = Node(util.IdentityInterface(fields=['session']),
name='session_infosource')
session_infosource.iterables=[('session', sessions)]
# select files
templates={'rest': 'final_struct_space/rest1_1_trans/{subject}_{session}_denoised_trans.nii.gz'
}
selectfiles = Node(nio.SelectFiles(templates, base_directory=data_dir),
name="selectfiles")
smooth.connect([(subject_infosource, selectfiles, [('subject', 'subject')]),
(session_infosource, selectfiles, [('session', 'session')])
def create_denoise_pipeline(name='denoise'):
# workflow
denoise = Workflow(name='denoise')
# Define nodes
inputnode = Node(interface=util.IdentityInterface(fields=['anat_brain',
'brain_mask',
'epi2anat_dat',
'unwarped_mean',
'epi_coreg',
'moco_par',
'highpass_sigma',
'lowpass_sigma',
'tr']),
name='inputnode')
outputnode = Node(interface=util.IdentityInterface(fields=['wmcsf_mask',
'brain_mask_resamp',
'brain_mask2epi',
'combined_motion',
'outlier_files',
'intensity_files',
'outlier_stats',
'outlier_plots',
'mc_regressor',
'mc_F',
'mc_pF',
'comp_regressor',
'comp_F',
'comp_pF',
# FL added fullspectrum
'ts_fullspectrum',
'normalized_file']),
name='outputnode')
# run fast to get tissue probability classes
fast = Node(fsl.FAST(), name='fast')
denoise.connect([(inputnode, fast, [('anat_brain', 'in_files')])])
# functions to select tissue classes
def selectindex(files, idx):
import numpy as np
from nipype.utils.filemanip import filename_to_list, list_to_filename
return list_to_filename(np.array(filename_to_list(files))[idx].tolist())
def selectsingle(files, idx):
return files[idx]
# resample tissue classes
resample_tissue = MapNode(afni.Resample(resample_mode='NN',
outputtype='NIFTI_GZ'),
iterfield=['in_file'],
name='resample_tissue')
denoise.connect([(inputnode, resample_tissue, [('epi_coreg', 'master')]),
(fast, resample_tissue, [(('partial_volume_files', selectindex, [0, 2]), 'in_file')]),
])
# binarize tissue classes
binarize_tissue = MapNode(fsl.ImageMaths(op_string='-nan -thr 0.99 -ero -bin'),
iterfield=['in_file'],
name='binarize_tissue')
denoise.connect([(resample_tissue, binarize_tissue, [('out_file', 'in_file')]),
])
# combine tissue classes to noise mask
wmcsf_mask = Node(fsl.BinaryMaths(operation='add',
out_file='wmcsf_mask_lowres.nii.gz'),
name='wmcsf_mask')
denoise.connect([(binarize_tissue, wmcsf_mask, [(('out_file', selectsingle, 0), 'in_file'),
(('out_file', selectsingle, 1), 'operand_file')]),
(wmcsf_mask, outputnode, [('out_file', 'wmcsf_mask')])])
# resample brain mask
resample_brain = Node(afni.Resample(resample_mode='NN',
outputtype='NIFTI_GZ',
out_file='T1_brain_mask_lowres.nii.gz'),
name='resample_brain')
denoise.connect([(inputnode, resample_brain, [('brain_mask', 'in_file'),
('epi_coreg', 'master')]),
(resample_brain, outputnode, [('out_file', 'brain_mask_resamp')])])
# project brain mask into original epi space fpr quality assessment
brainmask2epi = Node(fs.ApplyVolTransform(interp='nearest',
inverse=True,
transformed_file='T1_brain_mask2epi.nii.gz', ),
name='brainmask2epi')
denoise.connect([(inputnode, brainmask2epi, [('brain_mask', 'target_file'),
('epi2anat_dat', 'reg_file'),
('unwarped_mean', 'source_file')]),
(brainmask2epi, outputnode, [('transformed_file', 'brain_mask2epi')])])
# perform artefact detection
artefact = Node(ra.ArtifactDetect(save_plot=True,
use_norm=True,
parameter_source='FSL',
mask_type='file',
norm_threshold=1,
zintensity_threshold=3,
use_differences=[True, False]
),
name='artefact')
artefact.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, artefact, [('epi_coreg', 'realigned_files'),
('moco_par', 'realignment_parameters')]),
(resample_brain, artefact, [('out_file', 'mask_file')]),
(artefact, outputnode, [('norm_files', 'combined_motion'),
('outlier_files', 'outlier_files'),
('intensity_files', 'intensity_files'),
('statistic_files', 'outlier_stats'),
('plot_files', 'outlier_plots')])])
# Compute motion regressors
motreg = Node(util.Function(input_names=['motion_params', 'order', 'derivatives'],
output_names=['out_files'],
function=motion_regressors),
name='getmotionregress')
motreg.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, motreg, [('moco_par', 'motion_params')])])
# Create a filter to remove motion and art confounds
createfilter1 = Node(util.Function(input_names=['motion_params', 'comp_norm',
'outliers', 'detrend_poly'],
output_names=['out_files'],
function=build_filter1),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 2
createfilter1.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(motreg, createfilter1, [('out_files', 'motion_params')]),
(artefact, createfilter1, [ # ('norm_files', 'comp_norm'),
('outlier_files', 'outliers')]),
(createfilter1, outputnode, [('out_files', 'mc_regressor')])
])
# regress out motion and art confounds
filter1 = Node(fsl.GLM(out_f_name='F_mcart.nii.gz',
out_pf_name='pF_mcart.nii.gz',
out_res_name='rest_mc_denoised.nii.gz',
demean=True),
name='filtermotion')
filter1.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, filter1, [('epi_coreg', 'in_file')]),
(createfilter1, filter1, [(('out_files', list_to_filename), 'design')]),
(filter1, outputnode, [('out_f', 'mc_F'),
('out_pf', 'mc_pF')])])
# create filter with compcor components
createfilter2 = Node(util.Function(input_names=['realigned_file', 'mask_file',
'num_components',
'extra_regressors'],
output_names=['out_files'],
function=extract_noise_components),
name='makecompcorfilter')
createfilter2.inputs.num_components = 6
createfilter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(createfilter1, createfilter2, [(('out_files', list_to_filename), 'extra_regressors')]),
(filter1, createfilter2, [('out_res', 'realigned_file')]),
(wmcsf_mask, createfilter2, [('out_file', 'mask_file')]),
(createfilter2, outputnode, [('out_files', 'comp_regressor')]),
])
# regress compcor and other noise components
filter2 = Node(fsl.GLM(out_f_name='F_noise.nii.gz',
out_pf_name='pF_noise.nii.gz',
out_res_name='rest2anat_denoised.nii.gz',
demean=True),
name='filternoise')
filter2.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(filter1, filter2, [('out_res', 'in_file')]),
(createfilter2, filter2, [('out_files', 'design')]),
(resample_brain, filter2, [('out_file', 'mask')]),
(filter2, outputnode, [('out_f', 'comp_F'),
('out_pf', 'comp_pF')])
])
# bandpass filter denoised file
bandpass_filter = Node(fsl.TemporalFilter(out_file='rest_denoised_bandpassed.nii.gz'),
name='bandpass_filter')
bandpass_filter.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, bandpass_filter, [('highpass_sigma', 'highpass_sigma'),
('lowpass_sigma', 'lowpass_sigma')]),
(filter2, bandpass_filter, [('out_res', 'in_file')]),
# FL added fullspectrum to outputnoded
(filter2, outputnode, [('out_res', 'ts_fullspectrum')])
])
# time-normalize scans
normalize_time = Node(util.Function(input_names=['in_file', 'tr'],
output_names=['out_file'],
function=time_normalizer),
name='normalize_time')
normalize_time.plugin_args = {'submit_specs': 'request_memory = 17000'}
denoise.connect([(inputnode, normalize_time, [('tr', 'tr')]),
(bandpass_filter, normalize_time, [('out_file', 'in_file')]),
(normalize_time, outputnode, [('out_file', 'normalized_file')])
])
return denoise
def calc_local_metrics(
preprocessed_data_dir,
subject_id,
parcellations_dict,
bp_freq_list,
fd_thresh,
working_dir,
ds_dir,
use_n_procs,
plugin_name,
):
import os
from nipype import config
from nipype.pipeline.engine import Node, Workflow, MapNode
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
import utils as calc_metrics_utils
#####################################
# GENERAL SETTINGS
#####################################
fsl.FSLCommand.set_default_output_type("NIFTI_GZ")
wf = Workflow(name="LeiCA_LIFE_metrics")
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(
logging=dict(workflow_level="DEBUG"),
execution={"stop_on_first_crash": True, "remove_unnecessary_outputs": True, "job_finished_timeout": 15},
)
config.update_config(nipype_cfg)
wf.config["execution"]["crashdump_dir"] = os.path.join(working_dir, "crash")
ds = Node(nio.DataSink(base_directory=ds_dir), name="ds")
ds.inputs.regexp_substitutions = [
("MNI_resampled_brain_mask_calc.nii.gz", "falff.nii.gz"),
("residual_filtered_3dT.nii.gz", "alff.nii.gz"),
("_parcellation_", ""),
("_bp_freqs_", "bp_"),
]
#####################
# ITERATORS
#####################
# PARCELLATION ITERATOR
parcellation_infosource = Node(util.IdentityInterface(fields=["parcellation"]), name="parcellation_infosource")
parcellation_infosource.iterables = ("parcellation", parcellations_dict.keys())
bp_filter_infosource = Node(util.IdentityInterface(fields=["bp_freqs"]), name="bp_filter_infosource")
bp_filter_infosource.iterables = ("bp_freqs", bp_freq_list)
selectfiles = Node(
nio.SelectFiles(
{
"parcellation_time_series": "{subject_id}/con_mat/parcellated_time_series/bp_{bp_freqs}/{parcellation}/parcellation_time_series.npy"
},
base_directory=preprocessed_data_dir,
),
name="selectfiles",
)
selectfiles.inputs.subject_id = subject_id
wf.connect(parcellation_infosource, "parcellation", selectfiles, "parcellation")
wf.connect(bp_filter_infosource, "bp_freqs", selectfiles, "bp_freqs")
fd_file = Node(
nio.SelectFiles({"fd_p": "{subject_id}/QC/FD_P_ts"}, base_directory=preprocessed_data_dir), name="fd_file"
)
fd_file.inputs.subject_id = subject_id
##############
## CON MATS
##############
##############
## extract ts
##############
get_good_trs = Node(
util.Function(
input_names=["fd_file", "fd_thresh"],
output_names=["good_trs", "fd_scrubbed_file"],
function=calc_metrics_utils.get_good_trs,
),
name="get_good_trs",
)
wf.connect(fd_file, "fd_p", get_good_trs, "fd_file")
get_good_trs.inputs.fd_thresh = fd_thresh
parcellated_ts_scrubbed = Node(
util.Function(
input_names=["parcellation_time_series_file", "good_trs"],
output_names=["parcellation_time_series_scrubbed"],
function=calc_metrics_utils.parcellation_time_series_scrubbing,
),
name="parcellated_ts_scrubbed",
)
wf.connect(selectfiles, "parcellation_time_series", parcellated_ts_scrubbed, "parcellation_time_series_file")
wf.connect(get_good_trs, "good_trs", parcellated_ts_scrubbed, "good_trs")
##############
## get conmat
##############
con_mat = Node(
