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_structural():
# main workflow
struct_preproc = Workflow(name='anat_preproc')
#struct_preproc.config['execution']['crashdump_dir'] = struct_preproc.base_dir + "/crash_files"
#inputnode
inputnode = Node(util.IdentityInterface(fields=[
'subject', 'anat', 'out_dir', 'freesurfer_dir', 'standard_brain'
]),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=[
'brain', 'brainmask', 'anat2std_transforms', 'std2anat_transforms',
'anat2std', 'anat_head', 'wmseg', 'wmedge'
]),
name='outputnode')
# workflow to run freesurfer reconall
reconall = create_reconall_pipeline()
# workflow to get brain, head and wmseg from freesurfer and convert to nifti
mgzconvert = create_mgzconvert_pipeline()
normalize = create_normalize_pipeline()
# sink to store files
#sink = Node(nio.DataSink(parameterization=False,
# substitutions=[
# ('transform_Warped', 'T1_brain2mni')]),
# name='sink')
# connections
struct_preproc.connect([
(inputnode, reconall, [('anat', 'inputnode.anat')]),
(inputnode, reconall, [('subject', 'inputnode.fs_subject_id')]),
(inputnode, reconall, [('freesurfer_dir', 'inputnode.fs_subjects_dir')
]),
(reconall, mgzconvert,
[('outputnode.fs_subject_id', 'inputnode.fs_subject_id'),
('outputnode.fs_subjects_dir', 'inputnode.fs_subjects_dir')]),
(inputnode, normalize, [('standard_brain', 'inputnode.standard')]),
(mgzconvert, normalize, [('outputnode.anat_brain', 'inputnode.anat')]),
(normalize, outputnode,
[('outputnode.anat2std', 'anat2std'),
('outputnode.anat2std_transforms', 'anat2std_transforms'),
('outputnode.std2anat_transforms', 'std2anat_transforms')]),
(mgzconvert, outputnode, [('outputnode.anat_brain', 'brain')]),
(mgzconvert, outputnode, [('outputnode.anat_brain_mask', 'brainmask')
]),
(mgzconvert, outputnode, [('outputnode.anat_head', 'anat_head')]),
(mgzconvert, outputnode, [('outputnode.wmseg', 'wmseg')]),
(mgzconvert, outputnode, [('outputnode.wmedge', 'wmedge')])
])
return struct_preproc
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"
# 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(
[(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')]),
(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='CondorDAGMan', plugin_args = {'initial_specs': 'request_memory = 1500'}) #
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"
#########-----------------------------------------------------------#######
#if freesurfer doesn't exists --> run freesurfer additionally, uncomment
######### this section
#########-----------------------------------------------------------#######
# select files
#templates={'anat': 'anat/MPRAGE_t1.nii'}
#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
#########-----------------------------------------------------------#######
#if freesurfer already exists --> start directly with mgzconvert
#########-----------------------------------------------------------#######
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([
#########-----------------------------------------------------------#######
#if freesurfer doesn't exist --> uncomment this section
#########-----------------------------------------------------------#######
#(selectfiles, reconall, [('anat', 'inputnode.anat')]),
#(reconall, mgzconvert, [('outputnode.fs_subject_id', 'inputnode.fs_subject_id'),
# ('outputnode.fs_subjects_dir', 'inputnode.fs_subjects_dir')]),
#########-----------------------------------------------------------#######
#if freesurfer already exists
#########-----------------------------------------------------------#######
(mgzconvert, normalize, [('outputnode.anat_brain', 'inputnode.anat')]),
(mgzconvert, sink, [('outputnode.anat_head',
'preprocessed.mod.anat.@head')]),
(mgzconvert, sink, [('outputnode.anat_brain',
'preprocessed.mod.anat.@brain')]),
(mgzconvert, sink, [('outputnode.anat_brain_mask',
'preprocessed.mod.anat.@mask')]),
(normalize, sink,
[('outputnode.anat2std', 'preprocessed.mod.anat.@anat2std'),
('outputnode.anat2std_transforms',
'preprocessed.mod.anat.transforms2mni.@anat2std_transforms'),
('outputnode.std2anat_transforms',
'preprocessed.mod.anat.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='CondorDAGMan') #
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"
#########-----------------------------------------------------------#######
#if freesurfer doesn't exists --> run freesurfer additionally, uncomment
######### this section
#########-----------------------------------------------------------#######
# select files
#templates={'anat': 'anat/MPRAGE_t1.nii'}
#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
#########-----------------------------------------------------------#######
#if freesurfer already exists --> start directly with mgzconvert
#########-----------------------------------------------------------#######
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(
[
#########-----------------------------------------------------------#######
#if freesurfer doesn't exist --> uncomment this section
#########-----------------------------------------------------------#######
#(selectfiles, reconall, [('anat', 'inputnode.anat')]),
#(reconall, mgzconvert, [('outputnode.fs_subject_id', 'inputnode.fs_subject_id'),
# ('outputnode.fs_subjects_dir', 'inputnode.fs_subjects_dir')]),
#########-----------------------------------------------------------#######
#if freesurfer already exists
#########-----------------------------------------------------------#######
(mgzconvert, normalize, [('outputnode.anat_brain', 'inputnode.anat')]),
(mgzconvert, sink, [('outputnode.anat_head', 'preprocessed.mod.anat.@head')]),
(mgzconvert, sink, [('outputnode.anat_brain', 'preprocessed.mod.anat.@brain')]),
(mgzconvert, sink, [('outputnode.anat_brain_mask', 'preprocessed.mod.anat.@mask')]),
(normalize, sink, [('outputnode.anat2std', 'preprocessed.mod.anat.@anat2std'),
('outputnode.anat2std_transforms', 'preprocessed.mod.anat.transforms2mni.@anat2std_transforms'),
('outputnode.std2anat_transforms', 'preprocessed.mod.anat.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='CondorDAGMan')#
