def build_core_nodes(self):
"""Build and connect the core nodes of the pipeline.
Notes:
- If `FSLOUTPUTTYPE` environment variable is not set, `nipype` takes
NIFTI by default.
Todo:
- [x] Detect space automatically.
- [ ] Allow for custom parcellations (See TODOs in utils).
"""
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as npe
import nipype.interfaces.fsl as fsl
import nipype.interfaces.freesurfer as fs
import nipype.interfaces.mrtrix3 as mrtrix3
from clinica.lib.nipype.interfaces.mrtrix.preprocess import MRTransform
from clinica.lib.nipype.interfaces.mrtrix3.reconst import EstimateFOD
from clinica.lib.nipype.interfaces.mrtrix3.tracking import Tractography
from clinica.utils.exceptions import ClinicaException, ClinicaCAPSError
from clinica.utils.stream import cprint
import clinica.pipelines.dwi_connectome.dwi_connectome_utils as utils
from clinica.utils.mri_registration import convert_flirt_transformation_to_mrtrix_transformation
# cprint('Building the pipeline...')
# Nodes
# =====
# B0 Extraction (only if space=b0)
# -------------
split_node = npe.Node(name="Reg-0-DWI-B0Extraction",
interface=fsl.Split())
split_node.inputs.output_type = "NIFTI_GZ"
split_node.inputs.dimension = 't'
select_node = npe.Node(name="Reg-0-DWI-B0Selection",
interface=niu.Select())
select_node.inputs.index = 0
# B0 Brain Extraction (only if space=b0)
# -------------------
mask_node = npe.Node(name="Reg-0-DWI-BrainMasking",
interface=fsl.ApplyMask())
mask_node.inputs.output_type = "NIFTI_GZ"
# T1-to-B0 Registration (only if space=b0)
# ---------------------
t12b0_reg_node = npe.Node(name="Reg-1-T12B0Registration",
interface=fsl.FLIRT(
dof=6,
interp='spline',
cost='normmi',
cost_func='normmi',
))
t12b0_reg_node.inputs.output_type = "NIFTI_GZ"
# MGZ File Conversion (only if space=b0)
# -------------------
t1_brain_conv_node = npe.Node(name="Reg-0-T1-T1BrainConvertion",
interface=fs.MRIConvert())
wm_mask_conv_node = npe.Node(name="Reg-0-T1-WMMaskConvertion",
interface=fs.MRIConvert())
# WM Transformation (only if space=b0)
# -----------------
wm_transform_node = npe.Node(name="Reg-2-WMTransformation",
interface=fsl.ApplyXFM())
wm_transform_node.inputs.apply_xfm = True
# Nodes Generation
# ----------------
label_convert_node = npe.MapNode(
name="0-LabelsConversion",
iterfield=['in_file', 'in_config', 'in_lut', 'out_file'],
interface=mrtrix3.LabelConvert())
label_convert_node.inputs.in_config = utils.get_conversion_luts()
label_convert_node.inputs.in_lut = utils.get_luts()
# FSL flirt matrix to MRtrix matrix Conversion (only if space=b0)
# --------------------------------------------
fsl2mrtrix_conv_node = npe.Node(
name='Reg-2-FSL2MrtrixConversion',
interface=niu.Function(
input_names=[
'in_source_image', 'in_reference_image', 'in_flirt_matrix',
'name_output_matrix'
],
output_names=['out_mrtrix_matrix'],
function=convert_flirt_transformation_to_mrtrix_transformation)
)
# Parc. Transformation (only if space=b0)
# --------------------
parc_transform_node = npe.MapNode(
name="Reg-2-ParcTransformation",
iterfield=["in_files", "out_filename"],
interface=MRTransform())
# Response Estimation
# -------------------
resp_estim_node = npe.Node(name="1a-ResponseEstimation",
interface=mrtrix3.ResponseSD())
resp_estim_node.inputs.algorithm = 'tournier'
# FOD Estimation
# --------------
fod_estim_node = npe.Node(name="1b-FODEstimation",
interface=EstimateFOD())
fod_estim_node.inputs.algorithm = 'csd'
# Tracts Generation
# -----------------
tck_gen_node = npe.Node(name="2-TractsGeneration",
interface=Tractography())
tck_gen_node.inputs.n_tracks = self.parameters['n_tracks']
tck_gen_node.inputs.algorithm = 'iFOD2'