util.Function(
input_names=["in_data", "extraction_method"],
output_names=["matrix", "matrix_file"],
function=calc_metrics_utils.calculate_connectivity_matrix,
),
name="con_mat",
)
con_mat.inputs.extraction_method = "correlation"
wf.connect(parcellated_ts_scrubbed, "parcellation_time_series_scrubbed", con_mat, "in_data")
##############
## ds
##############
wf.connect(get_good_trs, "fd_scrubbed_file", ds, "QC.@fd_scrubbed_file")
fd_str = ("%.1f" % fd_thresh).replace(".", "_")
wf.connect(con_mat, "matrix_file", ds, "con_mat.matrix_scrubbed_%s.@mat" % fd_str)
# wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
# wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
# wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == "CondorDAGMan":
wf.run(plugin=plugin_name, plugin_args={"initial_specs": "request_memory = 1500"})
if plugin_name == "MultiProc":
wf.run(plugin=plugin_name, plugin_args={"n_procs": use_n_procs})
reference_image=template,
terminal_output='file'),
name='apply2mean')
# Initiation of the ANTS normalization workflow
normflow = Workflow(name='normflow')
normflow.base_dir = opj(experiment_dir, working_dir)
# Connect up ANTS normalization components
normflow.connect([(antsreg, apply2con, [('composite_transform', 'transforms')]),
(antsreg, apply2mean, [('composite_transform',
'transforms')])
])
# 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('freesurfer', '{subject_id}', 'mri/brain.mgz')
func_file = opj(input_dir_1st, 'contrasts', '{subject_id}',
'_mriconvert*/*_out.nii.gz')
func_orig_file = opj(input_dir_1st, 'contrasts', '{subject_id}', '[ce]*.nii')
mean_file = opj(input_dir_1st, 'preprocout', '{subject_id}', 'mean*.nii')
templates = {'anat': anat_file,
'func': func_file,
'func_orig': func_orig_file,
'mean': mean_file,
}
# resample anatomy
resamp_anat = Node(fsl.FLIRT(apply_isoxfm=2.3),
name = 'resample_anat')
apply_ts.connect([(inputnode, resamp_anat, [('anat_head', 'in_file'),
('anat_head', 'reference'),
]),
])
# apply fmap fullwarp
apply_fmap = Node(fsl.ApplyWarp(interp='spline',
relwarp=True,
out_file='fmap_ts.nii.gz',
datatype='float'),
name='apply_fmap')
apply_ts.connect([(inputnode, apply_fmap, [('moco_ts', 'in_file'),
('fmap_fullwarp', 'field_file')]),
(resamp_anat, apply_fmap, [('out_file', 'ref_file')]),
(apply_fmap, outputnode, [('out_file', 'fmap_ts')])
])
apply_fmap.plugin_args={'initial_specs': 'request_memory = 8000'}
# apply topup fullwarp
apply_topup = Node(fsl.ApplyWarp(interp='spline',
relwarp=True,
out_file='topup_ts.nii.gz',
def make_func_subcortical_masks(name = 'func_subcortical'):
# Define Workflow
flow = Workflow(name=name)
inputnode = Node(util.IdentityInterface(fields=['func_first']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['left_nacc', 'left_amygdala', 'left_caudate', 'left_hipoocampus', 'left_pallidum', 'left_putamen', 'left_thalamus',
'right_nacc','right_amygdala', 'right_caudate', 'right_hipoocampus', 'right_pallidum', 'right_putamen','right_thalamus',
'midbrain', 'right_striatum', 'left_striatum']),
name = 'outputnode')
left_nacc = Node(interface=fsl.ExtractROI(), name = 'left_nacc')
left_nacc.inputs.t_min = 0
left_nacc.inputs.t_size = 1
left_nacc.inputs.roi_file = 'left_nacc.nii.gz'
left_amygdala = Node(interface=fsl.ExtractROI(), name = 'left_amygdala')
left_amygdala.inputs.t_min = 1
left_amygdala.inputs.t_size = 1
left_amygdala.inputs.roi_file = 'left_amygdala.nii.gz'
left_caudate = Node(interface=fsl.ExtractROI(), name = 'left_caudate')
left_caudate.inputs.t_min = 2
left_caudate.inputs.t_size = 1
left_caudate.inputs.roi_file = 'left_caudate.nii.gz'
left_hipoocampus = Node(interface=fsl.ExtractROI(), name = 'left_hipoocampus')
left_hipoocampus.inputs.t_min = 3
left_hipoocampus.inputs.t_size = 1
left_hipoocampus.inputs.roi_file = 'left_hipoocampus.nii.gz'
left_pallidum = Node(interface=fsl.ExtractROI(), name = 'left_pallidum')
left_pallidum.inputs.t_min = 4
left_pallidum.inputs.t_size = 1
left_pallidum.inputs.roi_file = 'left_pallidum.nii.gz'
left_putamen = Node(interface=fsl.ExtractROI(), name = 'left_putamen')
left_putamen.inputs.t_min = 5
left_putamen.inputs.t_size = 1
left_putamen.inputs.roi_file = 'left_putamen.nii.gz'
left_thalamus = Node(interface=fsl.ExtractROI(), name = 'left_thalamus')
left_thalamus.inputs.t_min = 6
left_thalamus.inputs.t_size = 1
left_thalamus.inputs.roi_file = 'left_thalamus.nii.gz'
###############
right_nacc = Node(interface=fsl.ExtractROI(), name = 'right_nacc')
right_nacc.inputs.t_min = 7
right_nacc.inputs.t_size = 1
right_nacc.inputs.roi_file = 'right_nacc.nii.gz'
right_amygdala = Node(interface=fsl.ExtractROI(), name = 'right_amygdala')
right_amygdala.inputs.t_min = 8
right_amygdala.inputs.t_size = 1
right_amygdala.inputs.roi_file = 'right_amygdala.nii.gz'
right_caudate = Node(interface=fsl.ExtractROI(), name = 'right_caudate')
right_caudate.inputs.t_min = 9
right_caudate.inputs.t_size = 1
right_caudate.inputs.roi_file = 'right_caudate.nii.gz'
right_hipoocampus = Node(interface=fsl.ExtractROI(), name = 'right_hipoocampus')
right_hipoocampus.inputs.t_min = 10
right_hipoocampus.inputs.t_size = 1
right_hipoocampus.inputs.roi_file = 'right_hipoocampus.nii.gz'
right_pallidum = Node(interface=fsl.ExtractROI(), name = 'right_pallidum')
right_pallidum.inputs.t_min = 11
right_pallidum.inputs.t_size = 1
right_pallidum.inputs.roi_file = 'right_pallidum.nii.gz'
right_putamen = Node(interface=fsl.ExtractROI(), name = 'right_putamen')
right_putamen.inputs.t_min = 12
right_putamen.inputs.t_size = 1
right_putamen.inputs.roi_file = 'right_putamen.nii.gz'
right_thalamus = Node(interface=fsl.ExtractROI(), name = 'right_thalamus')
right_thalamus.inputs.t_min = 13
right_thalamus.inputs.t_size = 1
right_thalamus.inputs.roi_file = 'right_thalamus.nii.gz'
midbrain = Node(interface=fsl.ExtractROI(), name = 'midbrain')
midbrain.inputs.t_min = 14
midbrain.inputs.t_size = 1
midbrain.inputs.roi_file = 'midbrain.nii.gz'
flow.connect( inputnode , 'func_first' , left_nacc, 'in_file' )
flow.connect( inputnode , 'func_first' , left_amygdala, 'in_file' )
flow.connect( inputnode , 'func_first' , left_caudate, 'in_file' )
flow.connect( inputnode , 'func_first' , left_hipoocampus,'in_file' )
flow.connect( inputnode , 'func_first' , left_pallidum, 'in_file' )
flow.connect( inputnode , 'func_first' , left_putamen, 'in_file' )
flow.connect( inputnode , 'func_first' , left_thalamus, 'in_file' )
flow.connect( inputnode , 'func_first' , right_nacc, 'in_file' )
flow.connect( inputnode , 'func_first' , right_amygdala, 'in_file' )
flow.connect( inputnode , 'func_first' , right_caudate, 'in_file' )
flow.connect( inputnode , 'func_first' , right_hipoocampus,'in_file' )
flow.connect( inputnode , 'func_first' , right_pallidum, 'in_file' )
flow.connect( inputnode , 'func_first' , right_putamen, 'in_file' )
flow.connect( inputnode , 'func_first' , right_thalamus, 'in_file' )
flow.connect( inputnode , 'func_first' , midbrain, 'in_file' )
flow.connect( left_nacc , 'roi_file' ,outputnode , 'left_nacc' )
flow.connect( left_amygdala , 'roi_file' ,outputnode , 'left_amygdala' )
flow.connect( left_caudate , 'roi_file' ,outputnode , 'left_caudate' )
flow.connect( left_hipoocampus , 'roi_file' ,outputnode , 'left_hipoocampus')
flow.connect( left_pallidum , 'roi_file' ,outputnode , 'left_pallidum')
flow.connect( left_putamen , 'roi_file' ,outputnode , 'left_putamen' )
flow.connect( left_thalamus , 'roi_file' ,outputnode , 'left_thalamus' )
flow.connect( right_nacc , 'roi_file' ,outputnode , 'right_nacc' )
flow.connect( right_amygdala , 'roi_file' ,outputnode , 'right_amygdala' )
flow.connect( right_caudate , 'roi_file' ,outputnode , 'right_caudate' )
flow.connect( right_hipoocampus, 'roi_file' ,outputnode , 'right_hipoocampus')
flow.connect( right_pallidum , 'roi_file' ,outputnode , 'right_pallidum')
flow.connect( right_putamen , 'roi_file' ,outputnode , 'right_putamen' )
flow.connect( right_thalamus , 'roi_file' ,outputnode , 'right_thalamus' )
flow.connect( midbrain , 'roi_file' ,outputnode , 'midbrain' )
# add images together
right_striatum = Node(interface=fsl.MultiImageMaths(), name = 'right_striatum')
right_striatum.inputs.op_string = '-add %s -add %s -bin'
right_striatum.out_file = 'right_striatum.nii.gz'
list_R_str = Node(util.Function(input_names = ['file_1', 'file_2'],
output_names= ['list'],
function = return_list),
name = 'list_str_r')
flow.connect( right_pallidum , 'roi_file' ,list_R_str , 'file_1' )
flow.connect( right_putamen , 'roi_file' ,list_R_str , 'file_2' )
flow.connect( right_caudate , 'roi_file' ,right_striatum , 'in_file' )
flow.connect( list_R_str , 'list' ,right_striatum , 'operand_files' )
flow.connect( right_striatum , 'out_file' ,outputnode , 'right_striatum' )
left_striatum = Node(interface=fsl.MultiImageMaths(), name = 'left_striatum')
left_striatum.inputs.op_string = '-add %s -add %s'
left_striatum.out_file = 'left_striatum.nii.gz'
list_L_str = list_R_str.clone('list_str_l')
flow.connect( left_pallidum , 'roi_file' ,list_L_str , 'file_1' )
flow.connect( left_putamen , 'roi_file' ,list_L_str , 'file_2' )
flow.connect( left_caudate , 'roi_file' ,left_striatum , 'in_file' )
flow.connect( list_L_str , 'list' ,left_striatum , 'operand_files' )
flow.connect( left_striatum , 'out_file' ,outputnode , 'left_striatum' )
return flow
###################################################################################################################################
# # artefact detection
# ad = Node(ra.ArtifactDetect(save_plot=False,
# norm_threshold=1,
# zintensity_threshold=3,
# mask_type='spm_global',
# use_differences = [True, False],
# parameter_source='FSL'),
# name='artefactdetect')
#
# #wf.connect(getmask, 'outputspec.mask',ad, 'mask_file') mask_type='file'
###################################################################################################################################
# tsnr (input is timeseries from inputnode)
tsnr = Node(TSNR(regress_poly=2), name="tsnr")
tsnr.plugin_args = {"initial_specs": "request_memory = 30000"}
###################################################################################################################################
