def synthstrip_wf(name="synthstrip_wf", omp_nthreads=None):
"""Create a brain-extraction workflow using SynthStrip."""
from nipype.interfaces.ants import N4BiasFieldCorrection
from niworkflows.interfaces.nibabel import IntensityClip, ApplyMask
from mriqc.interfaces.synthstrip import SynthStrip
inputnode = pe.Node(niu.IdentityInterface(fields=["in_files"]),
name="inputnode")
outputnode = pe.Node(
niu.IdentityInterface(
fields=["out_corrected", "out_brain", "bias_image", "out_mask"]),
name="outputnode",
)
# truncate target intensity for N4 correction
pre_clip = pe.Node(IntensityClip(p_min=10, p_max=99.9), name="pre_clip")
pre_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
num_threads=omp_nthreads,
rescale_intensities=True,
copy_header=True,
),
name="pre_n4",
)
post_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
save_bias=True,
num_threads=omp_nthreads,
n_iterations=[50] * 4,
copy_header=True,
),
name="post_n4",
)
synthstrip = pe.Node(
SynthStrip(),
name="synthstrip",
)
final_masked = pe.Node(ApplyMask(), name="final_masked")
final_inu = pe.Node(niu.Function(function=_apply_bias_correction),
name="final_inu")
workflow = pe.Workflow(name=name)
# fmt: off
workflow.connect([
(inputnode, final_inu, [("in_files", "in_file")]),
(inputnode, pre_clip, [("in_files", "in_file")]),
(pre_clip, pre_n4, [("out_file", "input_image")]),
(pre_n4, synthstrip, [("output_image", "in_file")]),
(synthstrip, post_n4, [("out_mask", "weight_image")]),
(synthstrip, final_masked, [("out_mask", "in_mask")]),
(pre_clip, post_n4, [("out_file", "input_image")]),
(post_n4, final_inu, [("bias_image", "bias_image")]),
(post_n4, final_masked, [("output_image", "in_file")]),
(final_masked, outputnode, [("out_file", "out_brain")]),
(post_n4, outputnode, [("bias_image", "bias_image")]),
(synthstrip, outputnode, [("out_mask", "out_mask")]),
(post_n4, outputnode, [("output_image", "out_corrected")]),
])
# fmt: on
return workflow
def init_rodent_brain_extraction_wf(
ants_affine_init=False,
factor=20,
arc=0.12,
step=4,
grid=(0, 4, 4),
debug=False,
interim_checkpoints=True,
mem_gb=3.0,
mri_scheme="T2w",
name="rodent_brain_extraction_wf",
omp_nthreads=None,
output_dir=None,
template_id="Fischer344",
template_specs=None,
use_float=True,
):
"""
Build an atlas-based brain extraction pipeline for rodent T1w and T2w MRI data.
Parameters
----------
ants_affine_init : :obj:`bool`, optional
Set-up a pre-initialization step with ``antsAI`` to account for mis-oriented images.
"""
inputnode = pe.Node(niu.IdentityInterface(fields=["in_files", "in_mask"]),
name="inputnode")
outputnode = pe.Node(
niu.IdentityInterface(
fields=["out_corrected", "out_brain", "out_mask"]),
name="outputnode",
)
template_specs = template_specs or {}
if template_id == "WHS" and "resolution" not in template_specs:
template_specs["resolution"] = 2
# Find a suitable target template in TemplateFlow
tpl_target_path = get_template(
template_id,
suffix=mri_scheme,
**template_specs,
)
if not tpl_target_path:
raise RuntimeError(
f"An instance of template <tpl-{template_id}> with MR scheme '{mri_scheme}'"
" could not be found.")
