def legacy(
bids_base,
template,
debug=False,
functional_blur_xy=False,
functional_match={},
keep_work=False,
n_jobs=False,
n_jobs_percentage=0.8,
out_base=None,
realign="time",
registration_mask=False,
sessions=[],
structural_match={},
subjects=[],
tr=1,
workflow_name='legacy',
enforce_dummy_scans=DUMMY_SCANS,
exclude={},
):
'''
Legacy realignment and registration workflow representative of the tweaks and workarounds commonly used in the pre-SAMRI period.
Parameters
----------
bids_base : str
Path to the BIDS data set root.
template : str
Path to the template to register the data to.
debug : bool, optional
Whether to enable nipype debug mode.
This increases logging.
exclude : dict
A dictionary with any combination of "sessions", "subjects", "tasks" as keys and corresponding identifiers as values.
If this is specified matching entries will be excluded in the analysis.
functional_blur_xy : float, optional
Factor by which to smooth data in the xy-plane; if parameter evaluates to false, no smoothing will be applied.
Ideally this value should correspond to the resolution or smoothness in the z-direction (assuing z represents the lower-resolution slice-encoding direction).
functional_match : dict, optional
Dictionary specifying a whitelist to use for functional data inclusion into the workflow; if dictionary is empty no whitelist is present and all data will be considered.
The dictionary should have keys which are 'acquisition', 'task', or 'modality', and values which are lists of acceptable strings for the respective BIDS field.
keep_work : bool, str
Whether to keep the work directory after workflow conclusion (this directory contains all the intermediary processing commands, inputs, and outputs --- it is invaluable for debugging but many times larger in size than the actual output).
n_jobs : int, optional
Number of processors to maximally use for the workflow; if unspecified a best guess will be estimate based on `n_jobs_percentage` and hardware (but not on current load).
n_jobs_percentage : float, optional
Percentage of available processors (as in available hardware, not available free load) to maximally use for the workflow (this is overriden by `n_jobs`).
out_base : str, optional
Output base directory - inside which a directory named `workflow_name` (as well as associated directories) will be created.
realign : {"space","time","spacetime",""}, optional
Parameter that dictates slictiming correction and realignment of slices. "time" (FSL.SliceTimer) is default, since it works safely. Use others only with caution!
registration_mask : str, optional
Mask to use for the registration process.
This mask will constrain the area for similarity metric evaluation, but the data will not be cropped.
sessions : list, optional
A whitelist of sessions to include in the workflow, if the list is empty there is no whitelist and all sessions will be considered.
structural_match : dict, optional
Dictionary specifying a whitelist to use for structural data inclusion into the workflow; if dictionary is empty no whitelist is present and all data will be considered.
The dictionary should have keys which are 'acquisition', or 'modality', and values which are lists of acceptable strings for the respective BIDS field.
subjects : list, optional
A whitelist of subjects to include in the workflow, if the list is empty there is no whitelist and all sessions will be considered.
tr : float, optional
Repetition time, explicitly.
WARNING! This is a parameter waiting for deprecation.
workflow_name : str, optional
Top level name for the output directory.
'''
try:
import nipype.interfaces.ants.legacy as antslegacy
except ModuleNotFoundError:
print('''
The `nipype.interfaces.ants.legacy` was not found on this system.
You may want to downgrade nipype to e.g. 1.1.1, as this module has been removed in more recent versions:
https://github.com/nipy/nipype/issues/3197
''')
bids_base, out_base, out_dir, template, registration_mask, data_selection, functional_scan_types, structural_scan_types, subjects_sessions, func_ind, struct_ind = common_select(
bids_base,
out_base,
workflow_name,
template,
registration_mask,
functional_match,
structural_match,
subjects,
sessions,
exclude,
)
if not n_jobs:
n_jobs = max(int(round(mp.cpu_count() * n_jobs_percentage)), 2)
get_f_scan = pe.Node(name='get_f_scan',
interface=util.Function(
function=get_bids_scan,
input_names=inspect.getargspec(get_bids_scan)[0],
output_names=[
'scan_path', 'scan_type', 'task', 'nii_path',
'nii_name', 'events_name', 'subject_session',
'metadata_filename', 'dict_slice', 'ind_type'
]))
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = data_selection
get_f_scan.inputs.bids_base = bids_base
get_f_scan.iterables = ("ind_type", func_ind)
dummy_scans = pe.Node(
name='dummy_scans',
interface=util.Function(
function=force_dummy_scans,
input_names=inspect.getargspec(force_dummy_scans)[0],
output_names=['out_file', 'deleted_scans']))
dummy_scans.inputs.desired_dummy_scans = enforce_dummy_scans
events_file = pe.Node(
name='events_file',
interface=util.Function(
function=write_bids_events_file,
input_names=inspect.getargspec(write_bids_events_file)[0],
output_names=['out_file']))
temporal_mean = pe.Node(interface=fsl.MeanImage(), name="temporal_mean")
