# Normally something like:
# subjects_dir = os.environ["SUBJECTS_DIR"]
subject_list = ['TMS007']
infosource = pe.Node(interface=util.IdentityInterface(
fields=['subject_id', 'subjects_dir']), name="infosource")
infosource.iterables = ('subject_id', subject_list)
infosource.inputs.subjects_dir = subjects_dir
datasink = pe.Node(interface=nio.DataSink(),
name="datasink")
datasink.inputs.base_directory = op.abspath('structural_datasink')
datasink.inputs.container = 'subject'
preproc = create_structural_mesh_workflow()
struct_proc = pe.Workflow(name="struct_proc")
struct_proc.base_dir = op.abspath('struct_proc')
struct_proc.connect([
(infosource,preproc,[('subject_id', 'inputnode.subject_id')]),
(infosource,preproc,[('subjects_dir', 'inputnode.subjects_dir')]),
])
struct_proc.connect([
(preproc,datasink,[('outputnode.volumes', 'volumes')]),
(preproc,datasink,[('outputnode.surfaces', 'surfaces')]),
(preproc,datasink,[('outputnode.volume_mesh', 'volume_mesh')]),
(preproc,datasink,[('outputnode.t1_fsl_space', 't1_fsl_space')]),
])
datasource.inputs.template = "%s/%s"
datasource.inputs.base_directory = data_path
datasource.inputs.field_template = dict(t2=op.join(data_path,
'mesh/%s%s.nii.gz'),
t2fs=op.join(data_path,
'mesh/%s%s.nii.gz'),
t1=op.join(data_path,
'mesh/%s%s.nii.gz'))
datasource.inputs.template_args = info
datasink = pe.Node(interface=nio.DataSink(), name="datasink")
datasink.inputs.base_directory = op.abspath(name + 'structural_datasink')
datasink.inputs.container = 'subject'
preproc = create_structural_mesh_workflow(include_t1=True,
include_t2=True,
include_t2fs=True)
struct_proc = pe.Workflow(name="struct_proc")
struct_proc.base_dir = op.abspath(name + 'struct_proc')
struct_proc.connect([
(infosource, preproc, [('subject_id', 'inputnode.subject_id')]),
(infosource, preproc, [('subjects_dir', 'inputnode.subjects_dir')]),
(infosource, datasource, [('subject_id', 'subject_id')]),
])
struct_proc.connect([
(datasource, preproc, [('t2', 'inputnode.t2_file')]),
(datasource, preproc, [('t2fs', 'inputnode.t2fs_file')]),
(datasource, preproc, [('t1', 'inputnode.t1_file')]),
])
datasource.inputs.sort_filelist = True
datasource.inputs.template = "%s/%s"
datasource.inputs.base_directory = data_path
datasource.inputs.field_template = dict(
t2=op.join(data_path,'mesh/%s%s.nii.gz'),
t2fs=op.join(data_path,'mesh/%s%s.nii.gz'),
t1=op.join(data_path,'mesh/%s%s.nii.gz'))
datasource.inputs.template_args = info
datasink = pe.Node(interface=nio.DataSink(),
name="datasink")
datasink.inputs.base_directory = op.abspath(name + 'structural_datasink')
datasink.inputs.container = 'subject'
preproc = create_structural_mesh_workflow(include_t1=True, include_t2=True, include_t2fs=True)
struct_proc = pe.Workflow(name="struct_proc")
struct_proc.base_dir = op.abspath(name + 'struct_proc')
struct_proc.connect([
(infosource,preproc,[('subject_id', 'inputnode.subject_id')]),
(infosource,preproc,[('subjects_dir', 'inputnode.subjects_dir')]),
(infosource,datasource,[('subject_id', 'subject_id')]),
])
struct_proc.connect([
(datasource,preproc,[('t2', 'inputnode.t2_file')]),
(datasource,preproc,[('t2fs', 'inputnode.t2fs_file')]),
(datasource,preproc,[('t1', 'inputnode.t1_file')]),
])
# Normally something like:
# subjects_dir = os.environ["SUBJECTS_DIR"]
subject_list = ['TMS007']
infosource = pe.Node(
interface=util.IdentityInterface(fields=['subject_id', 'subjects_dir']),
name="infosource")
infosource.iterables = ('subject_id', subject_list)
infosource.inputs.subjects_dir = subjects_dir
datasink = pe.Node(interface=nio.DataSink(), name="datasink")
datasink.inputs.base_directory = op.abspath('structural_datasink')
datasink.inputs.container = 'subject'
preproc = create_structural_mesh_workflow()
struct_proc = pe.Workflow(name="struct_proc")
struct_proc.base_dir = op.abspath('struct_proc')
struct_proc.connect([
(infosource, preproc, [('subject_id', 'inputnode.subject_id')]),
(infosource, preproc, [('subjects_dir', 'inputnode.subjects_dir')]),
])
struct_proc.connect([
(preproc, datasink, [('outputnode.volumes', 'volumes')]),
(preproc, datasink, [('outputnode.surfaces', 'surfaces')]),
(preproc, datasink, [('outputnode.volume_mesh', 'volume_mesh')]),
(preproc, datasink, [('outputnode.t1_fsl_space', 't1_fsl_space')]),
])