# create noise mask file
getthresh = Node(interface=fsl.ImageStats(op_string="-p 98"), name="getthreshold")
getthresh.plugin_args = {"initial_specs": "request_memory = 30000"}
threshold_stddev = Node(fsl.Threshold(), name="threshold")
threshold_stddev.plugin_args = {"initial_specs": "request_memory = 30000"}
preproc.connect(tsnr, "stddev_file", threshold_stddev, "in_file")
preproc.connect(tsnr, "stddev_file", getthresh, "in_file")
preproc.connect(getthresh, "out_stat", threshold_stddev, "thresh")
preproc.connect(threshold_stddev, "out_file", outputnode, "noise_mask_file")
def create_registration_pipeline(working_dir, freesurfer_dir, ds_dir, name='registration'):
"""
find transformations between struct, funct, and MNI
"""
# initiate workflow
reg_wf = Workflow(name=name)
reg_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting', 'rsfMRI_preprocessing')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
freesurfer.FSCommand.set_default_subjects_dir(freesurfer_dir)
# inputnode
inputnode = Node(util.IdentityInterface(fields=['initial_mean_epi_moco',
't1w',
't1w_brain',
'subject_id',
'wm_mask_4_bbr',
'struct_brain_mask']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['struct_2_MNI_warp',
'epi_2_struct_mat',
'struct_2_epi_mat',
'epi_2_MNI_warp',
'MNI_2_epi_warp',
'fs_2_struct_mat',
'mean_epi_structSpace',
'mean_epi_MNIspace',
'struct_MNIspace']),
name='outputnode')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
##########################################
# TOC REGISTRATION MATS AND WARPS
##########################################
# I. STRUCT -> MNI
## 1. STRUCT -> MNI with FLIRT
## 2. CALC. WARP STRUCT -> MNI with FNIRT
# II.EPI -> STRUCT
## 3. calc EPI->STRUCT initial registration
## 4. run EPI->STRUCT via bbr
## 5. INVERT to get: STRUCT -> EPI
# III. COMBINE I. & II.: EPI -> MNI
## 6. COMBINE MATS: EPI -> MNI
## 7. MNI -> EPI
##########################################
# CREATE REGISTRATION MATS AND WARPS
##########################################
# I. STRUCT -> MNI
##########################################
# 1. REGISTER STRUCT -> MNI with FLIRT
struct_2_MNI_mat = Node(fsl.FLIRT(dof=12), name='struct_2_MNI_mat')
struct_2_MNI_mat.inputs.reference = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
reg_wf.connect(inputnode, 't1w_brain', struct_2_MNI_mat, 'in_file')
reg_wf.connect(struct_2_MNI_mat, 'out_matrix_file', outputnode, 'struct_2_MNI_mat_flirt')
# 2. CALC. WARP STRUCT -> MNI with FNIRT
# cf. wrt. 2mm
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=FSL&P=R86108&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
struct_2_MNI_warp = Node(fsl.FNIRT(), name='struct_2_MNI_warp')
struct_2_MNI_warp.inputs.config_file = 'T1_2_MNI152_2mm'
struct_2_MNI_warp.inputs.ref_file = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
struct_2_MNI_warp.inputs.field_file = 'struct_2_MNI_warp.nii.gz'
struct_2_MNI_warp.plugin_args = {'submit_specs': 'request_memory = 4000'}
reg_wf.connect(inputnode, 't1w', struct_2_MNI_warp, 'in_file')
reg_wf.connect(struct_2_MNI_mat, 'out_matrix_file', struct_2_MNI_warp, 'affine_file')
reg_wf.connect(struct_2_MNI_warp, 'field_file', ds, 'registration.struct_2_MNI_warp')
reg_wf.connect(struct_2_MNI_warp, 'field_file', outputnode, 'struct_2_MNI_warp')
reg_wf.connect(struct_2_MNI_warp, 'warped_file', outputnode, 'struct_MNIspace')
reg_wf.connect(struct_2_MNI_warp, 'warped_file', ds, 'registration.struct_MNIspace')
# II.EPI -> STRUCT (via bbr)
##########################################
# 3. calc EPI->STRUCT initial registration with flirt dof=6 and corratio
epi_2_struct_flirt6_mat = Node(fsl.FLIRT(dof=6, cost='corratio'), name='epi_2_struct_flirt6_mat')
epi_2_struct_flirt6_mat.inputs.out_file = 'epi_structSpace_flirt6.nii.gz'
reg_wf.connect(inputnode, 't1w_brain', epi_2_struct_flirt6_mat, 'reference')
reg_wf.connect(inputnode, 'initial_mean_epi_moco', epi_2_struct_flirt6_mat, 'in_file')
# 4. run EPI->STRUCT via bbr
bbr_shedule = os.path.join(os.getenv('FSLDIR'), 'etc/flirtsch/bbr.sch')
epi_2_struct_bbr_mat = Node(interface=fsl.FLIRT(dof=6, cost='bbr'), name='epi_2_struct_bbr_mat')
epi_2_struct_bbr_mat.inputs.schedule = bbr_shedule
epi_2_struct_bbr_mat.inputs.out_file = 'epi_structSpace.nii.gz'
reg_wf.connect(inputnode, 'initial_mean_epi_moco', epi_2_struct_bbr_mat, 'in_file')
reg_wf.connect(inputnode, 't1w_brain', epi_2_struct_bbr_mat, 'reference')
reg_wf.connect(epi_2_struct_flirt6_mat, 'out_matrix_file', epi_2_struct_bbr_mat, 'in_matrix_file')
reg_wf.connect(inputnode, 'wm_mask_4_bbr', epi_2_struct_bbr_mat, 'wm_seg')
reg_wf.connect(epi_2_struct_bbr_mat, 'out_matrix_file', ds, 'registration.epi_2_struct_mat')
reg_wf.connect(epi_2_struct_bbr_mat, 'out_file', outputnode, 'mean_epi_structSpace')
# 5. INVERT to get: STRUCT -> EPI
struct_2_epi_mat = Node(fsl.ConvertXFM(invert_xfm=True), name='struct_2_epi_mat')
reg_wf.connect(epi_2_struct_bbr_mat, 'out_matrix_file', struct_2_epi_mat, 'in_file')
reg_wf.connect(struct_2_epi_mat, 'out_file', outputnode, 'struct_2_epi_mat')
# III. COMBINE I. & II.: EPI -> MNI
##########################################
# 6. COMBINE MATS: EPI -> MNI
epi_2_MNI_warp = Node(fsl.ConvertWarp(), name='epi_2_MNI_warp')
epi_2_MNI_warp.inputs.reference = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
reg_wf.connect(epi_2_struct_bbr_mat, 'out_matrix_file', epi_2_MNI_warp, 'premat') # epi2struct
reg_wf.connect(struct_2_MNI_warp, 'field_file', epi_2_MNI_warp, 'warp1') # struct2mni
reg_wf.connect(epi_2_MNI_warp, 'out_file', outputnode, 'epi_2_MNI_warp')
reg_wf.connect(epi_2_MNI_warp, 'out_file', ds, 'registration.epi_2_MNI_warp')
# output: out_file
# 7. MNI -> EPI
MNI_2_epi_warp = Node(fsl.InvWarp(), name='MNI_2_epi_warp')
MNI_2_epi_warp.inputs.reference = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
reg_wf.connect(epi_2_MNI_warp, 'out_file', MNI_2_epi_warp, 'warp')
reg_wf.connect(inputnode, 'initial_mean_epi_moco', MNI_2_epi_warp, 'reference')
reg_wf.connect(MNI_2_epi_warp, 'inverse_warp', outputnode, 'MNI_2_epi_warp')
# output: inverse_warp
##########################################
# TRANSFORM VOLUMES
##########################################
# CREATE STRUCT IN EPI SPACE FOR DEBUGGING
struct_epiSpace = Node(fsl.ApplyXfm(), name='struct_epiSpace')
struct_epiSpace.inputs.out_file = 'struct_brain_epiSpace.nii.gz'
reg_wf.connect(inputnode, 't1w_brain', struct_epiSpace, 'in_file')
reg_wf.connect(inputnode, 'initial_mean_epi_moco', struct_epiSpace, 'reference')
reg_wf.connect(struct_2_epi_mat, 'out_file', struct_epiSpace, 'in_matrix_file')
reg_wf.connect(struct_epiSpace, 'out_file', ds, 'QC.struct_brain_epiSpace')
# CREATE EPI IN MNI SPACE
mean_epi_MNIspace = Node(fsl.ApplyWarp(), name='mean_epi_MNIspace')
mean_epi_MNIspace.inputs.ref_file = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
mean_epi_MNIspace.inputs.out_file = 'mean_epi_MNIspace.nii.gz'
reg_wf.connect(inputnode, 'initial_mean_epi_moco', mean_epi_MNIspace, 'in_file')
reg_wf.connect(epi_2_MNI_warp, 'out_file', mean_epi_MNIspace, 'field_file')
reg_wf.connect(mean_epi_MNIspace, 'out_file', ds, 'registration.mean_epi_MNIspace')
reg_wf.connect(mean_epi_MNIspace, 'out_file', outputnode, 'mean_epi_MNIspace')
# CREATE MNI IN EPI SPACE FOR DEBUGGING
MNI_epiSpace = Node(fsl.ApplyWarp(), name='MNI_epiSpace')
MNI_epiSpace.inputs.in_file = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
MNI_epiSpace.inputs.out_file = 'MNI_epiSpace.nii.gz'
reg_wf.connect(inputnode, 'initial_mean_epi_moco', MNI_epiSpace, 'ref_file')
reg_wf.connect(MNI_2_epi_warp, 'inverse_warp', MNI_epiSpace, 'field_file')
reg_wf.connect(MNI_epiSpace, 'out_file', ds, 'registration.MNI_epiSpace')
reg_wf.write_graph(dotfilename=reg_wf.name, graph2use='flat', format='pdf')
return reg_wf
def learning_predict_data_2samp_wf(working_dir,
ds_dir,
in_data_name_list,
subjects_selection_crit_dict,
subjects_selection_crit_names_list,
aggregated_subjects_dir,
target_list,
use_n_procs,
plugin_name,
confound_regression=[False, True],
run_cv=False,
n_jobs_cv=1,
run_tuning=False,
run_2sample_training=False,
aggregated_subjects_dir_nki=None,
subjects_selection_crit_dict_nki=None,
subjects_selection_crit_name_nki=None,
reverse_split=False,
random_state_nki=666,
run_learning_curve=False,
life_test_size=0.5):
import os
from nipype import config
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
from itertools import chain
from learning_utils import aggregate_multimodal_metrics_fct, run_prediction_split_fct, \
backproject_and_split_weights_fct, select_subjects_fct, select_multimodal_X_fct, learning_curve_plot
import pandas as pd
###############################################################################################################
# GENERAL SETTINGS
wf = Workflow(name='learning_predict_data_2samp_wf')
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(logging=dict(workflow_level='DEBUG'),
execution={'stop_on_first_crash': False,
'remove_unnecessary_outputs': False,
'job_finished_timeout': 120})
config.update_config(nipype_cfg)
wf.config['execution']['crashdump_dir'] = os.path.join(working_dir, 'crash')
ds = Node(nio.DataSink(), name='ds')
ds.inputs.base_directory = os.path.join(ds_dir, 'group_learning_prepare_data')
ds.inputs.regexp_substitutions = [
# ('subject_id_', ''),
('_parcellation_', ''),
('_bp_freqs_', 'bp_'),
('_extraction_method_', ''),
('_subject_id_[A0-9]*/', '')
]
ds_pdf = Node(nio.DataSink(), name='ds_pdf')
ds_pdf.inputs.base_directory = os.path.join(ds_dir, 'pdfs')
ds_pdf.inputs.parameterization = False
###############################################################################################################
# ensure in_data_name_list is list of lists
in_data_name_list = [i if type(i) == list else [i] for i in in_data_name_list]
in_data_name_list_unique = list(set(chain.from_iterable(in_data_name_list)))
###############################################################################################################
# SET ITERATORS
in_data_name_infosource = Node(util.IdentityInterface(fields=['in_data_name']), name='in_data_name_infosource')
in_data_name_infosource.iterables = ('in_data_name', in_data_name_list_unique)
multimodal_in_data_name_infosource = Node(util.IdentityInterface(fields=['multimodal_in_data_name']),