tpl_brainmask_path = get_template(
template_id,
atlas=None,
hemi=None,
desc="brain",
suffix="probseg",
**template_specs,
) or get_template(
template_id,
atlas=None,
hemi=None,
desc="brain",
suffix="mask",
**template_specs,
)
tpl_regmask_path = get_template(
template_id,
atlas=None,
desc="BrainCerebellumExtraction",
suffix="mask",
**template_specs,
)
denoise = pe.Node(DenoiseImage(dimension=3, copy_header=True),
name="denoise",
n_procs=omp_nthreads)
# Resample template to a controlled, isotropic resolution
res_tmpl = pe.Node(RegridToZooms(zooms=HIRES_ZOOMS, smooth=True),
name="res_tmpl")
# Create Laplacian images
lap_tmpl = pe.Node(ImageMath(operation="Laplacian", copy_header=True),
name="lap_tmpl")
tmpl_sigma = pe.Node(niu.Function(function=_lap_sigma),
name="tmpl_sigma",
run_without_submitting=True)
norm_lap_tmpl = pe.Node(niu.Function(function=_norm_lap),
name="norm_lap_tmpl")
lap_target = pe.Node(ImageMath(operation="Laplacian", copy_header=True),
name="lap_target")
target_sigma = pe.Node(niu.Function(function=_lap_sigma),
name="target_sigma",
run_without_submitting=True)
norm_lap_target = pe.Node(niu.Function(function=_norm_lap),
name="norm_lap_target")
# Set up initial spatial normalization
ants_params = "testing" if debug else "precise"
norm = pe.Node(
Registration(from_file=pkgr_fn(
"nirodents",
f"data/artsBrainExtraction_{ants_params}_{mri_scheme}.json")),
name="norm",
n_procs=omp_nthreads,
mem_gb=mem_gb,
)
norm.inputs.float = use_float
# main workflow
wf = pe.Workflow(name)
# truncate target intensity for N4 correction
clip_target = pe.Node(IntensityClip(p_min=15, p_max=99.9),
name="clip_target")
# truncate template intensity to match target
clip_tmpl = pe.Node(IntensityClip(p_min=5, p_max=98), name="clip_tmpl")
clip_tmpl.inputs.in_file = _pop(tpl_target_path)
# set INU bspline grid based on voxel size
bspline_grid = pe.Node(niu.Function(function=_bspline_grid),
name="bspline_grid")
# INU correction of the target image
init_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
save_bias=False,
copy_header=True,
n_iterations=[50] * (4 - debug),
convergence_threshold=1e-7,
shrink_factor=4,
rescale_intensities=True,
),
n_procs=omp_nthreads,
name="init_n4",
)
clip_inu = pe.Node(IntensityClip(p_min=1, p_max=99.8), name="clip_inu")
# Create a buffer interface as a cache for the actual inputs to registration
buffernode = pe.Node(niu.IdentityInterface(fields=["hires_target"]),
name="buffernode")
# Merge image nodes
mrg_target = pe.Node(niu.Merge(2), name="mrg_target")
mrg_tmpl = pe.Node(niu.Merge(2), name="mrg_tmpl")
# fmt: off
wf.connect([
# Target image massaging
(inputnode, denoise, [(("in_files", _pop), "input_image")]),
(inputnode, bspline_grid, [(("in_files", _pop), "in_file")]),
(bspline_grid, init_n4, [("out", "args")]),
(denoise, clip_target, [("output_image", "in_file")]),
(clip_target, init_n4, [("out_file", "input_image")]),
(init_n4, clip_inu, [("output_image", "in_file")]),
(clip_inu, target_sigma, [("out_file", "in_file")]),
(clip_inu, buffernode, [("out_file", "hires_target")]),
(buffernode, lap_target, [("hires_target", "op1")]),
(target_sigma, lap_target, [("out", "op2")]),
(lap_target, norm_lap_target, [("output_image", "in_file")]),
(buffernode, mrg_target, [("hires_target", "in1")]),
(norm_lap_target, mrg_target, [("out", "in2")]),