# BUG: Info package does not exist
# from nipype.interfaces.mrtrix3.base import Info
# from distutils.version import LooseVersion
#
# if Info.looseversion() >= LooseVersion("3.0"):
# tck_gen_node.inputs.select = self.parameters['n_tracks']
# elif Info.looseversion() <= LooseVersion("0.4"):
# tck_gen_node.inputs.n_tracks = self.parameters['n_tracks']
# else:
# from clinica.utils.exceptions import ClinicaException
# raise ClinicaException("Your MRtrix version is not supported.")
# Connectome Generation
# ---------------------
# only the parcellation and output filename should be iterable, the tck
# file stays the same.
conn_gen_node = npe.MapNode(name="3-ConnectomeGeneration",
iterfield=['in_parc', 'out_file'],
interface=mrtrix3.BuildConnectome())
# Print begin message
# -------------------
print_begin_message = npe.MapNode(interface=niu.Function(
input_names=['in_bids_or_caps_file'],
function=utils.print_begin_pipeline),
iterfield='in_bids_or_caps_file',
name='WriteBeginMessage')
# Print end message
# -----------------
print_end_message = npe.MapNode(interface=niu.Function(
input_names=['in_bids_or_caps_file', 'final_file'],
function=utils.print_end_pipeline),
iterfield=['in_bids_or_caps_file'],
name='WriteEndMessage')
# CAPS File names Generation
# --------------------------
caps_filenames_node = npe.Node(
name='CAPSFilenamesGeneration',
interface=niu.Function(input_names='dwi_file',
output_names=self.get_output_fields(),
function=utils.get_caps_filenames))
# Connections
# ===========
# Computation of the diffusion model, tractography & connectome
# -------------------------------------------------------------
self.connect([
(self.input_node, print_begin_message,
[('dwi_file', 'in_bids_or_caps_file')]), # noqa
(self.input_node, caps_filenames_node, [('dwi_file', 'dwi_file')]),
# Response Estimation
(self.input_node, resp_estim_node, [('dwi_file', 'in_file')]
), # Preproc. DWI # noqa
(self.input_node, resp_estim_node,
[('dwi_brainmask_file', 'in_mask')]), # B0 brain mask # noqa
(self.input_node, resp_estim_node, [('grad_fsl', 'grad_fsl')
]), # bvecs and bvals # noqa
(caps_filenames_node, resp_estim_node,
[('response', 'wm_file')]), # output response filename # noqa
# FOD Estimation
(self.input_node, fod_estim_node, [('dwi_file', 'in_file')]
), # Preproc. DWI # noqa
(resp_estim_node, fod_estim_node,
[('wm_file', 'wm_txt')]), # Response (txt file) # noqa
(self.input_node, fod_estim_node,
[('dwi_brainmask_file', 'mask_file')]), # B0 brain mask # noqa
(self.input_node, fod_estim_node,
[('grad_fsl', 'grad_fsl')]), # T1-to-B0 matrix file # noqa
(caps_filenames_node, fod_estim_node,
[('fod', 'wm_odf')]), # output odf filename # noqa
# Tracts Generation
(fod_estim_node, tck_gen_node, [('wm_odf', 'in_file')]
), # ODF file # noqa
(caps_filenames_node, tck_gen_node,
[('tracts', 'out_file')]), # output tck filename # noqa
# Label Conversion
(self.input_node, label_convert_node, [('atlas_files', 'in_file')]
), # atlas image files # noqa
(caps_filenames_node, label_convert_node, [
('nodes', 'out_file')
]), # converted atlas image filenames # noqa
# Connectomes Generation
(tck_gen_node, conn_gen_node, [('out_file', 'in_file')]), # noqa
(caps_filenames_node, conn_gen_node, [('connectomes', 'out_file')
]), # noqa
])
# Registration T1-DWI (only if space=b0)
# -------------------
if self.parameters['dwi_space'] == 'b0':
self.connect([
# MGZ Files Conversion
(self.input_node, t1_brain_conv_node, [('t1_brain_file',
'in_file')]), # noqa
(self.input_node, wm_mask_conv_node, [('wm_mask_file',
'in_file')]), # noqa
# B0 Extraction
(self.input_node, split_node, [('dwi_file', 'in_file')]
), # noqa
(split_node, select_node, [('out_files', 'inlist')]), # noqa
# Masking
(select_node, mask_node, [('out', 'in_file')]), # B0 # noqa