name='multimodal_in_data_name_infosource')
multimodal_in_data_name_infosource.iterables = ('multimodal_in_data_name', in_data_name_list)
subject_selection_infosource = Node(util.IdentityInterface(fields=['selection_criterium']),
name='subject_selection_infosource')
subject_selection_infosource.iterables = ('selection_criterium', subjects_selection_crit_names_list)
target_infosource = Node(util.IdentityInterface(fields=['target_name']), name='target_infosource')
target_infosource.iterables = ('target_name', target_list)
###############################################################################################################
# COMPILE LIFE DATA
###############################################################################################################
###############################################################################################################
# GET INFO AND SELECT FILES
df_all_subjects_pickle_file = os.path.join(aggregated_subjects_dir, 'df_all_subjects_pickle_file/df_all.pkl')
df = pd.read_pickle(df_all_subjects_pickle_file)
# build lookup dict for unimodal data
X_file_template = 'X_file/_in_data_name_{in_data_name}/vectorized_aggregated_data.npy'
info_file_template = 'unimodal_backprojection_info_file/_in_data_name_{in_data_name}/unimodal_backprojection_info.pkl'
unimodal_lookup_dict = {}
for k in in_data_name_list_unique:
unimodal_lookup_dict[k] = {'X_file': os.path.join(aggregated_subjects_dir, X_file_template.format(
in_data_name=k)),
'unimodal_backprojection_info_file': os.path.join(aggregated_subjects_dir,
info_file_template.format(
in_data_name=k))
}
###############################################################################################################
# AGGREGATE MULTIMODAL METRICS
# stack single modality arrays horizontally
aggregate_multimodal_metrics = Node(util.Function(input_names=['multimodal_list', 'unimodal_lookup_dict'],
output_names=['X_multimodal_file',
'multimodal_backprojection_info',
'multimodal_name'],
function=aggregate_multimodal_metrics_fct),
name='aggregate_multimodal_metrics')
wf.connect(multimodal_in_data_name_infosource, 'multimodal_in_data_name', aggregate_multimodal_metrics,
'multimodal_list')
aggregate_multimodal_metrics.inputs.unimodal_lookup_dict = unimodal_lookup_dict
###############################################################################################################
# GET INDEXER FOR SUBJECTS OF INTEREST (as defined by selection criterium)
select_subjects = Node(util.Function(input_names=['df_all_subjects_pickle_file',
'subjects_selection_crit_dict',
'selection_criterium'],
output_names=['df_use_file',
'df_use_pickle_file',
'subjects_selection_index'],
function=select_subjects_fct),
name='select_subjects')
select_subjects.inputs.df_all_subjects_pickle_file = df_all_subjects_pickle_file
select_subjects.inputs.subjects_selection_crit_dict = subjects_selection_crit_dict
wf.connect(subject_selection_infosource, 'selection_criterium', select_subjects, 'selection_criterium')
###############################################################################################################
# SELECT MULITMODAL X
# select subjects (rows) from multimodal X according indexer
select_multimodal_X = Node(util.Function(input_names=['X_multimodal_file', 'subjects_selection_index',
'selection_criterium'],
output_names=['X_multimodal_selected_file'],
function=select_multimodal_X_fct),
name='select_multimodal_X')
wf.connect(aggregate_multimodal_metrics, 'X_multimodal_file', select_multimodal_X, 'X_multimodal_file')
wf.connect(select_subjects, 'subjects_selection_index', select_multimodal_X, 'subjects_selection_index')
###############################################################################################################
# COMPILE NKI DATA
###############################################################################################################
if run_2sample_training:
###############################################################################################################
# GET INFO AND SELECT FILES
df_all_subjects_pickle_file_nki = os.path.join(aggregated_subjects_dir_nki,
'df_all_subjects_pickle_file/df_all.pkl')
df_nki = pd.read_pickle(df_all_subjects_pickle_file_nki)
# build lookup dict for unimodal data
X_file_template = 'X_file/_in_data_name_{in_data_name}/vectorized_aggregated_data.npy'
info_file_template = 'unimodal_backprojection_info_file/_in_data_name_{in_data_name}/unimodal_backprojection_info.pkl'
unimodal_lookup_dict_nki = {}
for k in in_data_name_list_unique:
unimodal_lookup_dict_nki[k] = {'X_file': os.path.join(aggregated_subjects_dir_nki, X_file_template.format(
in_data_name=k)),
'unimodal_backprojection_info_file': os.path.join(
aggregated_subjects_dir_nki,
info_file_template.format(
in_data_name=k))
}
###############################################################################################################
# AGGREGATE MULTIMODAL METRICS
# stack single modality arrays horizontally
aggregate_multimodal_metrics_nki = Node(util.Function(input_names=['multimodal_list', 'unimodal_lookup_dict'],
output_names=['X_multimodal_file',
'multimodal_backprojection_info',
'multimodal_name'],
function=aggregate_multimodal_metrics_fct),
name='aggregate_multimodal_metrics_nki')
wf.connect(multimodal_in_data_name_infosource, 'multimodal_in_data_name', aggregate_multimodal_metrics_nki,
'multimodal_list')
aggregate_multimodal_metrics_nki.inputs.unimodal_lookup_dict = unimodal_lookup_dict_nki
###############################################################################################################
# GET INDEXER FOR SUBJECTS OF INTEREST (as defined by selection criterium)
select_subjects_nki = Node(util.Function(input_names=['df_all_subjects_pickle_file',
'subjects_selection_crit_dict',
'selection_criterium'],
output_names=['df_use_file',
'df_use_pickle_file',
'subjects_selection_index'],
function=select_subjects_fct),
name='select_subjects_nki')
select_subjects_nki.inputs.df_all_subjects_pickle_file = df_all_subjects_pickle_file_nki
select_subjects_nki.inputs.subjects_selection_crit_dict = subjects_selection_crit_dict_nki
select_subjects_nki.inputs.selection_criterium = subjects_selection_crit_name_nki
###############################################################################################################
# SELECT MULITMODAL X
# select subjects (rows) from multimodal X according indexer
select_multimodal_X_nki = Node(util.Function(input_names=['X_multimodal_file', 'subjects_selection_index',
'selection_criterium'],
output_names=['X_multimodal_selected_file'],
function=select_multimodal_X_fct),
name='select_multimodal_X_nki')
wf.connect(aggregate_multimodal_metrics_nki, 'X_multimodal_file', select_multimodal_X_nki, 'X_multimodal_file')
wf.connect(select_subjects_nki, 'subjects_selection_index', select_multimodal_X_nki, 'subjects_selection_index')
###############################################################################################################
# RUN PREDICTION
#
prediction_node_dict = {}
backprojection_node_dict = {}
prediction_split = Node(util.Function(input_names=['X_file',
'target_name',
'selection_criterium',
'df_file',
'data_str',
'regress_confounds',
'run_cv',
'n_jobs_cv',
'run_tuning',
'X_file_nki',
'df_file_nki',
'reverse_split',
'random_state_nki',
'run_learning_curve',
'life_test_size'],
output_names=['scatter_file',
'brain_age_scatter_file',
'df_life_out_file',
'df_nki_out_file',
'df_big_out_file',
'model_out_file',
'df_res_out_file',
'tuning_curve_file',
'scatter_file_cv',
'learning_curve_plot_file',
'learning_curve_df_file'],
function=run_prediction_split_fct),
name='prediction_split')
backproject_and_split_weights = Node(util.Function(input_names=['trained_model_file',
'multimodal_backprojection_info',
'data_str',
'target_name'],
output_names=['out_file_list',
'out_file_render_list'],
function=backproject_and_split_weights_fct),
name='backproject_and_split_weights')
i = 0
for reg in confound_regression:
the_out_node_str = 'single_source_model_reg_%s_' % (reg)
prediction_node_dict[i] = prediction_split.clone(the_out_node_str)
the_in_node = prediction_node_dict[i]
the_in_node.inputs.regress_confounds = reg
the_in_node.inputs.run_cv = run_cv
the_in_node.inputs.n_jobs_cv = n_jobs_cv
the_in_node.inputs.run_tuning = run_tuning
the_in_node.inputs.reverse_split = reverse_split
the_in_node.inputs.random_state_nki = random_state_nki
the_in_node.inputs.run_learning_curve = run_learning_curve
the_in_node.inputs.life_test_size = life_test_size
wf.connect(select_multimodal_X, 'X_multimodal_selected_file', the_in_node, 'X_file')
wf.connect(target_infosource, 'target_name', the_in_node, 'target_name')
wf.connect(subject_selection_infosource, 'selection_criterium', the_in_node, 'selection_criterium')
wf.connect(select_subjects, 'df_use_pickle_file', the_in_node, 'df_file')
wf.connect(aggregate_multimodal_metrics, 'multimodal_name', the_in_node, 'data_str')
wf.connect(the_in_node, 'model_out_file', ds, the_out_node_str + 'trained_model')
wf.connect(the_in_node, 'scatter_file', ds_pdf, the_out_node_str + 'scatter')
wf.connect(the_in_node, 'brain_age_scatter_file', ds_pdf, the_out_node_str + 'brain_age_scatter')
wf.connect(the_in_node, 'df_life_out_file', ds_pdf, the_out_node_str + 'predicted_life')
wf.connect(the_in_node, 'df_nki_out_file', ds_pdf, the_out_node_str + 'predicted_nki')
wf.connect(the_in_node, 'df_big_out_file', ds_pdf, the_out_node_str + 'predicted')
wf.connect(the_in_node, 'df_res_out_file', ds_pdf, the_out_node_str + 'results_error')
wf.connect(the_in_node, 'tuning_curve_file', ds_pdf, the_out_node_str + 'tuning_curve')
wf.connect(the_in_node, 'scatter_file_cv', ds_pdf, the_out_node_str + 'scatter_cv')
wf.connect(the_in_node, 'learning_curve_plot_file', ds_pdf, the_out_node_str + 'learning_curve_plot_file.@plot')
wf.connect(the_in_node, 'learning_curve_df_file', ds_pdf, the_out_node_str + 'learning_curve_df_file.@df')
# NKI
if run_2sample_training:
wf.connect(select_multimodal_X_nki, 'X_multimodal_selected_file', the_in_node, 'X_file_nki')
wf.connect(select_subjects_nki, 'df_use_pickle_file', the_in_node, 'df_file_nki')
else:
the_in_node.inputs.df_file_nki = None