f_resize = pe.Node(interface=VoxelResize(), name="f_resize")
f_resize.inputs.resize_factors = [10, 10, 10]
f_percentile = pe.Node(interface=fsl.ImageStats(), name="f_percentile")
f_percentile.inputs.op_string = '-p 98'
f_threshold = pe.Node(interface=fsl.Threshold(), name="f_threshold")
f_fast = pe.Node(interface=fsl.FAST(), name="f_fast")
f_fast.inputs.no_pve = True
f_fast.inputs.output_biascorrected = True
f_bet = pe.Node(interface=fsl.BET(), name="f_BET")
f_swapdim = pe.Node(interface=fsl.SwapDimensions(), name="f_swapdim")
f_swapdim.inputs.new_dims = ('x', '-z', '-y')
f_deleteorient = pe.Node(interface=FSLOrient(), name="f_deleteorient")
f_deleteorient.inputs.main_option = 'deleteorient'
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = out_dir
datasink.inputs.parameterization = False
workflow_connections = [
(get_f_scan, dummy_scans, [('nii_path', 'in_file')]),
(dummy_scans, events_file, [('deleted_scans', 'forced_dummy_scans')]),
(dummy_scans, f_resize, [('out_file', 'in_file')]),
(get_f_scan, events_file, [('nii_path', 'timecourse_file'),
('task', 'task'),
('scan_path', 'scan_dir')]),
(events_file, datasink, [('out_file', 'func.@events')]),
(get_f_scan, events_file, [('events_name', 'out_file')]),
(get_f_scan, datasink, [(('subject_session', ss_to_path), 'container')
]),
(temporal_mean, f_percentile, [('out_file', 'in_file')]),
# here we divide by 10 assuming 10 percent noise
(f_percentile, f_threshold, [(('out_stat', divideby_10), 'thresh')]),
(temporal_mean, f_threshold, [('out_file', 'in_file')]),
(f_threshold, f_fast, [('out_file', 'in_files')]),
(f_fast, f_bet, [('restored_image', 'in_file')]),
(f_resize, f_deleteorient, [('out_file', 'in_file')]),
(f_deleteorient, f_swapdim, [('out_file', 'in_file')]),
]
if realign == "space":
realigner = pe.Node(interface=spm.Realign(), name="realigner")
realigner.inputs.register_to_mean = True
workflow_connections.extend([
(f_swapdim, realigner, [('out_file', 'in_file')]),
])
elif realign == "spacetime":
realigner = pe.Node(interface=nipy.SpaceTimeRealigner(),
name="realigner")
realigner.inputs.slice_times = "asc_alt_2"
realigner.inputs.tr = tr
realigner.inputs.slice_info = 3 #3 for coronal slices (2 for horizontal, 1 for sagittal)
workflow_connections.extend([
(f_swapdim, realigner, [('out_file', 'in_file')]),
])
elif realign == "time":
realigner = pe.Node(interface=fsl.SliceTimer(), name="slicetimer")
realigner.inputs.time_repetition = tr
workflow_connections.extend([
(f_swapdim, realigner, [('out_file', 'in_file')]),
])
f_antsintroduction = pe.Node(interface=antslegacy.antsIntroduction(),
name='ants_introduction')
f_antsintroduction.inputs.dimension = 3
f_antsintroduction.inputs.reference_image = template
#will need updating to `1`
f_antsintroduction.inputs.bias_field_correction = True
f_antsintroduction.inputs.transformation_model = 'GR'
f_antsintroduction.inputs.max_iterations = [8, 15, 8]
f_warp = pe.Node(interface=ants.WarpTimeSeriesImageMultiTransform(),
name='f_warp')
f_warp.inputs.reference_image = template
f_warp.inputs.dimension = 4
f_copysform2qform = pe.Node(interface=FSLOrient(),
name='f_copysform2qform')
f_copysform2qform.inputs.main_option = 'copysform2qform'
warp_merge = pe.Node(util.Merge(2), name='warp_merge')
workflow_connections.extend([
(f_bet, f_antsintroduction, [('out_file', 'input_image')]),
(f_antsintroduction, warp_merge, [('warp_field', 'in1')]),
(f_antsintroduction, warp_merge, [('affine_transformation', 'in2')]),
(warp_merge, f_warp, [('out', 'transformation_series')]),
(f_warp, f_copysform2qform, [('output_image', 'in_file')]),
])
if realign == "space":
workflow_connections.extend([
(realigner, temporal_mean, [('realigned_files', 'in_file')]),
(realigner, f_warp, [('realigned_files', 'input_image')]),
])
elif realign == "spacetime":
workflow_connections.extend([
(realigner, temporal_mean, [('out_file', 'in_file')]),
(realigner, f_warp, [('out_file', 'input_image')]),
])
elif realign == "time":
workflow_connections.extend([
(realigner, temporal_mean, [('slice_time_corrected_file',
'in_file')]),
(realigner, f_warp, [('slice_time_corrected_file', 'input_image')
]),
])
else:
workflow_connections.extend([
(f_resize, temporal_mean, [('out_file', 'in_file')]),
(f_swapdim, f_warp, [('out_file', 'input_image')]),
])
if functional_blur_xy:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(get_f_scan, blur, [('nii_name', 'out_file')]),
(f_copysform2qform, blur, [('out_file', 'in_file')]),
(blur, datasink, [('out_file', 'func')]),
])
else:
f_rename = pe.Node(util.Rename(), name='f_rename')
workflow_connections.extend([
(get_f_scan, f_rename, [('nii_name', 'format_string')]),
(f_copysform2qform, f_rename, [('out_file', 'in_file')]),
(f_rename, datasink, [('out_file', 'func')]),
])
workflow_config = {
'execution': {
'crashdump_dir': path.join(out_base, 'crashdump'),
}
}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workdir_name = workflow_name + "_work"
#this gives the name of the workdir, the output name is passed to the datasink
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = out_base
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,
workdir_name, "graph.dot"),
graph2use="hierarchical",
format="png")
except OSError:
print(
'We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.'