(self.input_node, mask_node,
[('dwi_brainmask_file', 'mask_file')]), # Brain mask # noqa
# T1-to-B0 Registration
(t1_brain_conv_node, t12b0_reg_node, [('out_file', 'in_file')]
), # Brain # noqa
(mask_node, t12b0_reg_node, [('out_file', 'reference')
]), # B0 brain-masked # noqa
# WM Transformation
(wm_mask_conv_node, wm_transform_node,
[('out_file', 'in_file')]), # Brain mask # noqa
(mask_node, wm_transform_node, [('out_file', 'reference')
]), # BO brain-masked # noqa
(t12b0_reg_node, wm_transform_node, [
('out_matrix_file', 'in_matrix_file')
]), # T1-to-B0 matrix file # noqa
# FSL flirt matrix to MRtrix matrix Conversion
(t1_brain_conv_node, fsl2mrtrix_conv_node,
[('out_file', 'in_source_image')]), # noqa
(mask_node, fsl2mrtrix_conv_node,
[('out_file', 'in_reference_image')]), # noqa
(t12b0_reg_node, fsl2mrtrix_conv_node,
[('out_matrix_file', 'in_flirt_matrix')]), # noqa
# Apply registration without resampling on parcellations
(label_convert_node, parc_transform_node,
[('out_file', 'in_files')]), # noqa
(fsl2mrtrix_conv_node, parc_transform_node,
[('out_mrtrix_matrix', 'linear_transform')]), # noqa
(caps_filenames_node, parc_transform_node,
[('nodes', 'out_filename')]), # noqa
])
# Special care for Parcellation & WM mask
# ---------------------------------------
if self.parameters['dwi_space'] == 'b0':
self.connect([
(wm_transform_node, tck_gen_node, [('out_file', 'seed_image')
]), # noqa
(parc_transform_node, conn_gen_node, [('out_file', 'in_parc')
]), # noqa
(parc_transform_node, self.output_node, [('out_file', 'nodes')
]), # noqa
])
elif self.parameters['dwi_space'] == 'T1w':
self.connect([
(self.input_node, tck_gen_node, [('wm_mask_file', 'seed_image')
]), # noqa
(label_convert_node, conn_gen_node, [('out_file', 'in_parc')
]), # noqa
(label_convert_node, self.output_node, [('out_file', 'nodes')
]), # noqa
])
else:
raise ClinicaCAPSError(
'Bad preprocessed DWI space. Please check your CAPS '
'folder.')
# Outputs
# -------
self.connect([
(resp_estim_node, self.output_node, [('wm_file', 'response')]),
(fod_estim_node, self.output_node, [('wm_odf', 'fod')]),
(tck_gen_node, self.output_node, [('out_file', 'tracts')]),
(conn_gen_node, self.output_node, [('out_file', 'connectomes')]),
(self.input_node, print_end_message, [('dwi_file',
'in_bids_or_caps_file')]),
(conn_gen_node, print_end_message, [('out_file', 'final_file')]),
])
def build_core_nodes(self):
"""Build and connect the core nodes of the pipeline.
Notes:
- If `FSLOUTPUTTYPE` environment variable is not set, `nipype` takes
NIFTI by default.
Todo:
- [x] Detect space automatically.
- [ ] Allow for custom parcellations (See TODOs in utils).
"""
import nipype.interfaces.freesurfer as fs
import nipype.interfaces.fsl as fsl
import nipype.interfaces.mrtrix3 as mrtrix3
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as npe
from nipype.interfaces.mrtrix3.tracking import Tractography
from nipype.interfaces.mrtrix.preprocess import MRTransform
import clinica.pipelines.dwi_connectome.dwi_connectome_utils as utils
from clinica.lib.nipype.interfaces.mrtrix3.reconst import EstimateFOD
from clinica.utils.exceptions import ClinicaCAPSError
from clinica.utils.mri_registration import (
convert_flirt_transformation_to_mrtrix_transformation,
)
# Nodes
# =====
# B0 Extraction (only if space=b0)
# -------------
split_node = npe.Node(name="Reg-0-DWI-B0Extraction", interface=fsl.Split())
split_node.inputs.output_type = "NIFTI_GZ"
split_node.inputs.dimension = "t"
select_node = npe.Node(name="Reg-0-DWI-B0Selection", interface=niu.Select())
select_node.inputs.index = 0
# B0 Brain Extraction (only if space=b0)
# -------------------
mask_node = npe.Node(name="Reg-0-DWI-BrainMasking", interface=fsl.ApplyMask())
mask_node.inputs.output_type = "NIFTI_GZ"
