def create_longitudinal(project, subject, session, master_config, interpMode='Linear',
pipeline_name=''):
"""
create longitudinal workflow on a single session
This is the main function to call when processing a data set with T1 & T2
data. ExperimentBaseDirectoryPrefix is the base of the directory to place results, T1Images & T2Images
are the lists of images to be used in the auto-workup. atlas_fname_wpath is
the path and filename of the atlas to use.
"""
from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, Directory
from nipype.interfaces.base import traits, isdefined, BaseInterface
from nipype.interfaces.utility import Split, Rename, IdentityInterface, Function
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from atlasNode import MakeAtlasNode
from baseline import baseline_workflow as create_baseline
baw201 = create_baseline(project, subject, session, master_config,
phase='longitudinal',
interpMode=interpMode,
pipeline_name=pipeline_name)
template_DG = pe.Node(interface=nio.DataGrabber(infields=['subject'],
outfields=['template_t1', 'outAtlasFullPath']),
name='Template_DG')
template_DG.inputs.base_directory = master_config['previousresult']
template_DG.inputs.subject = subject
template_DG.inputs.template = 'SUBJECT_TEMPLATES/%s/AVG_%s.nii.gz'
template_DG.inputs.template_args['template_t1'] = [['subject', 'T1']]
template_DG.inputs.field_template = {'outAtlasFullPath': 'Atlas/definitions/AtlasDefinition_%s.xml'}
template_DG.inputs.template_args['outAtlasFullPath'] = [['subject']]
template_DG.inputs.sort_filelist = True
template_DG.inputs.raise_on_empty = True
inputsSpec = baw201.get_node('inputspec')
baw201.connect([(template_DG, inputsSpec, [('outAtlasFullPath', 'atlasDefinition'),
('template_t1', 'template_t1')]),
])
if 'segmentation' in master_config['components']:
from workflows.segmentation import segmentation
sname = 'segmentation'
# sname = GenerateWFName(project, subject, session, 'segmentation')
onlyT1 = not(len(inputsSpec.inputs.T2s) > 0)
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas')
segWF = segmentation(project, subject, session, master_config, atlasNode, onlyT1, pipeline_name=sname)
outputSpec = baw201.get_node('outputspec')
baw201.connect([(outputSpec, segWF, [('t1_average', 'inputspec.t1_average'),
('LMIatlasToSubject_tx', 'inputspec.LMIatlasToSubject_tx'),
('outputLabels', 'inputspec.inputLabels'),
('posteriorImages', 'inputspec.posteriorImages'),
('tc_atlas2sessionInverse_tx', 'inputspec.TissueClassifyatlasToSubjectInverseTransform'),
('UpdatedPosteriorsList', 'inputspec.UpdatedPosteriorsList'),
('outputHeadLabels', 'inputspec.inputHeadLabels')])
])
if not onlyT1:
baw201.connect([(outputSpec, segWF, [('t1_average', 'inputspec.t2_average')])])
return baw201
def create_longitudinal(project, subject, session, master_config, interpMode='Linear', pipeline_name=''):
"""
create longitudinal workflow on a single session
This is the main function to call when processing a data set with T1 & T2
data. ExperimentBaseDirectoryPrefix is the base of the directory to place results, T1Images & T2Images
are the lists of images to be used in the auto-workup. atlas_fname_wpath is
the path and filename of the atlas to use.