)
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_jobs})
copy_bids_files(bids_base, os.path.join(out_base, workflow_name))
if not keep_work:
workdir = path.join(workflow.base_dir, workdir_name)
try:
shutil.rmtree(workdir)
except OSError as e:
if str(e) == 'Cannot call rmtree on a symbolic link':
print(
'Not deleting top level workdir (`{}`), as it is a symlink. Deleting only contents instead'
.format(workdir))
for file_object in os.listdir(workdir):
file_object_path = os.path.join(workdir, file_object)
if os.path.isfile(file_object_path):
os.unlink(file_object_path)
else:
shutil.rmtree(file_object_path)
else:
raise OSError(str(e))
def create_apply_ants_xfm(dimension, mapnode, name='apply_ants_xfm'):
"""
Takes in the results of the FSL-based functional-to-anatomical registration,
and the results of the ANTS-based anatomical-to-template registration, and
applies these transformations to register functional to template.
The FSL-based functional-to-anatomical registration output transformations
are first converted from FSL format to ITK format - this step can and
should be separated into their own workflows in the future.
NOTE: The dimension of the input image (3 or 4) must be specified in the
function call, as well as whether or not the apply warp must be
treated as a mapnode (0 - no, 1 - yes).
Parameters
----------
name : string, optional
Name of the workflow.
Returns
-------
apply_ants_xfm : nipype.pipeline.engine.Workflow
Notes
-----
Workflow Inputs::
inputspec.in_file : string (nifti file)
File of functional brain data to be registered
inputspec.warp_reference : string (nifti file)
File of template to be used
inputspec.use_nearest : boolean (True or False)
Whether or not to use nearest neighbor interpolation
inputspec.func_anat_affine : .mat file (affine matrix)
Output matrix of FSL-based functional to anatomical registration
inputspec.conversion_reference : string (nifti file)
File of skull-stripped anatomical brain to be used in affine conversion
inputspec.conversion_source : string (nifti file)
Should match the input of the apply warp (in_file) unless you are
applying the warp to a 4-d file, in which case this file should
be a mean_functional file
inputspec.nonlinear_field : string (nifti file)
Output field file of the anatomical to template ANTS registration
inputspec.ants_affine : text file
Output matrix of the anatomical to template ANTS registration
Workflow Outputs::
outputspec.out_file : string (nifti file)
Normalizion of input functional file
Registration Procedure:
1. Convert the FSL-based functional-to-anatomical output affine matrix into ANTS (ITK) format.
2. Collect this converted affine, and the ants_affine.txt and nonlinear field file from
the anatomical-to-template ANTS registration into one transformation series string.
3. Apply the warp to the input file using WarpImageMultiTransform (for 3d files) or
WarpTimeSeriesImageMultiTransform (for 4d files with timeseries).
Workflow Graph:
.. image::
:width: 500
Detailed Workflow Graph:
.. image::
:width: 500
"""
apply_ants_xfm = pe.Workflow(name=name)
inputspec = pe.Node(util.IdentityInterface(fields=[
'warp_reference', 'in_file', 'use_nearest', 'func_anat_affine',
'conversion_reference', 'conversion_source', 'nonlinear_field',
'ants_affine'
]),
name='inputspec')
outputspec = pe.Node(util.IdentityInterface(fields=['out_file']),
name='outputspec')
if dimension == 4:
if mapnode == 0:
# converts FSL-format .mat affine xfm into ANTS-format .txt
# .mat affine comes from Func->Anat registration
fsl_reg_2_itk = create_fsl_to_itk_conversion(
mapnode, 'fsl_reg_2_itk')
#collects series of transformations to be applied to the moving images
collect_transforms = pe.Node(util.Merge(3),
name='collect_transforms')
# performs series of transformations on moving images
warp_images = pe.Node(
interface=ants.WarpTimeSeriesImageMultiTransform(),
name='ants_apply_4d_warp')
warp_images.inputs.dimension = 4
apply_ants_xfm.connect(inputspec, 'warp_reference', warp_images,
'reference_image')
apply_ants_xfm.connect(inputspec, 'use_nearest', warp_images,
'use_nearest')
elif mapnode == 1:
# in this case with 4-d images (timeseries), fsl_reg_2_itk and collect_transforms are not
# map nodes due to the fact that the affine conversion (fsl_reg_2_itk) cannot take in a
# 4-d image as its conversion_source (ordinarily the input image and the conversion source
# are the same image, however with timeseries, mean_functional should be used as the
# conversion source and the 4-d image used as the input image to the apply warp.
# (this is why in_file and conversion_source are separated into two inputs)
# converts FSL-format .mat affine xfm into ANTS-format .txt
# .mat affine comes from Func->Anat registration
fsl_reg_2_itk = create_fsl_to_itk_conversion(
mapnode, 'fsl_reg_2_itk')
#collects series of transformations to be applied to the moving images
collect_transforms = pe.Node(util.Merge(3),
name='collect_transforms')
# performs series of transformations on moving images
warp_images = pe.MapNode(
interface=ants.WarpTimeSeriesImageMultiTransform(),
name='ants_apply_4d_warp',
iterfield=['in_file'])
warp_images.inputs.dimension = 4
apply_ants_xfm.connect(inputspec, 'warp_reference', warp_images,
'reference_image')
apply_ants_xfm.connect(inputspec, 'use_nearest', warp_images,
'use_nearest')
elif dimension == 3:
if mapnode == 0:
# converts FSL-format .mat affine xfm into ANTS-format .txt
# .mat affine comes from Func->Anat registration
fsl_reg_2_itk = create_fsl_to_itk_conversion(
mapnode, 'fsl_reg_2_itk')
#collects series of transformations to be applied to the moving images
collect_transforms = pe.Node(util.Merge(3),
name='collect_transforms')
# performs series of transformations on moving images
warp_images = pe.Node(interface=ants.WarpImageMultiTransform(),
name='apply_ants_3d_warp')
warp_images.inputs.dimension = 3
apply_ants_xfm.connect(inputspec, 'warp_reference', warp_images,
'reference_image')
apply_ants_xfm.connect(inputspec, 'use_nearest', warp_images,
'use_nearest')
elif mapnode == 1:
# converts FSL-format .mat affine xfm into ANTS-format .txt
# .mat affine comes from Func->Anat registration
fsl_reg_2_itk = create_fsl_to_itk_conversion(
mapnode, 'fsl_reg_2_itk')
#collects series of transformations to be applied to the moving images
collect_transforms = pe.MapNode(util.Merge(3),
name='collect_transforms',
iterfield=['in3'])
# performs series of transformations on moving images
warp_images = pe.MapNode(
interface=ants.WarpImageMultiTransform(),
name='apply_ants_3d_warp',
iterfield=['input_image', 'transformation_series'])
warp_images.inputs.dimension = 3
apply_ants_xfm.connect(inputspec, 'warp_reference', warp_images,
'reference_image')
apply_ants_xfm.connect(inputspec, 'use_nearest', warp_images,
'use_nearest')
# convert the .mat from linear Func->Anat to ANTS format
apply_ants_xfm.connect(inputspec, 'func_anat_affine', fsl_reg_2_itk,
'inputspec.transform_file')
apply_ants_xfm.connect(inputspec, 'conversion_reference', fsl_reg_2_itk,
'inputspec.reference_file')
apply_ants_xfm.connect(inputspec, 'conversion_source', fsl_reg_2_itk,
'inputspec.source_file')
# Premat from Func->Anat linear reg and bbreg (if bbreg is enabled)
apply_ants_xfm.connect(fsl_reg_2_itk, 'outputspec.itk_transform',
collect_transforms, 'in3')
# Field file from anatomical nonlinear registration
apply_ants_xfm.connect(inputspec, 'nonlinear_field', collect_transforms,
'in1')
# affine transformation from anatomical registration
apply_ants_xfm.connect(inputspec, 'ants_affine', collect_transforms, 'in2')
apply_ants_xfm.connect(inputspec, 'in_file', warp_images, 'input_image')
apply_ants_xfm.connect(collect_transforms, 'out', warp_images,
'transformation_series')
apply_ants_xfm.connect(warp_images, 'output_image', outputspec, 'out_file')
return apply_ants_xfm
def get_post_struct_norm_workflow(name='normalize_post_struct'):
""" Base post-structural workflow for normalization
Parameters
----------
name : name of workflow. Default = 'normalize_post_struct'
Inputs
------
inputspec.template_file :
inputspec.unwarped_brain :
inputspec.warp_field :
inputspec.affine_transformation :
inputspec.out_fsl_file :
inputspec.moving_image :
inputspec.mean_func :
inputspec.use_nearest:
Outputs
-------
outputspec.warped_image :
Returns
-------
workflow : post-structural normalization workflow
"""
#inputs to workflow
import nipype.interfaces.freesurfer as fs
import nipype.interfaces.ants as ants
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
inputspec = pe.Node(util.IdentityInterface(fields=[
'template_file', 'unwarped_brain', 'warp_field',
'affine_transformation', 'out_fsl_file', 'moving_image', 'mean_func',
"use_nearest"
]),
name='inputspec')
#makes fsl-style coregistration ANTS compatible
fsl_reg_2_itk = pe.Node(c3.C3dAffineTool(fsl2ras=True),
name='fsl_reg_2_itk')
#collects series of transformations to be applied to the moving images
collect_transforms = pe.Node(util.Merge(3), name='collect_transforms')