# Template massaging
(clip_tmpl, res_tmpl, [("out_file", "in_file")]),
(res_tmpl, tmpl_sigma, [("out_file", "in_file")]),
(res_tmpl, lap_tmpl, [("out_file", "op1")]),
(tmpl_sigma, lap_tmpl, [("out", "op2")]),
(lap_tmpl, norm_lap_tmpl, [("output_image", "in_file")]),
(res_tmpl, mrg_tmpl, [("out_file", "in1")]),
(norm_lap_tmpl, mrg_tmpl, [("out", "in2")]),
# Setup inputs to spatial normalization
(mrg_target, norm, [("out", "moving_image")]),
(mrg_tmpl, norm, [("out", "fixed_image")]),
])
# fmt: on
# Graft a template registration-mask if present
if tpl_regmask_path:
hires_mask = pe.Node(
ApplyTransforms(
input_image=_pop(tpl_regmask_path),
transforms="identity",
interpolation="Gaussian",
float=True,
),
name="hires_mask",
mem_gb=1,
)
# fmt: off
wf.connect([
(res_tmpl, hires_mask, [("out_file", "reference_image")]),
(hires_mask, norm, [("output_image", "fixed_image_masks")]),
])
# fmt: on
# Finally project brain mask and refine INU correction
map_brainmask = pe.Node(
ApplyTransforms(interpolation="Gaussian", float=True),
name="map_brainmask",
mem_gb=1,
)
map_brainmask.inputs.input_image = str(tpl_brainmask_path)
thr_brainmask = pe.Node(Binarize(thresh_low=0.50), name="thr_brainmask")
final_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
save_bias=True,
copy_header=True,
n_iterations=[50] * 4,
convergence_threshold=1e-7,
rescale_intensities=True,
shrink_factor=4,
),
n_procs=omp_nthreads,
name="final_n4",
)
final_mask = pe.Node(ApplyMask(), name="final_mask")
# fmt: off
wf.connect([
(inputnode, map_brainmask, [(("in_files", _pop), "reference_image")]),
(bspline_grid, final_n4, [("out", "args")]),
(denoise, final_n4, [("output_image", "input_image")]),
# Project template's brainmask into subject space
(norm, map_brainmask, [("reverse_transforms", "transforms"),
("reverse_invert_flags",
"invert_transform_flags")]),
(map_brainmask, thr_brainmask, [("output_image", "in_file")]),
# take a second pass of N4
(map_brainmask, final_n4, [("output_image", "mask_image")]),
(final_n4, final_mask, [("output_image", "in_file")]),
(thr_brainmask, final_mask, [("out_mask", "in_mask")]),
(final_n4, outputnode, [("output_image", "out_corrected")]),
(thr_brainmask, outputnode, [("out_mask", "out_mask")]),
(final_mask, outputnode, [("out_file", "out_brain")]),
])
# fmt: on
if interim_checkpoints:
final_apply = pe.Node(
ApplyTransforms(interpolation="BSpline", float=True),
name="final_apply",
mem_gb=1,
)
final_report = pe.Node(
SimpleBeforeAfter(after_label="target",
before_label=f"tpl-{template_id}"),
name="final_report",
)
# fmt: off
wf.connect([
(inputnode, final_apply, [(("in_files", _pop), "reference_image")
]),
(res_tmpl, final_apply, [("out_file", "input_image")]),
(norm, final_apply, [("reverse_transforms", "transforms"),
("reverse_invert_flags",
"invert_transform_flags")]),
(final_apply, final_report, [("output_image", "before")]),
(outputnode, final_report, [("out_corrected", "after"),
("out_mask", "wm_seg")]),
])
# fmt: on
if ants_affine_init:
# Initialize transforms with antsAI
lowres_tmpl = pe.Node(RegridToZooms(zooms=LOWRES_ZOOMS, smooth=True),
name="lowres_tmpl")
lowres_trgt = pe.Node(RegridToZooms(zooms=LOWRES_ZOOMS, smooth=True),
name="lowres_trgt")
init_aff = pe.Node(
AI(
convergence=(100, 1e-6, 10),
metric=("Mattes", 32, "Random", 0.25),
