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 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_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 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_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_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 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_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 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_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')
def rename_subject_for_fu(input_id):
output_id=input_id+"_fu"
return output_id
#modify subject name so it can be saved in the same folder as other LIFE- freesurfer data
rename=Node(util.Function(input_names=['input_id'],
output_names=['output_id'],
function = rename_subject_for_fu), name="rename")
# run reconall
recon_all = Node(fs.ReconAll(args='-all -hippo-subfields -no-isrunning', openmp=24), #FS version 6.0: -hippocampal-subfields-T1, version 5.3.. -hippo-subfields
name="recon_all")
#recon_all.inputs.directive= 'autorecon2-wm' # -autorecon3
recon_all.plugin_args={'submit_specs': 'request_memory = 9000'}
reconall.connect([
(inputnode, rename, [('fs_subject_id', 'input_id')]),
(rename, recon_all, [('output_id', 'subject_id')]),
(inputnode, recon_all, [('fs_subjects_dir', 'subjects_dir'),
('anat', 'T1_files')]),
(recon_all, outputnode, [('subject_id', 'fs_subject_id'),
('subjects_dir', 'fs_subjects_dir')])
])
return reconall
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 create_bet_mask_from_dwi(name, do_realignment=True):
wf = Workflow(name=name)
inputnode = Node(interface=IdentityInterface(fields=["dwi", "bvec", "bval"]),
name="inputnode")
b0s = Node(DwiextractB0(), "b0s")
wf.connect(inputnode, "dwi", b0s, "in_file")
wf.connect(inputnode, "bvec", b0s, "bvec")
wf.connect(inputnode, "bval", b0s, "bval")
meanb0 = Node(fsl.ImageMaths(op_string='-Tmean', suffix='_mean'), name="meanb0")
wf.connect(b0s, "out_file", meanb0, "in_file")
mcflirt = Node(fsl.MCFLIRT(), "mcflirt")
bet = Node(fsl.BET(), "bet")
bet.inputs.frac = 0.3
bet.inputs.robust = True
bet.inputs.mask = True
if do_realignment:
wf.connect(meanb0, "out_file", mcflirt, "in_file")
wf.connect(mcflirt, "out_file", bet, "in_file")
else:
wf.connect(meanb0, "out_file", bet, "in_file")
outputnode = Node(interface=IdentityInterface(fields=["mask_file"]), name="outputnode")
wf.connect(bet, "mask_file", outputnode, "mask_file")
return wf
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_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_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 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_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 create_workflow():
workflow = Workflow(
name='transform_manual_mask')
inputs = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'refsubject_id',
'ref_funcmask',
'ref_func',
'funcs',
]), name='in')
# Find the transformation matrix func_ref -> func
# First find transform from func to manualmask's ref func
# first take the median (flirt functionality has changed and no longer automatically takes the first volume when given 4D files)
median_func = MapNode(
interface=fsl.maths.MedianImage(dimension="T"),
name='median_func',
iterfield=('in_file'),
)
findtrans = MapNode(fsl.FLIRT(),
iterfield=['in_file'],
name='findtrans'
)
# Invert the matrix transform
invert = MapNode(fsl.ConvertXFM(invert_xfm=True),
name='invert',
iterfield=['in_file'],
)
workflow.connect(findtrans, 'out_matrix_file',
invert, 'in_file')
# Transform the manualmask to be aligned with func
funcreg = MapNode(ApplyXFMRefName(),
name='funcreg',
iterfield=['in_matrix_file', 'reference'],
)
workflow.connect(inputs, 'funcs',
median_func, 'in_file')
workflow.connect(median_func, 'out_file',
findtrans, 'in_file')
workflow.connect(inputs, 'ref_func',
findtrans, 'reference')
workflow.connect(invert, 'out_file',
funcreg, 'in_matrix_file')
workflow.connect(inputs, 'ref_func',
funcreg, 'in_file')
workflow.connect(inputs, 'funcs',
funcreg, 'reference')
return workflow
def create(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 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 create_mgzconvert_pipeline(name='mgzconvert'):
# workflow
mgzconvert = Workflow(name='mgzconvert')
# inputnode
inputnode = Node(
util.IdentityInterface(fields=['fs_subjects_dir', 'fs_subject_id']),
name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'anat_head', 'anat_brain', 'anat_brain_mask', 'wmseg', 'wmedge'
]),
name='outputnode')
# import files from freesurfer
fs_import = Node(interface=nio.FreeSurferSource(), name='fs_import')
# convert Freesurfer T1 file to nifti
head_convert = Node(fs.MRIConvert(out_type='niigz', out_file='T1.nii.gz'),
name='head_convert')
# create brainmask from aparc+aseg with single dilation
def get_aparc_aseg(files):
for name in files:
if 'aparc+aseg' in name:
return name
# create brain by converting only freesurfer output
brain_convert = Node(fs.MRIConvert(out_type='niigz',
out_file='brain.nii.gz'),
name='brain_convert')
brain_binarize = Node(fsl.ImageMaths(op_string='-bin -fillh',
out_file='T1_brain_mask.nii.gz'),
name='brain_binarize')
# cortical and cerebellar white matter volumes to construct wm edge
# [lh cerebral wm, lh cerebellar wm, rh cerebral wm, rh cerebellar wm, brain stem]
wmseg = Node(fs.Binarize(out_type='nii.gz',