#performs series of transformations on moving images
warp_images = pe.MapNode(ants.WarpTimeSeriesImageMultiTransform(),
name='warp_images',
iterfield=['input_image', 'dimension'])
#collects workflow outputs
outputspec = pe.Node(util.IdentityInterface(fields=['warped_image']),
name='outputspec')
#initializes and connects workflow nodes
normalize_post_struct = pe.Workflow(name=name)
normalize_post_struct.connect([
(inputspec, fsl_reg_2_itk, [('unwarped_brain', 'reference_file')]),
(inputspec, fsl_reg_2_itk, [('out_fsl_file', 'transform_file')]),
(inputspec, fsl_reg_2_itk, [('mean_func', 'source_file')]),
(fsl_reg_2_itk, collect_transforms, [('itk_transform', 'in3')]),
(inputspec, collect_transforms, [('warp_field', 'in1'),
('affine_transformation', 'in2')]),
(inputspec, warp_images, [('moving_image', 'input_image')]),
(inputspec, warp_images, [(('moving_image', get_image_dimensions),
'dimension')]),
(inputspec, warp_images, [('template_file', 'reference_image'),
('use_nearest', 'use_nearest')]),
(collect_transforms, warp_images, [('out', 'transformation_series')]),
(warp_images, outputspec, [('output_image', 'warped_image')])
])
return normalize_post_struct
def legacy(
bids_base,
template,
autorotate=False,
debug=False,
functional_blur_xy=False,
functional_match={},
keep_work=False,
negative_contrast_agent=False,
n_procs=N_PROCS,
out_base=None,
realign="time",
registration_mask=False,
sessions=[],
structural_match={},
subjects=[],
tr=1,
workflow_name='legacy',
):
'''
Legacy realignment and registration workflow representative of the tweaks and workarounds commonly used in the pre-SAMRI period.
Parameters
----------
bids_base : str
Path to the BIDS data set root.
template : str
Path to the template to register the data to.
autorotate : bool, optional
Whether to use a multi-rotation-state transformation start.
This allows the registration to commence with the best rotational fit, and may help if the orientation of the data is malformed with respect to the header.
debug : bool, optional
Whether to enable nipype debug mode.
This increases logging.
functional_blur_xy : float, optional
Factor by which to smooth data in the xy-plane; if parameter evaluates to false, no smoothing will be applied.
Ideally this value should correspond to the resolution or smoothness in the z-direction (assuing z represents the lower-resolution slice-encoding direction).
functional_match : dict, optional
Dictionary specifying a whitelist to use for functional data inclusion into the workflow; if dictionary is empty no whitelist is present and all data will be considered.
The dictionary should have keys which are 'acquisition', 'task', or 'modality', and values which are lists of acceptable strings for the respective BIDS field.
keep_work : bool, str
Whether to keep the work directory after workflow conclusion (this directory contains all the intermediary processing commands, inputs, and outputs --- it is invaluable for debugging but many times larger in size than the actual output).
negative_contrast_agent : bool, optional
Whether the scan was acquired witn a negative contrast agent given the imaging modality; if true the values will be inverted with respect to zero.
This is commonly used for iron nano-particle Cerebral Blood Volume (CBV) measurements.
n_procs : int, optional
Number of processors to maximally use for the workflow; if unspecified a best guess will be estimate based on hardware (but not on current load).
out_base : str, optional
Output base directory --- inside which a directory named `workflow_name` (as well as associated directories) will be created.
realign : {"space","time","spacetime",""}, optional
Parameter that dictates slictiming correction and realignment of slices. "time" (FSL.SliceTimer) is default, since it works safely. Use others only with caution!
registration_mask : str, optional
Mask to use for the registration process.
This mask will constrain the area for similarity metric evaluation, but the data will not be cropped.
sessions : list, optional
A whitelist of sessions to include in the workflow, if the list is empty there is no whitelist and all sessions will be considered.
structural_match : dict, optional
Dictionary specifying a whitelist to use for structural data inclusion into the workflow; if dictionary is empty no whitelist is present and all data will be considered.
The dictionary should have keys which are 'acquisition', or 'modality', and values which are lists of acceptable strings for the respective BIDS field.
subjects : list, optional
A whitelist of subjects to include in the workflow, if the list is empty there is no whitelist and all sessions will be considered.
tr : float, optional
Repetition time, explicitly.
WARNING! This is a parameter waiting for deprecation.
workflow_name : str, optional
Top level name for the output directory.