# T1-to-B0 Registration (only if space=b0)
# ---------------------
t12b0_reg_node = npe.Node(
name="Reg-1-T12B0Registration",
interface=fsl.FLIRT(
dof=6,
interp="spline",
cost="normmi",
cost_func="normmi",
),
)
t12b0_reg_node.inputs.output_type = "NIFTI_GZ"
# MGZ File Conversion (only if space=b0)
# -------------------
t1_brain_conv_node = npe.Node(
name="Reg-0-T1-T1BrainConvertion", interface=fs.MRIConvert()
)
wm_mask_conv_node = npe.Node(
name="Reg-0-T1-WMMaskConvertion", interface=fs.MRIConvert()
)
# WM Transformation (only if space=b0)
# -----------------
wm_transform_node = npe.Node(
name="Reg-2-WMTransformation", interface=fsl.ApplyXFM()
)
wm_transform_node.inputs.apply_xfm = True
# Nodes Generation
# ----------------
label_convert_node = npe.MapNode(
name="0-LabelsConversion",
iterfield=["in_file", "in_config", "in_lut", "out_file"],
interface=mrtrix3.LabelConvert(),
)
label_convert_node.inputs.in_config = utils.get_conversion_luts()
label_convert_node.inputs.in_lut = utils.get_luts()
# FSL flirt matrix to MRtrix matrix Conversion (only if space=b0)
# --------------------------------------------
fsl2mrtrix_conv_node = npe.Node(
name="Reg-2-FSL2MrtrixConversion",
interface=niu.Function(
input_names=[
"in_source_image",
"in_reference_image",
"in_flirt_matrix",
"name_output_matrix",
],
output_names=["out_mrtrix_matrix"],
function=convert_flirt_transformation_to_mrtrix_transformation,
),
)
# Parc. Transformation (only if space=b0)
# --------------------
parc_transform_node = npe.MapNode(
name="Reg-2-ParcTransformation",
iterfield=["in_files", "out_filename"],
interface=MRTransform(),
)
# Response Estimation
# -------------------
resp_estim_node = npe.Node(
name="1a-ResponseEstimation", interface=mrtrix3.ResponseSD()
)
resp_estim_node.inputs.algorithm = "tournier"
# FOD Estimation
# --------------
fod_estim_node = npe.Node(name="1b-FODEstimation", interface=EstimateFOD())
fod_estim_node.inputs.algorithm = "csd"
# Tracts Generation
# -----------------
tck_gen_node = npe.Node(name="2-TractsGeneration", interface=Tractography())
tck_gen_node.inputs.select = self.parameters["n_tracks"]
tck_gen_node.inputs.algorithm = "iFOD2"
# Connectome Generation
# ---------------------
# only the parcellation and output filename should be iterable, the tck
# file stays the same.
conn_gen_node = npe.MapNode(
name="3-ConnectomeGeneration",
iterfield=["in_parc", "out_file"],
interface=mrtrix3.BuildConnectome(),
)
# Print begin message
# -------------------
print_begin_message = npe.MapNode(
interface=niu.Function(
input_names=["in_bids_or_caps_file"],
function=utils.print_begin_pipeline,
),
iterfield="in_bids_or_caps_file",
name="WriteBeginMessage",
)
# Print end message
# -----------------
print_end_message = npe.MapNode(
interface=niu.Function(
input_names=["in_bids_or_caps_file", "final_file"],
function=utils.print_end_pipeline,
),
iterfield=["in_bids_or_caps_file"],
name="WriteEndMessage",
)
# CAPS File names Generation
# --------------------------
caps_filenames_node = npe.Node(
name="CAPSFilenamesGeneration",
interface=niu.Function(
input_names="dwi_file",
output_names=self.get_output_fields(),
function=utils.get_caps_filenames,
),
)
# Connections
# ===========
# Computation of the diffusion model, tractography & connectome
# -------------------------------------------------------------
# fmt: off
self.connect(
[
(self.input_node, print_begin_message, [("dwi_file", "in_bids_or_caps_file")]),
(self.input_node, caps_filenames_node, [("dwi_file", "dwi_file")]),
# Response Estimation
(self.input_node, resp_estim_node, [("dwi_file", "in_file")]), # Preproc. DWI
(self.input_node, resp_estim_node, [("dwi_brainmask_file", "in_mask")]), # B0 brain mask
(self.input_node, resp_estim_node, [("grad_fsl", "grad_fsl")]), # bvecs and bvals