principal_axes=False,
search_factor=(factor, arc),
search_grid=(step, grid),
transform=("Affine", 0.1),
verbose=True,
),
name="init_aff",
n_procs=omp_nthreads,
)
# fmt: off
wf.connect([
(clip_inu, lowres_trgt, [("out_file", "in_file")]),
(lowres_trgt, init_aff, [("out_file", "moving_image")]),
(clip_tmpl, lowres_tmpl, [("out_file", "in_file")]),
(lowres_tmpl, init_aff, [("out_file", "fixed_image")]),
(init_aff, norm, [("output_transform", "initial_moving_transform")
]),
])
# fmt: on
if tpl_regmask_path:
lowres_mask = pe.Node(
ApplyTransforms(
input_image=_pop(tpl_regmask_path),
transforms="identity",
interpolation="MultiLabel",
),
name="lowres_mask",
mem_gb=1,
)
# fmt: off
wf.connect([
(lowres_tmpl, lowres_mask, [("out_file", "reference_image")]),
(lowres_mask, init_aff, [("output_image", "fixed_image_mask")
]),
])
# fmt: on
if interim_checkpoints:
init_apply = pe.Node(
ApplyTransforms(interpolation="BSpline",
invert_transform_flags=[True]),
name="init_apply",
mem_gb=1,
)
init_mask = pe.Node(
ApplyTransforms(interpolation="Gaussian",
invert_transform_flags=[True]),
name="init_mask",
mem_gb=1,
)
init_mask.inputs.input_image = str(tpl_brainmask_path)
init_report = pe.Node(
SimpleBeforeAfter(
out_report="init_report.svg",
before_label="target",
after_label="template",
),
name="init_report",
)
# fmt: off
wf.connect([
(lowres_trgt, init_apply, [("out_file", "reference_image")]),
(lowres_tmpl, init_apply, [("out_file", "input_image")]),
(init_aff, init_apply, [("output_transform", "transforms")]),
(lowres_trgt, init_report, [("out_file", "before")]),
(init_apply, init_report, [("output_image", "after")]),
(lowres_trgt, init_mask, [("out_file", "reference_image")]),
(init_aff, init_mask, [("output_transform", "transforms")]),
(init_mask, init_report, [("output_image", "wm_seg")]),
])
# fmt: on
else:
norm.inputs.initial_moving_transform_com = 1
if output_dir:
ds_final_inu = pe.Node(DerivativesDataSink(
base_directory=str(output_dir),
desc="preproc",
compress=True,
),
name="ds_final_inu",
run_without_submitting=True)
ds_final_msk = pe.Node(DerivativesDataSink(
base_directory=str(output_dir),
desc="brain",
suffix="mask",
compress=True,
),
name="ds_final_msk",
run_without_submitting=True)
# fmt: off
wf.connect([
(inputnode, ds_final_inu, [("in_files", "source_file")]),
(inputnode, ds_final_msk, [("in_files", "source_file")]),
(outputnode, ds_final_inu, [("out_corrected", "in_file")]),
(outputnode, ds_final_msk, [("out_mask", "in_file")]),
])
# fmt: on
if interim_checkpoints:
ds_report = pe.Node(DerivativesDataSink(
base_directory=str(output_dir),
desc="brain",
suffix="mask",
datatype="figures"),
name="ds_report",
run_without_submitting=True)
# fmt: off
wf.connect([
(inputnode, ds_report, [("in_files", "source_file")]),
(final_report, ds_report, [("out_report", "in_file")]),
])
# fmt: on
if ants_affine_init and interim_checkpoints:
ds_report_init = pe.Node(DerivativesDataSink(
base_directory=str(output_dir),
desc="init",
suffix="mask",
datatype="figures"),
name="ds_report_init",
run_without_submitting=True)
# fmt: off
wf.connect([
(inputnode, ds_report_init, [("in_files", "source_file")]),
(init_report, ds_report_init, [("out_report", "in_file")]),
])
# fmt: on
return wf
def test_syn_wf(tmpdir, datadir, workdir, outdir):
"""Build and run an SDC-SyN workflow."""