'''
bids_base, out_base, out_dir, template, registration_mask, data_selection, functional_scan_types, structural_scan_types, subjects_sessions, func_ind, struct_ind = common_select(
bids_base,
out_base,
workflow_name,
template,
registration_mask,
functional_match,
structural_match,
subjects,
sessions,
)
get_f_scan = pe.Node(name='get_f_scan',
interface=util.Function(
function=get_bids_scan,
input_names=inspect.getargspec(get_bids_scan)[0],
output_names=[
'scan_path', 'scan_type', 'task', 'nii_path',
'nii_name', 'file_name', 'events_name',
'subject_session'
]))
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = data_selection
get_f_scan.inputs.bids_base = bids_base
get_f_scan.iterables = ("ind_type", func_ind)
dummy_scans = pe.Node(
name='dummy_scans',
interface=util.Function(
function=force_dummy_scans,
input_names=inspect.getargspec(force_dummy_scans)[0],
output_names=['out_file', 'deleted_scans']))
dummy_scans.inputs.desired_dummy_scans = DUMMY_SCANS
events_file = pe.Node(
name='events_file',
interface=util.Function(
function=write_bids_events_file,
input_names=inspect.getargspec(write_bids_events_file)[0],
output_names=['out_file']))
temporal_mean = pe.Node(interface=fsl.MeanImage(), name="temporal_mean")
f_resize = pe.Node(interface=VoxelResize(), name="f_resize")
f_resize.inputs.resize_factors = [10, 10, 10]
f_percentile = pe.Node(interface=fsl.ImageStats(), name="f_percentile")
f_percentile.inputs.op_string = '-p 98'
f_threshold = pe.Node(interface=fsl.Threshold(), name="f_threshold")
f_fast = pe.Node(interface=fsl.FAST(), name="f_fast")
f_fast.inputs.no_pve = True
f_fast.inputs.output_biascorrected = True
f_bet = pe.Node(interface=fsl.BET(), name="f_BET")
f_swapdim = pe.Node(interface=fsl.SwapDimensions(), name="f_swapdim")
f_swapdim.inputs.new_dims = ('x', '-z', '-y')
f_deleteorient = pe.Node(interface=FSLOrient(), name="f_deleteorient")
f_deleteorient.inputs.main_option = 'deleteorient'
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = out_dir
datasink.inputs.parameterization = False
workflow_connections = [
(get_f_scan, dummy_scans, [('nii_path', 'in_file')]),
(get_f_scan, dummy_scans, [('scan_path', 'scan_dir')]),
(dummy_scans, events_file, [('deleted_scans', 'forced_dummy_scans')]),
(dummy_scans, f_resize, [('out_file', 'in_file')]),
(get_f_scan, events_file, [('nii_path', 'timecourse_file'),
('task', 'task'),
('scan_path', 'scan_dir')]),
(events_file, datasink, [('out_file', 'func.@events')]),
(get_f_scan, events_file, [('events_name', 'out_file')]),
(get_f_scan, datasink, [(('subject_session', ss_to_path), 'container')
]),
(temporal_mean, f_percentile, [('out_file', 'in_file')]),
# here we divide by 10 assuming 10 percent noise
(f_percentile, f_threshold, [(('out_stat', divideby_10), 'thresh')]),
(temporal_mean, f_threshold, [('out_file', 'in_file')]),
(f_threshold, f_fast, [('out_file', 'in_files')]),
(f_fast, f_bet, [('restored_image', 'in_file')]),
(f_resize, f_deleteorient, [('out_file', 'in_file')]),
(f_deleteorient, f_swapdim, [('out_file', 'in_file')]),
]
if realign == "space":
realigner = pe.Node(interface=spm.Realign(), name="realigner")
realigner.inputs.register_to_mean = True
workflow_connections.extend([
(f_swapdim, realigner, [('out_file', 'in_file')]),
])
elif realign == "spacetime":
realigner = pe.Node(interface=nipy.SpaceTimeRealigner(),
name="realigner")
realigner.inputs.slice_times = "asc_alt_2"
realigner.inputs.tr = tr
realigner.inputs.slice_info = 3 #3 for coronal slices (2 for horizontal, 1 for sagittal)
workflow_connections.extend([
(f_swapdim, realigner, [('out_file', 'in_file')]),
])
elif realign == "time":
realigner = pe.Node(interface=fsl.SliceTimer(), name="slicetimer")
realigner.inputs.time_repetition = tr
workflow_connections.extend([
(f_swapdim, realigner, [('out_file', 'in_file')]),
])
#if structural_scan_types.any():