the_in_node.inputs.X_file_nki = None
# BACKPROJECT PREDICTION WEIGHTS
# map weights back to single modality original format (e.g., nifti or matrix)
the_out_node_str = 'backprojection_single_source_model_reg_%s_' % (reg)
backprojection_node_dict[i] = backproject_and_split_weights.clone(the_out_node_str)
the_from_node = prediction_node_dict[i]
the_in_node = backprojection_node_dict[i]
wf.connect(the_from_node, 'model_out_file', the_in_node, 'trained_model_file')
wf.connect(aggregate_multimodal_metrics, 'multimodal_backprojection_info', the_in_node,
'multimodal_backprojection_info')
wf.connect(aggregate_multimodal_metrics, 'multimodal_name', the_in_node, 'data_str')
wf.connect(target_infosource, 'target_name', the_in_node, 'target_name')
wf.connect(the_in_node, 'out_file_list', ds_pdf, the_out_node_str + '.@weights')
wf.connect(the_in_node, 'out_file_render_list', ds_pdf, the_out_node_str + 'renders.@renders')
i += 1
###############################################################################################################
# # RUN WF
wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == 'CondorDAGMan':
wf.run(plugin=plugin_name)
if plugin_name == 'MultiProc':
wf.run(plugin=plugin_name, plugin_args={'n_procs': use_n_procs})
def learning_prepare_data_wf(working_dir,
ds_dir,
template_lookup_dict,
behav_file,
qc_file,
in_data_name_list,
data_lookup_dict,
use_n_procs,
plugin_name):
import os
from nipype import config
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
from prepare_data_utils import vectorize_and_aggregate
from itertools import chain
# ensure in_data_name_list is list of lists
in_data_name_list = [i if type(i) == list else [i] for i in in_data_name_list]
in_data_name_list_unique = list(set(chain.from_iterable(in_data_name_list)))
#####################################
# GENERAL SETTINGS
#####################################
wf = Workflow(name='learning_prepare_data_wf')
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(logging=dict(workflow_level='DEBUG'), execution={'stop_on_first_crash': False,
'remove_unnecessary_outputs': False,
'job_finished_timeout': 120,
'hash_method': 'timestamp'})
config.update_config(nipype_cfg)
wf.config['execution']['crashdump_dir'] = os.path.join(working_dir, 'crash')
ds = Node(nio.DataSink(), name='ds')
ds.inputs.base_directory = os.path.join(ds_dir, 'group_learning_prepare_data')
ds.inputs.regexp_substitutions = [
# ('subject_id_', ''),
('_parcellation_', ''),
('_bp_freqs_', 'bp_'),
('_extraction_method_', ''),
('_subject_id_[A0-9]*/', '')
]
ds_X = Node(nio.DataSink(), name='ds_X')
ds_X.inputs.base_directory = os.path.join(ds_dir, 'vectorized_aggregated_data')
ds_pdf = Node(nio.DataSink(), name='ds_pdf')
ds_pdf.inputs.base_directory = os.path.join(ds_dir, 'pdfs')
ds_pdf.inputs.parameterization = False
#####################################
# SET ITERATORS
#####################################
# SUBJECTS ITERATOR
in_data_name_infosource = Node(util.IdentityInterface(fields=['in_data_name']), name='in_data_name_infosource')
in_data_name_infosource.iterables = ('in_data_name', in_data_name_list_unique)
mulitmodal_in_data_name_infosource = Node(util.IdentityInterface(fields=['multimodal_in_data_name']),
name='mulitmodal_in_data_name_infosource')
mulitmodal_in_data_name_infosource.iterables = ('multimodal_in_data_name', in_data_name_list)
###############################################################################################################
# GET SUBJECTS INFO
# create subjects list based on selection criteria
def create_df_fct(behav_file, qc_file):
import pandas as pd
import os
df = pd.read_pickle(behav_file)
qc = pd.read_pickle(qc_file)
df_all = qc.join(df, how='inner')
assert df_all.index.is_unique, 'duplicates in df index. fix before cont.'
df_all_subjects_pickle_file = os.path.abspath('df_all.pkl')
df_all.to_pickle(df_all_subjects_pickle_file)
full_subjects_list = df_all.index.values
return df_all_subjects_pickle_file, full_subjects_list
create_df = Node(util.Function(input_names=['behav_file', 'qc_file'],
output_names=['df_all_subjects_pickle_file', 'full_subjects_list'],
function=create_df_fct),
name='create_df')
create_df.inputs.behav_file = behav_file
create_df.inputs.qc_file = qc_file
###############################################################################################################
# CREAE FILE LIST
# of files that will be aggregted
def create_file_list_fct(subjects_list, in_data_name, data_lookup_dict, template_lookup_dict):
file_list = []
for s in subjects_list:
file_list.append(data_lookup_dict[in_data_name]['path_str'].format(subject_id=s))
if 'matrix_name' in data_lookup_dict[in_data_name].keys():
matrix_name = data_lookup_dict[in_data_name]['matrix_name']
else:
matrix_name = None
if 'parcellation_path' in data_lookup_dict[in_data_name].keys():
parcellation_path = data_lookup_dict[in_data_name]['parcellation_path']
else:
parcellation_path = None
if 'fwhm' in data_lookup_dict[in_data_name].keys():
fwhm = data_lookup_dict[in_data_name]['fwhm']
if fwhm == 0:
fwhm = None
else:
fwhm = None
if 'mask_name' in data_lookup_dict[in_data_name].keys():
mask_path = template_lookup_dict[data_lookup_dict[in_data_name]['mask_name']]
else:
mask_path = None
if 'use_diagonal' in data_lookup_dict[in_data_name].keys():
use_diagonal = data_lookup_dict[in_data_name]['use_diagonal']
else:
use_diagonal = False
if 'use_fishers_z' in data_lookup_dict[in_data_name].keys():
use_fishers_z = data_lookup_dict[in_data_name]['use_fishers_z']
else:
use_fishers_z = False
if 'df_col_names' in data_lookup_dict[in_data_name].keys():
df_col_names = data_lookup_dict[in_data_name]['df_col_names']
else:
df_col_names = None
return file_list, matrix_name, parcellation_path, fwhm, mask_path, use_diagonal, use_fishers_z, df_col_names
create_file_list = Node(util.Function(input_names=['subjects_list',
'in_data_name',
'data_lookup_dict',
'template_lookup_dict',
],
output_names=['file_list',
'matrix_name',
'parcellation_path',
'fwhm',
'mask_path',
'use_diagonal',
'use_fishers_z',
'df_col_names'],
function=create_file_list_fct),
name='create_file_list')
wf.connect(create_df, 'full_subjects_list', create_file_list, 'subjects_list')
wf.connect(in_data_name_infosource, 'in_data_name', create_file_list, 'in_data_name')
create_file_list.inputs.data_lookup_dict = data_lookup_dict
create_file_list.inputs.template_lookup_dict = template_lookup_dict
###############################################################################################################
# VECTORIZE AND AGGREGATE SUBJECTS
# stack single subject np arrays vertically
vectorize_aggregate_subjects = Node(util.Function(input_names=['in_data_file_list',
'mask_file',
'matrix_name',
'parcellation_path',
'fwhm',
'use_diagonal',
'use_fishers_z',
'df_file',
'df_col_names'],
output_names=['vectorized_aggregated_file',
'unimodal_backprojection_info_file'],
function=vectorize_and_aggregate),
name='vectorize_aggregate_subjects')
wf.connect(create_file_list, 'file_list', vectorize_aggregate_subjects, 'in_data_file_list')
wf.connect(create_file_list, 'mask_path', vectorize_aggregate_subjects, 'mask_file')
wf.connect(create_file_list, 'matrix_name', vectorize_aggregate_subjects, 'matrix_name')
wf.connect(create_file_list, 'parcellation_path', vectorize_aggregate_subjects, 'parcellation_path')
wf.connect(create_file_list, 'fwhm', vectorize_aggregate_subjects, 'fwhm')
wf.connect(create_file_list, 'use_diagonal', vectorize_aggregate_subjects, 'use_diagonal')
wf.connect(create_file_list, 'use_fishers_z', vectorize_aggregate_subjects, 'use_fishers_z')
wf.connect(create_df, 'df_all_subjects_pickle_file', vectorize_aggregate_subjects, 'df_file')
wf.connect(create_file_list, 'df_col_names', vectorize_aggregate_subjects, 'df_col_names')
wf.connect(create_df, 'df_all_subjects_pickle_file', ds_X, 'df_all_subjects_pickle_file')
wf.connect(vectorize_aggregate_subjects, 'vectorized_aggregated_file', ds_X, 'X_file')
wf.connect(vectorize_aggregate_subjects, 'unimodal_backprojection_info_file', ds_X, 'unimodal_backprojection_info_file')
#####################################
# RUN WF
#####################################
wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == 'CondorDAGMan':
wf.run(plugin=plugin_name)
if plugin_name == 'MultiProc':
wf.run(plugin=plugin_name, plugin_args={'n_procs': use_n_procs})
def downsampel_surfs(subject_id,
working_dir,
freesurfer_dir,
ds_dir,
plugin_name,
use_n_procs):
'''
Workflow resamples e.g. native thickness maps to fsaverage5 space
'''
#####################################
# GENERAL SETTINGS
#####################################
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
fs.FSCommand.set_default_subjects_dir(freesurfer_dir)
wf = Workflow(name='freesurfer_downsample')
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(logging=dict(workflow_level='DEBUG'), execution={'stop_on_first_crash': True,
'remove_unnecessary_outputs': True,
'job_finished_timeout': 15})
config.update_config(nipype_cfg)
wf.config['execution']['crashdump_dir'] = os.path.join(working_dir, 'crash')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.parameterization = False
#####################
# ITERATORS
#####################
# PARCELLATION ITERATOR
infosource = Node(util.IdentityInterface(fields=['hemi', 'surf_measure', 'fwhm', 'target']), name='infosource')
infosource.iterables = [('hemi', ['lh', 'rh']),
('surf_measure', ['thickness', 'area']),
('fwhm', [0, 5, 10, 20]),
('target', ['fsaverage3', 'fsaverage4', 'fsaverage5']),
]
downsample = Node(fs.model.MRISPreproc(), name='downsample')
downsample.inputs.subjects = [subject_id]
wf.connect(infosource, 'target', downsample, 'target')
wf.connect(infosource, 'hemi', downsample, 'hemi')
wf.connect(infosource, 'surf_measure', downsample, 'surf_measure')
wf.connect(infosource, 'fwhm', downsample, 'fwhm_source')
rename = Node(util.Rename(format_string='%(hemi)s.%(surf_measure)s.%(target)s.%(fwhm)smm'), name='rename')
rename.inputs.keep_ext = True
wf.connect(infosource, 'target', rename, 'target')
wf.connect(infosource, 'hemi', rename, 'hemi')
wf.connect(infosource, 'surf_measure', rename, 'surf_measure')
wf.connect(infosource, 'fwhm', rename, 'fwhm')