derivs_path = datadir / "ds000054" / "derivatives"
smriprep = derivs_path / "smriprep-0.6" / "sub-100185" / "anat"
wf = pe.Workflow(name="syn_test")
syn_wf = init_syn_sdc_wf(debug=True, omp_nthreads=4)
syn_wf.inputs.inputnode.epi_ref = (
str(derivs_path / "sdcflows-tests" /
"sub-100185_task-machinegame_run-1_boldref.nii.gz"),
{
"PhaseEncodingDirection": "j-",
"TotalReadoutTime": 0.005
},
)
syn_wf.inputs.inputnode.epi_mask = str(
derivs_path / "sdcflows-tests" /
"sub-100185_task-machinegame_run-1_desc-brain_mask.nii.gz")
syn_wf.inputs.inputnode.anat2epi_xfm = str(derivs_path / "sdcflows-tests" /
"t1w2bold.txt")
syn_wf.inputs.inputnode.std2anat_xfm = str(
smriprep /
"sub-100185_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5")
t1w_mask = pe.Node(
ApplyMask(
in_file=str(smriprep / "sub-100185_desc-preproc_T1w.nii.gz"),
in_mask=str(smriprep / "sub-100185_desc-brain_mask.nii.gz"),
),
name="t1w_mask",
)
# fmt: off
wf.connect([
(t1w_mask, syn_wf, [("out_file", "inputnode.anat_brain")]),
])
# fmt: on
if outdir:
from ...outputs import init_fmap_derivatives_wf, init_fmap_reports_wf
outdir = outdir / "unittests" / "syn_test"
fmap_derivatives_wf = init_fmap_derivatives_wf(
output_dir=str(outdir),
write_coeff=True,
bids_fmap_id="sdcsyn",
)
fmap_derivatives_wf.inputs.inputnode.source_files = [
str(derivs_path / "sdcflows-tests" /
"sub-100185_task-machinegame_run-1_boldref.nii.gz")
]
fmap_derivatives_wf.inputs.inputnode.fmap_meta = {
"PhaseEncodingDirection": "j-"
}
fmap_reports_wf = init_fmap_reports_wf(
output_dir=str(outdir),
fmap_type="sdcsyn",
)
fmap_reports_wf.inputs.inputnode.source_files = [
str(derivs_path / "sdcflows-tests" /
"sub-100185_task-machinegame_run-1_boldref.nii.gz")
]
# fmt: off
wf.connect([
(syn_wf, fmap_reports_wf,
[("outputnode.fmap", "inputnode.fieldmap"),
("outputnode.fmap_ref", "inputnode.fmap_ref"),
("outputnode.fmap_mask", "inputnode.fmap_mask")]),
(syn_wf, fmap_derivatives_wf, [
("outputnode.fmap", "inputnode.fieldmap"),
("outputnode.fmap_ref", "inputnode.fmap_ref"),
("outputnode.fmap_coeff", "inputnode.fmap_coeff"),
]),
])
# fmt: on
if workdir:
wf.base_dir = str(workdir)
wf.run(plugin="Linear")
def init_bold_confs_wf(
mem_gb,
metadata,
regressors_all_comps,
regressors_dvars_th,
regressors_fd_th,
freesurfer=False,
name="bold_confs_wf",
):
"""
Build a workflow to generate and write out confounding signals.
This workflow calculates confounds for a BOLD series, and aggregates them
into a :abbr:`TSV (tab-separated value)` file, for use as nuisance
regressors in a :abbr:`GLM (general linear model)`.
The following confounds are calculated, with column headings in parentheses:
#. Region-wise average signal (``csf``, ``white_matter``, ``global_signal``)
#. DVARS - original and standardized variants (``dvars``, ``std_dvars``)
#. Framewise displacement, based on head-motion parameters
(``framewise_displacement``)
#. Temporal CompCor (``t_comp_cor_XX``)
#. Anatomical CompCor (``a_comp_cor_XX``)
#. Cosine basis set for high-pass filtering w/ 0.008 Hz cut-off
(``cosine_XX``)
#. Non-steady-state volumes (``non_steady_state_XX``)
#. Estimated head-motion parameters, in mm and rad
(``trans_x``, ``trans_y``, ``trans_z``, ``rot_x``, ``rot_y``, ``rot_z``)
Prior to estimating aCompCor and tCompCor, non-steady-state volumes are
censored and high-pass filtered using a :abbr:`DCT (discrete cosine
transform)` basis.