# get_s_scan = pe.Node(name='get_s_scan', interface=util.Function(function=get_bids_scan, input_names=inspect.getargspec(get_bids_scan)[0], output_names=['scan_path','scan_type','task', 'nii_path', 'nii_name', 'file_name', 'events_name', 'subject_session']))
# get_s_scan.inputs.ignore_exception = True
# get_s_scan.inputs.data_selection = data_selection
# get_s_scan.inputs.bids_base = bids_base
# s_cutoff = pe.Node(interface=fsl.ImageMaths(), name="s_cutoff")
# s_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
# s_resize = pe.Node(interface=VoxelResize(), name="s_resize")
# s_BET = pe.Node(interface=fsl.BET(), name="s_BET")
# s_BET.inputs.mask = True
# s_BET.inputs.frac = 0.3
# s_BET.inputs.robust = True
# ants_introduction = pe.Node(interface=legacy.antsIntroduction(), name='ants_introduction')
# ants_introduction.inputs.dimension = 3
# ants_introduction.inputs.reference_image = template
# #will need updating to `1`
# ants_introduction.inputs.bias_field_correction = True
# ants_introduction.inputs.transformation_model = 'GR'
# ants_introduction.inputs.max_iterations = [8,15,8]
# s_mask = pe.Node(interface=fsl.ApplyMask(), name="s_mask")
# s_register, s_warp, f_warp = structural_registration(template)
# workflow_connections.extend([
# (get_s_scan, s_reg_biascorrect, [('nii_path', 'input_image')]),
# (s_reg_biascorrect, s_cutoff, [('output_image', 'in_file')]),
# (s_cutoff, s_BET, [('out_file', 'in_file')]),
# (s_biascorrect, s_mask, [('output_image', 'in_file')]),
# (s_BET, s_mask, [('mask_file', 'mask_file')]),
# ])
# #TODO: incl. in func registration
# if autorotate:
# workflow_connections.extend([
# (s_mask, s_rotated, [('out_file', 'out_file')]),
# (s_rotated, s_register, [('out_file', 'moving_image')]),
# ])
# else:
# workflow_connections.extend([
# (s_mask, s_register, [('out_file', 'moving_image')]),
# (s_register, s_warp, [('composite_transform', 'transforms')]),
# (get_s_scan, s_warp, [('nii_path', 'input_image')]),
# (s_warp, datasink, [('output_image', 'anat')]),
# ])
# if autorotate:
# s_rotated = autorotate(template)
# workflow_connections.extend([
# (get_f_scan, get_s_scan, [('subject_session', 'selector')]),
# (get_s_scan, s_warp, [('nii_name','output_image')]),
# (get_s_scan, s_biascorrect, [('nii_path', 'input_image')]),
# ])
f_antsintroduction = pe.Node(interface=antslegacy.antsIntroduction(),
name='ants_introduction')
f_antsintroduction.inputs.dimension = 3
f_antsintroduction.inputs.reference_image = template
#will need updating to `1`
f_antsintroduction.inputs.bias_field_correction = True
f_antsintroduction.inputs.transformation_model = 'GR'
f_antsintroduction.inputs.max_iterations = [8, 15, 8]
f_warp = pe.Node(interface=ants.WarpTimeSeriesImageMultiTransform(),
name='f_warp')
f_warp.inputs.reference_image = template
f_warp.inputs.dimension = 4
f_copysform2qform = pe.Node(interface=FSLOrient(),
name='f_copysform2qform')
f_copysform2qform.inputs.main_option = 'copysform2qform'
warp_merge = pe.Node(util.Merge(2), name='warp_merge')
workflow_connections.extend([
(f_bet, f_antsintroduction, [('out_file', 'input_image')]),
(f_antsintroduction, warp_merge, [('warp_field', 'in1')]),
(f_antsintroduction, warp_merge, [('affine_transformation', 'in2')]),
(warp_merge, f_warp, [('out', 'transformation_series')]),
(f_warp, f_copysform2qform, [('output_image', 'in_file')]),
])
if realign == "space":
workflow_connections.extend([
(realigner, temporal_mean, [('realigned_files', 'in_file')]),
(realigner, f_warp, [('realigned_files', 'input_image')]),
])
elif realign == "spacetime":
workflow_connections.extend([
(realigner, temporal_mean, [('out_file', 'in_file')]),
(realigner, f_warp, [('out_file', 'input_image')]),
])
elif realign == "time":
workflow_connections.extend([
(realigner, temporal_mean, [('slice_time_corrected_file',
'in_file')]),
(realigner, f_warp, [('slice_time_corrected_file', 'input_image')
]),
])
else:
workflow_connections.extend([
(f_resize, temporal_mean, [('out_file', 'in_file')]),
(f_swapdim, f_warp, [('out_file', 'input_image')]),
])
invert = pe.Node(interface=fsl.ImageMaths(), name="invert")
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
if functional_blur_xy and negative_contrast_agent:
workflow_connections.extend([
(f_copysform2qform, blur, [('out_file', 'in_file')]),
(blur, invert, [(('out_file', fslmaths_invert_values), 'op_string')
]),
(blur, invert, [('out_file', 'in_file')]),
(get_f_scan, invert, [('nii_name', 'output_image')]),
(invert, datasink, [('out_file', 'func')]),
])
elif functional_blur_xy:
workflow_connections.extend([