wf.connect(downsample, 'out_file', rename, 'in_file')
wf.connect(rename, 'out_file', ds, 'surfs.@surfs')
#
wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == 'CondorDAGMan':
wf.run(plugin=plugin_name)
if plugin_name == 'MultiProc':
wf.run(plugin=plugin_name, plugin_args={'n_procs': use_n_procs})
Created on Tue Aug 25 11:39:05 2015
@author: craigmoodie
"""
from nipype.pipeline.engine import Workflow, Node, MapNode
from variables import data_dir, work_dir, subject_list, plugin, plugin_args
surface_workflow = Workflow(name="qc_workflow")
surface_workflow.base_dir = work_dir
from nipype import SelectFiles
templates = dict(T1="*_{subject_id}_*/T1w_MPR_BIC_v1/*00001.nii*")
file_list = Node(SelectFiles(templates), name = "EPI_and_T1_File_Selection")
file_list.inputs.base_directory = data_dir
file_list.iterables = [("subject_id", subject_list)]
from nipype.interfaces.freesurfer import ReconAll
reconall = Node(ReconAll(), name = "Recon_All")
reconall.inputs.subject_id = "subject_id"
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = data_dir
#reconall.inputs.T1_files = "T1"
#reconall.run()
surface_workflow.connect(file_list,"T1", reconall, "T1_files")
surface_workflow.run(plugin=plugin, plugin_args=plugin_args)
def calc_local_metrics(cfg):
import os
from nipype import config
from nipype.pipeline.engine import Node, Workflow, MapNode
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
import nipype.interfaces.freesurfer as freesurfer
import CPAC.alff.alff as cpac_alff
import CPAC.reho.reho as cpac_reho
import CPAC.utils.utils as cpac_utils
import CPAC.vmhc.vmhc as cpac_vmhc
import CPAC.registration.registration as cpac_registration
import CPAC.network_centrality.z_score as cpac_centrality_z_score
import utils as calc_metrics_utils
# INPUT PARAMETERS
dicom_dir = cfg['dicom_dir']
preprocessed_data_dir = cfg['preprocessed_data_dir']
working_dir = cfg['working_dir']
freesurfer_dir = cfg['freesurfer_dir']
template_dir = cfg['template_dir']
script_dir = cfg['script_dir']
ds_dir = cfg['ds_dir']
subject_id = cfg['subject_id']
TR_list = cfg['TR_list']
vols_to_drop = cfg['vols_to_drop']
rois_list = cfg['rois_list']
lp_cutoff_freq = cfg['lp_cutoff_freq']
hp_cutoff_freq = cfg['hp_cutoff_freq']
use_fs_brainmask = cfg['use_fs_brainmask']
use_n_procs = cfg['use_n_procs']
plugin_name = cfg['plugin_name']
#####################################
# GENERAL SETTINGS
#####################################
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
freesurfer.FSCommand.set_default_subjects_dir(freesurfer_dir)
wf = Workflow(name='LeiCA_metrics')
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(logging=dict(workflow_level='DEBUG'), execution={'stop_on_first_crash': True,
'remove_unnecessary_outputs': True,
'job_finished_timeout': 120})
config.update_config(nipype_cfg)
wf.config['execution']['crashdump_dir'] = os.path.join(working_dir, 'crash')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
ds.inputs.regexp_substitutions = [('_variabilty_MNIspace_3mm[0-9]*/', ''), ('_z_score[0-9]*/', '')]
#####################################
# SET ITERATORS
#####################################
# GET SCAN TR_ID ITERATOR
scan_infosource = Node(util.IdentityInterface(fields=['TR_id']), name='scan_infosource')
scan_infosource.iterables = ('TR_id', TR_list)
# get atlas data
templates_atlases = { # 'GM_mask_MNI_2mm': 'SPM_GM/SPM_GM_mask_2mm.nii.gz',
# 'GM_mask_MNI_3mm': 'SPM_GM/SPM_GM_mask_3mm.nii.gz',
'FSL_MNI_3mm_template': 'MNI152_T1_3mm_brain.nii.gz',
'vmhc_symm_brain': 'cpac_image_resources/symmetric/MNI152_T1_2mm_brain_symmetric.nii.gz',
'vmhc_symm_brain_3mm': 'cpac_image_resources/symmetric/MNI152_T1_3mm_brain_symmetric.nii.gz',
'vmhc_symm_skull': 'cpac_image_resources/symmetric/MNI152_T1_2mm_symmetric.nii.gz',
'vmhc_symm_brain_mask_dil': 'cpac_image_resources/symmetric/MNI152_T1_2mm_brain_mask_symmetric_dil.nii.gz',
'vmhc_config_file_2mm': 'cpac_image_resources/symmetric/T1_2_MNI152_2mm_symmetric.cnf'
}
selectfiles_anat_templates = Node(nio.SelectFiles(templates_atlases,
base_directory=template_dir),
name="selectfiles_anat_templates")
# GET SUBJECT SPECIFIC FUNCTIONAL AND STRUCTURAL DATA
selectfiles_templates = {
'epi_2_MNI_warp': '{subject_id}/rsfMRI_preprocessing/registration/epi_2_MNI_warp/TR_{TR_id}/*.nii.gz',
'epi_mask': '{subject_id}/rsfMRI_preprocessing/masks/brain_mask_epiSpace/TR_{TR_id}/*.nii.gz',
'preproc_epi_full_spectrum': '{subject_id}/rsfMRI_preprocessing/epis/01_denoised/TR_{TR_id}/*.nii.gz',
'preproc_epi_bp': '{subject_id}/rsfMRI_preprocessing/epis/02_denoised_BP/TR_{TR_id}/*.nii.gz',
'preproc_epi_bp_tNorm': '{subject_id}/rsfMRI_preprocessing/epis/03_denoised_BP_tNorm/TR_{TR_id}/*.nii.gz',
'epi_2_struct_mat': '{subject_id}/rsfMRI_preprocessing/registration/epi_2_struct_mat/TR_{TR_id}/*.mat',
't1w': '{subject_id}/raw_niftis/sMRI/t1w_reoriented.nii.gz',
't1w_brain': '{subject_id}/rsfMRI_preprocessing/struct_prep/t1w_brain/t1w_reoriented_maths.nii.gz',
}
selectfiles = Node(nio.SelectFiles(selectfiles_templates,
base_directory=preprocessed_data_dir),
name="selectfiles")
wf.connect(scan_infosource, 'TR_id', selectfiles, 'TR_id')
selectfiles.inputs.subject_id = subject_id
# CREATE TRANSFORMATIONS
# creat MNI 2 epi warp
MNI_2_epi_warp = Node(fsl.InvWarp(), name='MNI_2_epi_warp')
MNI_2_epi_warp.inputs.reference = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
wf.connect(selectfiles, 'epi_mask', MNI_2_epi_warp, 'reference')
wf.connect(selectfiles, 'epi_2_MNI_warp', MNI_2_epi_warp, 'warp')
# # CREATE GM MASK IN EPI SPACE
# GM_mask_epiSpace = Node(fsl.ApplyWarp(), name='GM_mask_epiSpace')
# GM_mask_epiSpace.inputs.out_file = 'GM_mask_epiSpace.nii.gz'
#
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_2mm', GM_mask_epiSpace, 'in_file')
# wf.connect(selectfiles, 'epi_mask', GM_mask_epiSpace, 'ref_file')
# wf.connect(MNI_2_epi_warp, 'inverse_warp', GM_mask_epiSpace, 'field_file')
# wf.connect(GM_mask_epiSpace, 'out_file', ds, 'GM_mask_epiSpace')
# fixme
# # CREATE TS IN MNI SPACE
# # is it ok to apply the 2mm warpfield to the 3mm template?
# # seems ok: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=FSL&P=R14011&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
# epi_bp_MNIspace_3mm = Node(fsl.ApplyWarp(), name='epi_bp_MNIspace_3mm')
# epi_bp_MNIspace_3mm.inputs.interp = 'spline'
# epi_bp_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
# wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', epi_bp_MNIspace_3mm, 'ref_file')
# wf.connect(selectfiles, 'preproc_epi_bp', epi_bp_MNIspace_3mm, 'in_file')
# wf.connect(selectfiles, 'epi_2_MNI_warp', epi_bp_MNIspace_3mm, 'field_file')
# CREATE EPI MASK IN MNI SPACE
epi_mask_MNIspace_3mm = Node(fsl.ApplyWarp(), name='epi_mask_MNIspace_3mm')
epi_mask_MNIspace_3mm.inputs.interp = 'nn'
epi_mask_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', epi_mask_MNIspace_3mm, 'ref_file')
wf.connect(selectfiles, 'epi_mask', epi_mask_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', epi_mask_MNIspace_3mm, 'field_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', ds, 'epi_mask_MNIspace_3mm')
#####################
# CALCULATE METRICS
#####################
# f/ALFF
alff = cpac_alff.create_alff('alff')
alff.inputs.hp_input.hp = 0.01
alff.inputs.lp_input.lp = 0.1
wf.connect(selectfiles, 'preproc_epi_full_spectrum', alff, 'inputspec.rest_res')
# wf.connect(GM_mask_epiSpace, 'out_file', alff, 'inputspec.rest_mask')
wf.connect(selectfiles, 'epi_mask', alff, 'inputspec.rest_mask')
wf.connect(alff, 'outputspec.alff_img', ds, 'alff.alff')
wf.connect(alff, 'outputspec.falff_img', ds, 'alff.falff')
# f/ALFF 2 MNI
# fixme spline or default?
alff_MNIspace_3mm = Node(fsl.ApplyWarp(), name='alff_MNIspace_3mm')
alff_MNIspace_3mm.inputs.interp = 'spline'
alff_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', alff_MNIspace_3mm, 'ref_file')
wf.connect(alff, 'outputspec.alff_img', alff_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', alff_MNIspace_3mm, 'field_file')
wf.connect(alff_MNIspace_3mm, 'out_file', ds, 'alff.alff_MNI_3mm')
falff_MNIspace_3mm = Node(fsl.ApplyWarp(), name='falff_MNIspace_3mm')
falff_MNIspace_3mm.inputs.interp = 'spline'
falff_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', falff_MNIspace_3mm, 'ref_file')
wf.connect(alff, 'outputspec.falff_img', falff_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', falff_MNIspace_3mm, 'field_file')
wf.connect(falff_MNIspace_3mm, 'out_file', ds, 'alff.falff_MNI_3mm')
# f/ALFF_MNI Z-SCORE
alff_MNIspace_3mm_Z = cpac_utils.get_zscore(input_name='alff_MNIspace_3mm', wf_name='alff_MNIspace_3mm_Z')
wf.connect(alff_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', alff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(alff_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'alff.alff_MNI_3mm_Z')
falff_MNIspace_3mm_Z = cpac_utils.get_zscore(input_name='falff_MNIspace_3mm', wf_name='falff_MNIspace_3mm_Z')
wf.connect(falff_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', falff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(falff_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'alff.falff_MNI_3mm_Z')
# f/ALFF_MNI STANDARDIZE BY MEAN
alff_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='alff_MNIspace_3mm_standardized_mean')
wf.connect(alff_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', alff_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(alff_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds, 'alff.alff_MNI_3mm_standardized_mean')
falff_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='falff_MNIspace_3mm_standardized_mean')
wf.connect(falff_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', falff_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(falff_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds, 'alff.falff_MNI_3mm_standardized_mean')
# REHO
reho = cpac_reho.create_reho()
reho.inputs.inputspec.cluster_size = 27
wf.connect(selectfiles, 'preproc_epi_bp', reho, 'inputspec.rest_res_filt')
# wf.connect(GM_mask_epiSpace, 'out_file', reho, 'inputspec.rest_mask')
wf.connect(selectfiles, 'epi_mask', reho, 'inputspec.rest_mask')
wf.connect(reho, 'outputspec.raw_reho_map', ds, 'reho.reho')