"""
from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, Directory
from nipype.interfaces.base import traits, isdefined, BaseInterface
from nipype.interfaces.utility import Split, Rename, IdentityInterface, Function
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from baseline import baseline_workflow as create_baseline
baw201 = create_baseline(project, subject, session, master_config,
phase='longitudinal',
interpMode=interpMode,
pipeline_name=pipeline_name)
inputsSpec = baw201.get_node('inputspec')
if 'segmentation' in master_config['components']:
from workflows.segmentation import segmentation
sname = 'segmentation'
# sname = GenerateWFName(project, subject, session, 'segmentation')
onlyT1 = not(len(inputsSpec.inputs.T2s) > 0)
segWF = segmentation(project, subject, session, master_config, onlyT1, pipeline_name=sname)
outputSpec = baw201.get_node('outputspec')
baw201.connect([(outputSpec, segWF, [('t1_average', 'inputspec.t1_average'),
('LMIatlasToSubject_tx', 'inputspec.LMIatlasToSubject_tx'),
('outputLabels', 'inputspec.inputLabels'),
('posteriorImages', 'inputspec.posteriorImages'),
('tc_atlas2sessionInverse_tx',
'inputspec.TissueClassifyatlasToSubjectInverseTransform'),
('UpdatedPosteriorsList', 'inputspec.UpdatedPosteriorsList'),
('outputHeadLabels', 'inputspec.inputHeadLabels')])
])
if not onlyT1:
baw201.connect([(outputSpec, segWF, [('t1_average', 'inputspec.t2_average')])])
return baw201
def create_longitudinal(project,
subject,
session,
master_config,
interpMode='Linear',
pipeline_name=''):
"""
create longitudinal workflow on a single session
This is the main function to call when processing a data set with T1 & T2
data. ExperimentBaseDirectoryPrefix is the base of the directory to place results, T1Images & T2Images
are the lists of images to be used in the auto-workup. atlas_fname_wpath is
the path and filename of the atlas to use.
"""
from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, Directory
from nipype.interfaces.base import traits, isdefined, BaseInterface
from nipype.interfaces.utility import Split, Rename, IdentityInterface, Function
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from atlasNode import MakeAtlasNode
from baseline import baseline_workflow as create_baseline
baw201 = create_baseline(project,
subject,
session,
master_config,
phase='longitudinal',
interpMode=interpMode,
pipeline_name=pipeline_name)
template_DG = pe.Node(interface=nio.DataGrabber(
infields=['subject'], outfields=['template_t1', 'outAtlasFullPath']),
name='Template_DG')
template_DG.inputs.base_directory = master_config['previousresult']
template_DG.inputs.subject = subject
template_DG.inputs.template = 'SUBJECT_TEMPLATES/%s/AVG_%s.nii.gz'
template_DG.inputs.template_args['template_t1'] = [['subject', 'T1']]
template_DG.inputs.field_template = {
'outAtlasFullPath': 'Atlas/definitions/AtlasDefinition_%s.xml'
}
template_DG.inputs.template_args['outAtlasFullPath'] = [['subject']]
template_DG.inputs.sort_filelist = True
template_DG.inputs.raise_on_empty = True
inputsSpec = baw201.get_node('inputspec')
baw201.connect([
(template_DG, inputsSpec, [('outAtlasFullPath', 'atlasDefinition'),
('template_t1', 'template_t1')]),
])
if 'segmentation' in master_config['components']:
from workflows.segmentation import segmentation
sname = 'segmentation'
# sname = GenerateWFName(project, subject, session, 'segmentation')
onlyT1 = not (len(inputsSpec.inputs.T2s) > 0)
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas')
segWF = segmentation(project,
subject,
session,
master_config,
atlasNode,
onlyT1,
pipeline_name=sname)
outputSpec = baw201.get_node('outputspec')
baw201.connect([(outputSpec, segWF, [
('t1_average', 'inputspec.t1_average'),
('LMIatlasToSubject_tx', 'inputspec.LMIatlasToSubject_tx'),
('outputLabels', 'inputspec.inputLabels'),
('posteriorImages', 'inputspec.posteriorImages'),
('tc_atlas2sessionInverse_tx',
'inputspec.TissueClassifyatlasToSubjectInverseTransform'),
('UpdatedPosteriorsList', 'inputspec.UpdatedPosteriorsList'),
('outputHeadLabels', 'inputspec.inputHeadLabels')
])])
if not onlyT1:
baw201.connect([(outputSpec, segWF, [('t1_average',
'inputspec.t2_average')])])
return baw201