match=[2, 7, 41, 46, 16],
binary_file='T1_brain_wmseg.nii.gz'),
name='wmseg')
# make edge from wmseg to visualize coregistration quality
edge = Node(fsl.ApplyMask(args='-edge -bin',
out_file='T1_brain_wmedge.nii.gz'),
name='edge')
# connections
mgzconvert.connect([
(inputnode, fs_import, [('fs_subjects_dir', 'subjects_dir'),
('fs_subject_id', 'subject_id')]),
(fs_import, head_convert, [('T1', 'in_file')]),
(fs_import, wmseg, [(('aparc_aseg', get_aparc_aseg), 'in_file')]),
(fs_import, brain_convert, [('brainmask', 'in_file')]),
(wmseg, edge, [('binary_file', 'in_file'),
('binary_file', 'mask_file')]),
(head_convert, outputnode, [('out_file', 'anat_head')]),
(brain_convert, outputnode, [('out_file', 'anat_brain')]),
(brain_convert, brain_binarize, [('out_file', 'in_file')]),
(brain_binarize, outputnode, [('out_file', 'anat_brain_mask')]),
(wmseg, outputnode, [('binary_file', 'wmseg')]),
(edge, outputnode, [('out_file', 'wmedge')])
])
return mgzconvert
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 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_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 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 create_moco_pipeline(name='motion_correction'):
# initiate workflow
moco = Workflow(name='motion_correction')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['epi']), name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'epi_moco', 'par_moco', 'mat_moco', 'rms_moco', 'epi_mean', 'rotplot',
'transplot', 'dispplots', 'tsnr_file'
]),
name='outputnode')
# mcflirt motion correction to 1st volume
mcflirt = Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
ref_vol=1,
out_file='rest_realigned.nii.gz'),
name='mcflirt')
# plot motion parameters
rotplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation_plot.png'),
name='rotplotter')
transplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation_plot.png'),
name='transplotter')
dispplotter = MapNode(interface=fsl.PlotMotionParams(
in_source='fsl',
plot_type='displacement',
),
name='dispplotter',
iterfield=['in_file'])
dispplotter.iterables = ('plot_type', ['displacement'])
# calculate tmean
tmean = Node(fsl.maths.MeanImage(dimension='T',
out_file='rest_realigned_mean.nii.gz'),
name='tmean')
# calculate tsnr
tsnr = Node(confounds.TSNR(), name='tsnr')
# create connections
moco.connect([(inputnode, mcflirt, [('epi', 'in_file')]),
(mcflirt, tmean, [('out_file', 'in_file')]),
(mcflirt, rotplotter, [('par_file', 'in_file')]),
(mcflirt, transplotter, [('par_file', 'in_file')]),
(mcflirt, dispplotter, [('rms_files', 'in_file')]),
(tmean, outputnode, [('out_file', 'epi_mean')]),
(mcflirt, outputnode, [('out_file', 'epi_moco'),
('par_file', 'par_moco'),
('mat_file', 'mat_moco'),
('rms_files', 'rms_moco')]),
(rotplotter, outputnode, [('out_file', 'rotplot')]),
(transplotter, outputnode, [('out_file', 'transplot')]),
(dispplotter, outputnode, [('out_file', 'dispplots')]),
(mcflirt, tsnr, [('out_file', 'in_file')]),
(tsnr, outputnode, [('tsnr_file', 'tsnr_file')])])
return moco
def 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 create_structural(subject, working_dir, data_dir, freesurfer_dir, out_dir,
standard_brain):
# main workflow
struct_preproc = Workflow(name='anat_preproc')
struct_preproc.base_dir = working_dir
struct_preproc.config['execution'][
'crashdump_dir'] = struct_preproc.base_dir + "/crash_files"
# select files
#templates={'anat': '3T/nifti/MPRAGEADNI32Ch.nii.gz'}
#selectfiles = Node(nio.SelectFiles(templates, base_directory=data_dir), name="selectfiles")
# workflow to run freesurfer reconall
reconall = create_reconall_pipeline()
reconall.inputs.inputnode.fs_subjects_dir = freesurfer_dir
reconall.inputs.inputnode.fs_subject_id = subject
# workflow to get brain, head and wmseg from freesurfer and convert to nifti
mgzconvert = create_mgzconvert_pipeline()
mgzconvert.inputs.inputnode.fs_subjects_dir = freesurfer_dir
mgzconvert.inputs.inputnode.fs_subject_id = subject
normalize = create_normalize_pipeline()
normalize.inputs.inputnode.standard = standard_brain
# sink to store files
sink = Node(nio.DataSink(base_directory=out_dir,
parameterization=False,
substitutions=[('transform_Warped',
'T1_brain2mni')]),
name='sink')
# connections
struct_preproc.connect([ #(selectfiles, sink, [('anat', 'outputnode.test')]),
#(selectfiles, reconall, [('anat', 'inputnode.anat')]),
#(reconall, mgzconvert, [('outputnode.fs_subject_id', 'inputnode.fs_subject_id'),
# ('outputnode.fs_subjects_dir', 'inputnode.fs_subjects_dir')]),
#for second round of structural don't redo FREESURFER
(mgzconvert, normalize, [('outputnode.anat_brain', 'inputnode.anat')]),
(mgzconvert, sink, [('outputnode.anat_head', '@head')]),
(mgzconvert, sink, [('outputnode.anat_brain', '@brain')]),
(mgzconvert, sink, [('outputnode.anat_brain_mask', '@mask')]),
(mgzconvert, sink, [('outputnode.wmedge', '@wmedge')]),
(normalize, sink, [('outputnode.anat2std', '@anat2std'),
('outputnode.anat2std_transforms',
'transforms2mni.@anat2std_transforms'),
('outputnode.std2anat_transforms',
'transforms2mni.@std2anat_transforms')])
])
struct_preproc.write_graph(dotfilename='struct_preproc.dot',
graph2use='colored',
format='pdf',
simple_form=True)
# struct_preproc.run()
struct_preproc.run(
) #, plugin_args = {'initial_specs': 'request_memory = 1500'}plugin='CondorDAGMan'
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