(caps_filenames_node, resp_estim_node, [("response", "wm_file")]), # output response filename
# FOD Estimation
(self.input_node, fod_estim_node, [("dwi_file", "in_file")]), # Preproc. DWI
(resp_estim_node, fod_estim_node, [("wm_file", "wm_txt")]), # Response (txt file)
(self.input_node, fod_estim_node, [("dwi_brainmask_file", "mask_file")]), # B0 brain mask
(self.input_node, fod_estim_node, [("grad_fsl", "grad_fsl")]), # T1-to-B0 matrix file
(caps_filenames_node, fod_estim_node, [("fod", "wm_odf")]), # output odf filename
# Tracts Generation
(fod_estim_node, tck_gen_node, [("wm_odf", "in_file")]), # ODF file
(caps_filenames_node, tck_gen_node, [("tracts", "out_file")]), # output tck filename
# Label Conversion
(self.input_node, label_convert_node, [("atlas_files", "in_file")]), # atlas image files
(caps_filenames_node, label_convert_node, [("nodes", "out_file")]), # converted atlas image filenames
# Connectomes Generation
(tck_gen_node, conn_gen_node, [("out_file", "in_file")]),
(caps_filenames_node, conn_gen_node, [("connectomes", "out_file")]),
]
)
# Registration T1-DWI (only if space=b0)
# -------------------
if self.parameters["dwi_space"] == "b0":
self.connect(
[
# MGZ Files Conversion
(self.input_node, t1_brain_conv_node, [("t1_brain_file", "in_file")]),
(self.input_node, wm_mask_conv_node, [("wm_mask_file", "in_file")]),
# B0 Extraction
(self.input_node, split_node, [("dwi_file", "in_file")]),
(split_node, select_node, [("out_files", "inlist")]),
# Masking
(select_node, mask_node, [("out", "in_file")]), # B0
(self.input_node, mask_node, [("dwi_brainmask_file", "mask_file")]), # Brain mask
# T1-to-B0 Registration
(t1_brain_conv_node, t12b0_reg_node, [("out_file", "in_file")]), # Brain
(mask_node, t12b0_reg_node, [("out_file", "reference")]), # B0 brain-masked
# WM Transformation
(wm_mask_conv_node, wm_transform_node, [("out_file", "in_file")]), # Brain mask
(mask_node, wm_transform_node, [("out_file", "reference")]), # BO brain-masked
(t12b0_reg_node, wm_transform_node, [("out_matrix_file", "in_matrix_file")]), # T1-to-B0 matrix file
# FSL flirt matrix to MRtrix matrix Conversion
(t1_brain_conv_node, fsl2mrtrix_conv_node, [("out_file", "in_source_image")]),
(mask_node, fsl2mrtrix_conv_node, [("out_file", "in_reference_image")]),
(t12b0_reg_node, fsl2mrtrix_conv_node, [("out_matrix_file", "in_flirt_matrix")]),
# Apply registration without resampling on parcellations
(label_convert_node, parc_transform_node, [("out_file", "in_files")]),
(fsl2mrtrix_conv_node, parc_transform_node, [("out_mrtrix_matrix", "linear_transform")]),
(caps_filenames_node, parc_transform_node, [("nodes", "out_filename")]),
]
)
# Special care for Parcellation & WM mask
# ---------------------------------------
if self.parameters["dwi_space"] == "b0":
self.connect(
[
(wm_transform_node, tck_gen_node, [("out_file", "seed_image")]),
(parc_transform_node, conn_gen_node, [("out_file", "in_parc")]),
(parc_transform_node, self.output_node, [("out_file", "nodes")]),
]
)
elif self.parameters["dwi_space"] == "T1w":
self.connect(
[
(self.input_node, tck_gen_node, [("wm_mask_file", "seed_image")]),
(label_convert_node, conn_gen_node, [("out_file", "in_parc")]),
(label_convert_node, self.output_node, [("out_file", "nodes")]),
]
)
else:
raise ClinicaCAPSError(
"Bad preprocessed DWI space. Please check your CAPS folder."
)
# Outputs
# -------
self.connect(
[
(resp_estim_node, self.output_node, [("wm_file", "response")]),
(fod_estim_node, self.output_node, [("wm_odf", "fod")]),
(tck_gen_node, self.output_node, [("out_file", "tracts")]),
(conn_gen_node, self.output_node, [("out_file", "connectomes")]),
(self.input_node, print_end_message, [("dwi_file", "in_bids_or_caps_file")]),
(conn_gen_node, print_end_message, [("out_file", "final_file")]),
]
)