The cosine basis, as well as one regressor per censored volume, are included
for convenience.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.bold.confounds import init_bold_confs_wf
wf = init_bold_confs_wf(
mem_gb=1,
metadata={},
regressors_all_comps=False,
regressors_dvars_th=1.5,
regressors_fd_th=0.5,
)
Parameters
----------
mem_gb : :obj:`float`
Size of BOLD file in GB - please note that this size
should be calculated after resamplings that may extend
the FoV
metadata : :obj:`dict`
BIDS metadata for BOLD file
name : :obj:`str`
Name of workflow (default: ``bold_confs_wf``)
regressors_all_comps : :obj:`bool`
Indicates whether CompCor decompositions should return all
components instead of the minimal number of components necessary
to explain 50 percent of the variance in the decomposition mask.
regressors_dvars_th : :obj:`float`
Criterion for flagging DVARS outliers
regressors_fd_th : :obj:`float`
Criterion for flagging framewise displacement outliers
Inputs
------
bold
BOLD image, after the prescribed corrections (STC, HMC and SDC)
when available.
bold_mask
BOLD series mask
movpar_file
SPM-formatted motion parameters file
rmsd_file
Framewise displacement as measured by ``fsl_motion_outliers``.
skip_vols
number of non steady state volumes
t1w_mask
Mask of the skull-stripped template image
t1w_tpms
List of tissue probability maps in T1w space
t1_bold_xform
Affine matrix that maps the T1w space into alignment with
the native BOLD space
Outputs
-------
confounds_file
TSV of all aggregated confounds
rois_report
Reportlet visualizing white-matter/CSF mask used for aCompCor,
the ROI for tCompCor and the BOLD brain mask.
confounds_metadata
Confounds metadata dictionary.
"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.confounds import ExpandModel, SpikeRegressors
from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
from niworkflows.interfaces.images import SignalExtraction
from niworkflows.interfaces.masks import ROIsPlot
from niworkflows.interfaces.nibabel import ApplyMask, Binarize
from niworkflows.interfaces.patches import (
RobustACompCor as ACompCor,
RobustTCompCor as TCompCor,
)
from niworkflows.interfaces.plotting import (CompCorVariancePlot,
ConfoundsCorrelationPlot)
from niworkflows.interfaces.utils import (AddTSVHeader, TSV2JSON,
DictMerge)
from ...interfaces.confounds import aCompCorMasks
gm_desc = (
"dilating a GM mask extracted from the FreeSurfer's *aseg* segmentation"
if freesurfer else
"thresholding the corresponding partial volume map at 0.05")
workflow = Workflow(name=name)
workflow.__desc__ = f"""\
Several confounding time-series were calculated based on the
*preprocessed BOLD*: framewise displacement (FD), DVARS and
three region-wise global signals.
FD was computed using two formulations following Power (absolute sum of
relative motions, @power_fd_dvars) and Jenkinson (relative root mean square
displacement between affines, @mcflirt).
FD and DVARS are calculated for each functional run, both using their
implementations in *Nipype* [following the definitions by @power_fd_dvars].
The three global signals are extracted within the CSF, the WM, and
the whole-brain masks.
Additionally, a set of physiological regressors were extracted to
allow for component-based noise correction [*CompCor*, @compcor].
Principal components are estimated after high-pass filtering the
*preprocessed BOLD* time-series (using a discrete cosine filter with
128s cut-off) for the two *CompCor* variants: temporal (tCompCor)
and anatomical (aCompCor).
tCompCor components are then calculated from the top 2% variable
voxels within the brain mask.
For aCompCor, three probabilistic masks (CSF, WM and combined CSF+WM)
are generated in anatomical space.
The implementation differs from that of Behzadi et al. in that instead
of eroding the masks by 2 pixels on BOLD space, the aCompCor masks are
subtracted a mask of pixels that likely contain a volume fraction of GM.
This mask is obtained by {gm_desc}, and it ensures components are not extracted
from voxels containing a minimal fraction of GM.