(get_f_scan, blur, [('nii_name', 'output_image')]),
(f_copysform2qform, blur, [('out_file', 'in_file')]),
(blur, datasink, [('out_file', 'func')]),
])
elif negative_contrast_agent:
workflow_connections.extend([
(get_f_scan, invert, [('nii_name', 'out_file')]),
(f_copysform2qform, invert, [(('out_file', fslmaths_invert_values),
'op_string')]),
(f_copysform2qform, invert, [('out_file', 'in_file')]),
(invert, datasink, [('out_file', 'func')]),
])
else:
f_rename = pe.Node(util.Rename(), name='f_rename')
workflow_connections.extend([
(get_f_scan, f_rename, [('nii_name', 'format_string')]),
(f_copysform2qform, f_rename, [('out_file', 'in_file')]),
(f_rename, datasink, [('out_file', 'func')]),
])
workflow_config = {
'execution': {
'crashdump_dir': path.join(bids_base, 'preprocessing/crashdump'),
}
}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workdir_name = workflow_name + "_work"
#this gives the name of the workdir, the output name is passed to the datasink
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = out_base
workflow.config = workflow_config
workflow.write_graph(dotfilename=path.join(workflow.base_dir, workdir_name,
"graph.dot"),
graph2use="hierarchical",
format="png")
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
if not keep_work:
workdir = path.join(workflow.base_dir, workdir_name)
try:
shutil.rmtree(workdir)
except OSError as e:
if str(e) == 'Cannot call rmtree on a symbolic link':
print(
'Not deleting top level workdir (`{}`), as it is a symlink. Deleting only contents instead'
.format(workdir))
for file_object in os.listdir(workdir):
file_object_path = os.path.join(workdir, file_object)
if os.path.isfile(file_object_path):
os.unlink(file_object_path)
else:
shutil.rmtree(file_object_path)
else:
raise OSError(str(e))
preproc.connect(fsl2ras_downsample_atlas_from_struct_to_func, 'itk_transform', cmb_tfm_func_to_ds_atlas, 'in1')
# from structural to atlas (with struct resolution)
preproc.connect(structs_to_atlas_coreg_output, ('forward_transforms', get_sec), cmb_tfm_func_to_ds_atlas, 'in2')
preproc.connect(structs_to_atlas_coreg_output, ('forward_transforms', get_first), cmb_tfm_func_to_ds_atlas, 'in3')
# transform from functional to structural
#preproc.connect(ants_mbRef_to_t2_output, ('forward_transforms', get_sec), cmb_tfm_func_to_ds_atlas, 'in4')
preproc.connect(sep_tfms, 'out_list', cmb_tfm_func_to_ds_atlas, 'in4')
# apply transformation from mbRef all the way to caltech atlas (in func resolution)
mbRef_to_ds_atlas = pe.MapNode(interface=ants.WarpImageMultiTransform(use_nearest = True), name = 'mbRef_to_ds_atlas', iterfield=['input_image', 'transformation_series'])
preproc.connect(mask_mbRef, 'out_file', mbRef_to_ds_atlas, 'input_image')
preproc.connect(downsample_atlas_t2_to_func, 'out_file', mbRef_to_ds_atlas, 'reference_image')
preproc.connect(cmb_tfm_func_to_ds_atlas, 'out', mbRef_to_ds_atlas, 'transformation_series')
# apply transformation to 4D func
func_to_ds_atlas = pe.MapNode(interface=ants.WarpTimeSeriesImageMultiTransform(use_nearest = True), name = 'func_to_ds_atlas', iterfield=['transformation_series','input_image'])
preproc.connect(unwarp_func, 'unwarped_file', func_to_ds_atlas, 'input_image')
preproc.connect(downsample_atlas_t2_to_func, 'out_file', func_to_ds_atlas, 'reference_image')
preproc.connect(cmb_tfm_func_to_ds_atlas, 'out', func_to_ds_atlas, 'transformation_series')
# combine transformations (t2 to atlas)
cmb_tfm_t2_to_ds_atlas = pe.Node(interface=util.Merge(3, axis='hstack'), name='cmb_tfm_t2_to_ds_atlas')
# from structural to atlas (with struct resolution)
preproc.connect(structs_to_atlas_coreg_output, ('forward_transforms', get_sec), cmb_tfm_t2_to_ds_atlas, 'in1')
preproc.connect(structs_to_atlas_coreg_output, ('forward_transforms', get_first), cmb_tfm_t2_to_ds_atlas, 'in2')
# from atlas in struct resolution to t2 resolution
preproc.connect(fsl2ras_downsample_atlas_from_struct_to_func, 'itk_transform', cmb_tfm_t2_to_ds_atlas, 'in3')
# apply transformation from t2 all the way to caltech atlas (in func resolution)
t2_to_ds_atlas = pe.Node(interface=ants.WarpImageMultiTransform(use_nearest = True), name = 't2_to_ds_atlas')
preproc.connect(maskT2, 'out_file', t2_to_ds_atlas, 'input_image')