# REHO 2 MNI
# fixme spline or default?
reho_MNIspace_3mm = Node(fsl.ApplyWarp(), name='reho_MNIspace_3mm')
reho_MNIspace_3mm.inputs.interp = 'spline'
reho_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', reho_MNIspace_3mm, 'ref_file')
wf.connect(reho, 'outputspec.raw_reho_map', reho_MNIspace_3mm, 'in_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', reho_MNIspace_3mm, 'field_file')
wf.connect(reho_MNIspace_3mm, 'out_file', ds, 'reho.reho_MNI_3mm')
# REHO_MNI Z-SCORE
reho_MNIspace_3mm_Z = cpac_utils.get_zscore(input_name='reho_MNIspace_3mm', wf_name='reho_MNIspace_3mm_Z')
wf.connect(alff_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', reho_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(reho_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'reho.reho_MNI_3mm_Z')
# REHO_MNI STANDARDIZE BY MEAN
reho_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='reho_MNIspace_3mm_standardized_mean')
wf.connect(reho_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', reho_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(reho_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds, 'reho.reho_MNI_3mm_standardized_mean')
# VMHC
# create registration to symmetrical MNI template
struct_2_MNI_symm = cpac_registration.create_nonlinear_register(name='struct_2_MNI_symm')
wf.connect(selectfiles_anat_templates, 'vmhc_config_file_2mm', struct_2_MNI_symm, 'inputspec.fnirt_config')
wf.connect(selectfiles_anat_templates, 'vmhc_symm_brain', struct_2_MNI_symm, 'inputspec.reference_brain')
wf.connect(selectfiles_anat_templates, 'vmhc_symm_skull', struct_2_MNI_symm, 'inputspec.reference_skull')
wf.connect(selectfiles_anat_templates, 'vmhc_symm_brain_mask_dil', struct_2_MNI_symm, 'inputspec.ref_mask')
wf.connect(selectfiles, 't1w', struct_2_MNI_symm, 'inputspec.input_skull')
wf.connect(selectfiles, 't1w_brain', struct_2_MNI_symm, 'inputspec.input_brain')
wf.connect(struct_2_MNI_symm, 'outputspec.output_brain', ds, 'vmhc.symm_reg.@output_brain')
wf.connect(struct_2_MNI_symm, 'outputspec.linear_xfm', ds, 'vmhc.symm_reg.@linear_xfm')
wf.connect(struct_2_MNI_symm, 'outputspec.invlinear_xfm', ds, 'vmhc.symm_reg.@invlinear_xfm')
wf.connect(struct_2_MNI_symm, 'outputspec.nonlinear_xfm', ds, 'vmhc.symm_reg.@nonlinear_xfm')
# fixme
vmhc = cpac_vmhc.create_vmhc(use_ants=False, name='vmhc')
vmhc.inputs.fwhm_input.fwhm = 4
wf.connect(selectfiles_anat_templates, 'vmhc_symm_brain_3mm', vmhc, 'inputspec.standard_for_func')
wf.connect(selectfiles, 'preproc_epi_bp_tNorm', vmhc, 'inputspec.rest_res')
wf.connect(selectfiles, 'epi_2_struct_mat', vmhc, 'inputspec.example_func2highres_mat')
wf.connect(struct_2_MNI_symm, 'outputspec.nonlinear_xfm', vmhc, 'inputspec.fnirt_nonlinear_warp')
# wf.connect(GM_mask_epiSpace, 'out_file', vmhc, 'inputspec.rest_mask')
wf.connect(selectfiles, 'epi_mask', vmhc, 'inputspec.rest_mask')
wf.connect(vmhc, 'outputspec.rest_res_2symmstandard', ds, 'vmhc.rest_res_2symmstandard')
wf.connect(vmhc, 'outputspec.VMHC_FWHM_img', ds, 'vmhc.VMHC_FWHM_img')
wf.connect(vmhc, 'outputspec.VMHC_Z_FWHM_img', ds, 'vmhc.VMHC_Z_FWHM_img')
wf.connect(vmhc, 'outputspec.VMHC_Z_stat_FWHM_img', ds, 'vmhc.VMHC_Z_stat_FWHM_img')
# VARIABILITY SCORES
variability = Node(util.Function(input_names=['in_file'],
output_names=['out_file_list'],
function=calc_metrics_utils.calc_variability),
name='variability')
wf.connect(selectfiles, 'preproc_epi_bp', variability, 'in_file')
wf.connect(variability, 'out_file_list', ds, 'variability.subjectSpace.@out_files')
# #fixme spline?
variabilty_MNIspace_3mm = MapNode(fsl.ApplyWarp(), iterfield=['in_file'], name='variabilty_MNIspace_3mm')
variabilty_MNIspace_3mm.inputs.interp = 'spline'
variabilty_MNIspace_3mm.plugin_args = {'submit_specs': 'request_memory = 4000'}
wf.connect(selectfiles_anat_templates, 'FSL_MNI_3mm_template', variabilty_MNIspace_3mm, 'ref_file')
wf.connect(selectfiles, 'epi_2_MNI_warp', variabilty_MNIspace_3mm, 'field_file')
wf.connect(variability, 'out_file_list', variabilty_MNIspace_3mm, 'in_file')
wf.connect(variabilty_MNIspace_3mm, 'out_file', ds, 'variability.MNI_3mm.@out_file')
# CALC Z SCORE
variabilty_MNIspace_3mm_Z = cpac_centrality_z_score.get_cent_zscore(wf_name='variabilty_MNIspace_3mm_Z')
wf.connect(variabilty_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_Z, 'inputspec.input_file')
# wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', variabilty_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_Z, 'inputspec.mask_file')
wf.connect(variabilty_MNIspace_3mm_Z, 'outputspec.z_score_img', ds, 'variability.MNI_3mm_Z.@out_file')
# STANDARDIZE BY MEAN
variabilty_MNIspace_3mm_standardized_mean = calc_metrics_utils.standardize_divide_by_mean(
wf_name='variabilty_MNIspace_3mm_standardized_mean')
wf.connect(variabilty_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_standardized_mean, 'inputnode.in_file')
wf.connect(epi_mask_MNIspace_3mm, 'out_file', variabilty_MNIspace_3mm_standardized_mean, 'inputnode.mask_file')
wf.connect(variabilty_MNIspace_3mm_standardized_mean, 'outputnode.out_file', ds,
'variability.MNI_3mm_standardized_mean.@out_file')
wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == 'CondorDAGMan':
wf.run(plugin=plugin_name)
if plugin_name == 'MultiProc':
wf.run(plugin=plugin_name, plugin_args={'n_procs': use_n_procs})
def calc_centrality_metrics(cfg):
import os
from nipype import config
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
import nipype.interfaces.freesurfer as freesurfer
import CPAC.network_centrality.resting_state_centrality as cpac_centrality
import CPAC.network_centrality.z_score as cpac_centrality_z_score
# INPUT PARAMETERS
dicom_dir = cfg['dicom_dir']
preprocessed_data_dir = cfg['preprocessed_data_dir']
working_dir = cfg['working_dir']
freesurfer_dir = cfg['freesurfer_dir']
template_dir = cfg['template_dir']
script_dir = cfg['script_dir']
ds_dir = cfg['ds_dir']
subjects_list = cfg['subjects_list']
TR_list = cfg['TR_list']
use_n_procs = cfg['use_n_procs']
plugin_name = cfg['plugin_name']
#####################################
# GENERAL SETTINGS
#####################################
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
freesurfer.FSCommand.set_default_subjects_dir(freesurfer_dir)
wf = Workflow(name='LeiCA_metrics')
wf.base_dir = os.path.join(working_dir)
nipype_cfg = dict(logging=dict(workflow_level='DEBUG'), execution={'stop_on_first_crash': False,
'remove_unnecessary_outputs': True,
'job_finished_timeout': 120})
config.update_config(nipype_cfg)
wf.config['execution']['crashdump_dir'] = os.path.join(working_dir, 'crash')
ds = Node(nio.DataSink(), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
ds.inputs.regexp_substitutions = [('_subject_id_[A0-9]*/', ''), (
'_z_score[0-9]*/', '')] # , #('dc/_TR_id_[0-9]*/', ''), ('evc/_TR_id_[0-9]*/','')]
#####################################
# SET ITERATORS
#####################################
# GET SCAN TR_ID ITERATOR
scan_infosource = Node(util.IdentityInterface(fields=['TR_id']), name='scan_infosource')
scan_infosource.iterables = ('TR_id', TR_list)
subjects_infosource = Node(util.IdentityInterface(fields=['subject_id']), name='subjects_infosource')
subjects_infosource.iterables = ('subject_id', subjects_list)
def add_subject_id_to_ds_dir_fct(subject_id, ds_path):
import os
out_path = os.path.join(ds_path, subject_id)
return out_path
add_subject_id_to_ds_dir = Node(util.Function(input_names=['subject_id', 'ds_path'],
output_names=['out_path'],
function=add_subject_id_to_ds_dir_fct),
name='add_subject_id_to_ds_dir')
wf.connect(subjects_infosource, 'subject_id', add_subject_id_to_ds_dir, 'subject_id')
add_subject_id_to_ds_dir.inputs.ds_path = ds_dir
wf.connect(add_subject_id_to_ds_dir, 'out_path', ds, 'base_directory')
# get atlas data
templates_atlases = {'GM_mask_MNI_2mm': 'SPM_GM/SPM_GM_mask_2mm.nii.gz',
'GM_mask_MNI_3mm': 'SPM_GM/SPM_GM_mask_3mm.nii.gz',
'FSL_MNI_3mm_template': 'MNI152_T1_3mm_brain.nii.gz',
'vmhc_symm_brain': 'cpac_image_resources/symmetric/MNI152_T1_2mm_brain_symmetric.nii.gz',
'vmhc_symm_brain_3mm': 'cpac_image_resources/symmetric/MNI152_T1_3mm_brain_symmetric.nii.gz',
'vmhc_symm_skull': 'cpac_image_resources/symmetric/MNI152_T1_2mm_symmetric.nii.gz',
'vmhc_symm_brain_mask_dil': 'cpac_image_resources/symmetric/MNI152_T1_2mm_brain_mask_symmetric_dil.nii.gz',
'vmhc_config_file_2mm': 'cpac_image_resources/symmetric/T1_2_MNI152_2mm_symmetric.cnf'
}
selectfiles_anat_templates = Node(nio.SelectFiles(templates_atlases,
base_directory=template_dir),
name="selectfiles_anat_templates")
# GET SUBJECT SPECIFIC FUNCTIONAL AND STRUCTURAL DATA
selectfiles_templates = {
'epi_2_MNI_warp': '{subject_id}/rsfMRI_preprocessing/registration/epi_2_MNI_warp/TR_{TR_id}/*.nii.gz',