Finally, these masks are resampled into BOLD space and binarized by
thresholding at 0.99 (as in the original implementation).
Components are also calculated separately within the WM and CSF masks.
For each CompCor decomposition, the *k* components with the largest singular
values are retained, such that the retained components' time series are
sufficient to explain 50 percent of variance across the nuisance mask (CSF,
WM, combined, or temporal). The remaining components are dropped from
consideration.
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file.
The confound time series derived from head motion estimates and global
signals were expanded with the inclusion of temporal derivatives and
quadratic terms for each [@confounds_satterthwaite_2013].
Frames that exceeded a threshold of {regressors_fd_th} mm FD or
{regressors_dvars_th} standardised DVARS were annotated as motion outliers.
"""
inputnode = pe.Node(niu.IdentityInterface(fields=[
'bold', 'bold_mask', 'movpar_file', 'rmsd_file', 'skip_vols',
't1w_mask', 't1w_tpms', 't1_bold_xform'
]),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=[
'confounds_file', 'confounds_metadata', 'acompcor_masks',
'tcompcor_mask'
]),
name='outputnode')
# DVARS
dvars = pe.Node(nac.ComputeDVARS(save_nstd=True,
save_std=True,
remove_zerovariance=True),
name="dvars",
mem_gb=mem_gb)
# Frame displacement
fdisp = pe.Node(nac.FramewiseDisplacement(parameter_source="SPM"),
name="fdisp",
mem_gb=mem_gb)
# Generate aCompCor probseg maps
acc_masks = pe.Node(aCompCorMasks(is_aseg=freesurfer), name="acc_masks")
# Resample probseg maps in BOLD space via T1w-to-BOLD transform
acc_msk_tfm = pe.MapNode(ApplyTransforms(interpolation='Gaussian',
float=False),
iterfield=["input_image"],
name='acc_msk_tfm',
mem_gb=0.1)
acc_msk_brain = pe.MapNode(ApplyMask(),
name="acc_msk_brain",
iterfield=["in_file"])
acc_msk_bin = pe.MapNode(Binarize(thresh_low=0.99),
name='acc_msk_bin',
iterfield=["in_file"])
acompcor = pe.Node(ACompCor(components_file='acompcor.tsv',
header_prefix='a_comp_cor_',
pre_filter='cosine',
save_pre_filter=True,
save_metadata=True,
mask_names=['CSF', 'WM', 'combined'],
merge_method='none',
failure_mode='NaN'),
name="acompcor",
mem_gb=mem_gb)
tcompcor = pe.Node(TCompCor(components_file='tcompcor.tsv',
header_prefix='t_comp_cor_',
pre_filter='cosine',
save_pre_filter=True,
save_metadata=True,
percentile_threshold=.02,
failure_mode='NaN'),
name="tcompcor",
mem_gb=mem_gb)
# Set number of components
if regressors_all_comps:
acompcor.inputs.num_components = 'all'
tcompcor.inputs.num_components = 'all'
else:
acompcor.inputs.variance_threshold = 0.5
tcompcor.inputs.variance_threshold = 0.5
# Set TR if present
if 'RepetitionTime' in metadata:
tcompcor.inputs.repetition_time = metadata['RepetitionTime']
acompcor.inputs.repetition_time = metadata['RepetitionTime']
# Global and segment regressors
signals_class_labels = [
"global_signal",
"csf",
"white_matter",
"csf_wm",
"tcompcor",
]
merge_rois = pe.Node(niu.Merge(3, ravel_inputs=True),
name='merge_rois',
run_without_submitting=True)
signals = pe.Node(SignalExtraction(class_labels=signals_class_labels),
name="signals",
mem_gb=mem_gb)
# Arrange confounds
add_dvars_header = pe.Node(AddTSVHeader(columns=["dvars"]),
name="add_dvars_header",
mem_gb=0.01,
run_without_submitting=True)
add_std_dvars_header = pe.Node(AddTSVHeader(columns=["std_dvars"]),
name="add_std_dvars_header",