'epi_mask': '{subject_id}/rsfMRI_preprocessing/masks/brain_mask_epiSpace/TR_{TR_id}/*.nii.gz',
'preproc_epi_full_spectrum': '{subject_id}/rsfMRI_preprocessing/epis/01_denoised/TR_{TR_id}/*.nii.gz',
'preproc_epi_bp': '{subject_id}/rsfMRI_preprocessing/epis/02_denoised_BP/TR_{TR_id}/*.nii.gz',
'preproc_epi_bp_tNorm': '{subject_id}/rsfMRI_preprocessing/epis/03_denoised_BP_tNorm/TR_{TR_id}/*.nii.gz',
'epi_2_struct_mat': '{subject_id}/rsfMRI_preprocessing/registration/epi_2_struct_mat/TR_{TR_id}/*.mat',
't1w': '{subject_id}/raw_niftis/sMRI/t1w_reoriented.nii.gz',
't1w_brain': '{subject_id}/rsfMRI_preprocessing/struct_prep/t1w_brain/t1w_reoriented_maths.nii.gz',
'epi_bp_tNorm_MNIspace_3mm': '{subject_id}/rsfMRI_preprocessing/epis_MNI_3mm/03_denoised_BP_tNorm/TR_645/residual_filt_norm_warp.nii.gz'
}
selectfiles = Node(nio.SelectFiles(selectfiles_templates,
base_directory=preprocessed_data_dir),
name="selectfiles")
wf.connect(scan_infosource, 'TR_id', selectfiles, 'TR_id')
wf.connect(subjects_infosource, 'subject_id', selectfiles, 'subject_id')
# selectfiles.inputs.subject_id = subject_id
# CREATE TRANSFORMATIONS
# creat MNI 2 epi warp
MNI_2_epi_warp = Node(fsl.InvWarp(), name='MNI_2_epi_warp')
MNI_2_epi_warp.inputs.reference = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
wf.connect(selectfiles, 'epi_mask', MNI_2_epi_warp, 'reference')
wf.connect(selectfiles, 'epi_2_MNI_warp', MNI_2_epi_warp, 'warp')
#####################
# CALCULATE METRICS
#####################
# DEGREE
# fixme
# a_mem = 5
# fixme
a_mem = 20
dc = cpac_centrality.create_resting_state_graphs(allocated_memory=a_mem,
wf_name='dc') # allocated_memory = a_mem, wf_name = 'dc')
# dc.plugin_args = {'submit_specs': 'request_memory = 6000'}
# fixme
dc.plugin_args = {'submit_specs': 'request_memory = 20000'}
dc.inputs.inputspec.method_option = 0 # 0 for degree centrality, 1 for eigenvector centrality, 2 for lFCD
dc.inputs.inputspec.threshold_option = 0 # 0 for probability p_value, 1 for sparsity threshold, any other for threshold value
dc.inputs.inputspec.threshold = 0.0001
dc.inputs.inputspec.weight_options = [True,
True] # list of two booleans for binarize and weighted options respectively
wf.connect(selectfiles, 'epi_bp_tNorm_MNIspace_3mm', dc, 'inputspec.subject')
wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', dc, 'inputspec.template')
wf.connect(dc, 'outputspec.centrality_outputs', ds, 'metrics.centrality.dc.@centrality_outputs')
wf.connect(dc, 'outputspec.correlation_matrix', ds, 'metrics.centrality.dc.@correlation_matrix')
wf.connect(dc, 'outputspec.graph_outputs', ds, 'metrics.centrality.dc.@graph_outputs')
# DC Z-SCORE
dc_Z = cpac_centrality_z_score.get_cent_zscore(wf_name='dc_Z')
wf.connect(dc, 'outputspec.centrality_outputs', dc_Z, 'inputspec.input_file')
wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', dc_Z, 'inputspec.mask_file')
wf.connect(dc_Z, 'outputspec.z_score_img', ds, 'metrics.centrality.dc_z.@output')
a_mem = 20
evc = cpac_centrality.create_resting_state_graphs(allocated_memory=a_mem, wf_name='evc')
evc.plugin_args = {'submit_specs': 'request_memory = 20000'}
evc.inputs.inputspec.method_option = 1 # 0 for degree centrality, 1 for eigenvector centrality, 2 for lFCD
evc.inputs.inputspec.threshold_option = 0 # 0 for probability p_value, 1 for sparsity threshold, any other for threshold value
evc.inputs.inputspec.threshold = 0.0001
evc.inputs.inputspec.weight_options = [True,
True] # list of two booleans for binarize and weighted options respectively
wf.connect(selectfiles, 'epi_bp_tNorm_MNIspace_3mm', evc, 'inputspec.subject')
wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', evc, 'inputspec.template')
wf.connect(evc, 'outputspec.centrality_outputs', ds, 'metrics.centrality.evc.@centrality_outputs')
wf.connect(evc, 'outputspec.correlation_matrix', ds, 'metrics.centrality.evc.@correlation_matrix')
wf.connect(evc, 'outputspec.graph_outputs', ds, 'metrics.centrality.evc.@graph_outputs')
# EVC Z-SCORE
evc_Z = cpac_centrality_z_score.get_cent_zscore(wf_name='evc_Z')
wf.connect(evc, 'outputspec.centrality_outputs', evc_Z, 'inputspec.input_file')
wf.connect(selectfiles_anat_templates, 'GM_mask_MNI_3mm', evc_Z, 'inputspec.mask_file')
wf.connect(evc_Z, 'outputspec.z_score_img', ds, 'metrics.centrality.evc_z.@output')
wf.write_graph(dotfilename=wf.name, graph2use='colored', format='pdf') # 'hierarchical')
wf.write_graph(dotfilename=wf.name, graph2use='orig', format='pdf')
wf.write_graph(dotfilename=wf.name, graph2use='flat', format='pdf')
if plugin_name == 'CondorDAGMan':
wf.run(plugin=plugin_name)
if plugin_name == 'MultiProc':
wf.run(plugin=plugin_name, plugin_args={'n_procs': use_n_procs})
def create(self): # , **kwargs):
""" Create the nodes and connections for the workflow """
# Preamble
csvReader = CSVReader()
csvReader.inputs.in_file = self.csv_file.default_value
csvReader.inputs.header = self.hasHeader.default_value
csvOut = csvReader.run()
print(("=" * 80))
print((csvOut.outputs.__dict__))
print(("=" * 80))
iters = OrderedDict()
label = list(csvOut.outputs.__dict__.keys())[0]
result = eval("csvOut.outputs.{0}".format(label))
iters["tests"], iters["trains"] = sample_crossvalidation_set(
result, self.sample_size.default_value
)
# Main event
out_fields = ["T1", "T2", "Label", "trainindex", "testindex"]
inputsND = Node(
interface=IdentityInterface(fields=out_fields),
run_without_submitting=True,
name="inputs",
)
inputsND.iterables = [
("trainindex", iters["trains"]),
("testindex", iters["tests"]),
]
if not self.hasHeader.default_value:
inputsND.inputs.T1 = csvOut.outputs.column_0
inputsND.inputs.Label = csvOut.outputs.column_1
inputsND.inputs.T2 = csvOut.outputs.column_2
else:
inputsND.inputs.T1 = csvOut.outputs.__dict__["t1"]
inputsND.inputs.Label = csvOut.outputs.__dict__["label"]
inputsND.inputs.T2 = csvOut.outputs.__dict__["t2"]
pass # TODO
metaflow = Workflow(name="metaflow")
metaflow.config["execution"] = {
"plugin": "Linear",
"stop_on_first_crash": "false",
"stop_on_first_rerun": "false",
# This stops at first attempt to rerun, before running, and before deleting previous results.
"hash_method": "timestamp",
"single_thread_matlab": "true", # Multi-core 2011a multi-core for matrix multiplication.
"remove_unnecessary_outputs": "true",
"use_relative_paths": "false", # relative paths should be on, require hash update when changed.
"remove_node_directories": "false", # Experimental
"local_hash_check": "false",
}
metaflow.add_nodes([inputsND])
"""import pdb; pdb.set_trace()"""
fusionflow = FusionLabelWorkflow()
self.connect(
[
(
metaflow,
fusionflow,
[
("inputs.trainindex", "trainT1s.index"),
("inputs.T1", "trainT1s.inlist"),
],
),
(
metaflow,
fusionflow,
[
("inputs.trainindex", "trainLabels.index"),
("inputs.Label", "trainLabels.inlist"),
],
),
(
metaflow,
fusionflow,
[
("inputs.testindex", "testT1s.index"),
("inputs.T1", "testT1s.inlist"),
],
),
]
)
'skullstrip_mask'
]),
name='outputnode')
# remove background noise
background = Node(JistIntensityMp2rageMasking(outMasked=True,
outMasked2=True,
outSignal2=True),
name='background')
# skullstrip
strip = Node(MedicAlgorithmSPECTRE2010(outStripped=True,
outMask=True,
outOriginal=True,
inOutput='true',
inFind='true',
#maxMemoryUsage = 6000,
#inMMC=4
),
name='strip')
strip.iterables=('inMMC',[2,4])
# connections
mp2rage.connect([(inputnode, background, [('inv2', 'inSecond'),
('t1map', 'inQuantitative'),
('uni', 'inT1weighted')]),
(background, strip, [('outMasked2','inInput')]),
(background, outputnode, [('outMasked2','uni_masked'),
('outMasked','t1map_masked'),
('outSignal2','background_mask')]),
(strip, outputnode, [('outStripped','uni_stripped'),
####
from nipype.pipeline.engine import Node, Workflow
import nipype.interfaces.io as nio
#from nipype.interfaces.ants.registration import RegistrationSynQuick
import os
os.chdir('/Users/franzliem/Desktop/antstest')
wf = Workflow(name='normalize')
wf.base_dir = os.path.join('/Users/franzliem/Desktop/antstest/wf')
ds = Node(nio.DataSink(), name='ds')
ds.inputs.base_directory = '/Users/franzliem/Desktop/antstest/ds'
s = Node(RegistrationSynQuick(), name='s_rigid')
s.base_dir = '/Users/franzliem/Desktop/antstest/node_test'
s.inputs.fixed_image = '/Applications/FSL/data/standard/FMRIB58_FA_1mm.nii.gz'
s.inputs.moving_image = '/Users/franzliem/Desktop/antstest/dtifit__FA_ero.nii.gz'
s.inputs.output_prefix = 'ants_mni'
s.inputs.num_threads=4
# s.inputs.use_histogram_matching = True
# s.inputs.transform_type = 'r'
# s.inputs.histogram_bins = 44
# s.inputs.spline_distance = 15
# s.inputs.precision_type = 'double'
for f in ['warped_image', 'out_matrix', 'forward_warp_field', 'inverse_warp_field']:
wf.connect(s, f, ds, f)
wf.run()