mem_gb=0.01,
run_without_submitting=True)
add_motion_headers = pe.Node(AddTSVHeader(
columns=["trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"]),
name="add_motion_headers",
mem_gb=0.01,
run_without_submitting=True)
add_rmsd_header = pe.Node(AddTSVHeader(columns=["rmsd"]),
name="add_rmsd_header",
mem_gb=0.01,
run_without_submitting=True)
concat = pe.Node(GatherConfounds(),
name="concat",
mem_gb=0.01,
run_without_submitting=True)
# CompCor metadata
tcc_metadata_fmt = pe.Node(TSV2JSON(
index_column='component',
drop_columns=['mask'],
output=None,
additional_metadata={'Method': 'tCompCor'},
enforce_case=True),
name='tcc_metadata_fmt')
acc_metadata_fmt = pe.Node(TSV2JSON(
index_column='component',
output=None,
additional_metadata={'Method': 'aCompCor'},
enforce_case=True),
name='acc_metadata_fmt')
mrg_conf_metadata = pe.Node(niu.Merge(3),
name='merge_confound_metadata',
run_without_submitting=True)
mrg_conf_metadata.inputs.in3 = {
label: {
'Method': 'Mean'
}
for label in signals_class_labels
}
mrg_conf_metadata2 = pe.Node(DictMerge(),
name='merge_confound_metadata2',
run_without_submitting=True)
# Expand model to include derivatives and quadratics
model_expand = pe.Node(
ExpandModel(model_formula='(dd1(rps + wm + csf + gsr))^^2 + others'),
name='model_expansion')
# Add spike regressors
spike_regress = pe.Node(SpikeRegressors(fd_thresh=regressors_fd_th,
dvars_thresh=regressors_dvars_th),
name='spike_regressors')
# Generate reportlet (ROIs)
mrg_compcor = pe.Node(niu.Merge(2, ravel_inputs=True),
name='mrg_compcor',
run_without_submitting=True)
rois_plot = pe.Node(ROIsPlot(colors=['b', 'magenta'],
generate_report=True),
name='rois_plot',
mem_gb=mem_gb)
ds_report_bold_rois = pe.Node(DerivativesDataSink(
desc='rois', datatype="figures", dismiss_entities=("echo", )),
name='ds_report_bold_rois',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB)
# Generate reportlet (CompCor)
mrg_cc_metadata = pe.Node(niu.Merge(2),
name='merge_compcor_metadata',
run_without_submitting=True)
compcor_plot = pe.Node(CompCorVariancePlot(
variance_thresholds=(0.5, 0.7, 0.9),
metadata_sources=['tCompCor', 'aCompCor']),
name='compcor_plot')
ds_report_compcor = pe.Node(DerivativesDataSink(
desc='compcorvar', datatype="figures", dismiss_entities=("echo", )),
name='ds_report_compcor',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB)
# Generate reportlet (Confound correlation)
conf_corr_plot = pe.Node(ConfoundsCorrelationPlot(
reference_column='global_signal', max_dim=20),
name='conf_corr_plot')
ds_report_conf_corr = pe.Node(DerivativesDataSink(
desc='confoundcorr', datatype="figures", dismiss_entities=("echo", )),
name='ds_report_conf_corr',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB)
def _last(inlist):
return inlist[-1]
def _select_cols(table):
import pandas as pd
return [
col for col in pd.read_table(table, nrows=2).columns
if not col.startswith(("a_comp_cor_", "t_comp_cor_", "std_dvars"))
]
workflow.connect([
# connect inputnode to each non-anatomical confound node
(inputnode, dvars, [('bold', 'in_file'), ('bold_mask', 'in_mask')]),
(inputnode, fdisp, [('movpar_file', 'in_file')]),
# aCompCor
(inputnode, acompcor, [("bold", "realigned_file"),
("skip_vols", "ignore_initial_volumes")]),
(inputnode, acc_masks, [("t1w_tpms", "in_vfs"),
(("bold", _get_zooms), "bold_zooms")]),
(inputnode, acc_msk_tfm, [("t1_bold_xform", "transforms"),
("bold_mask", "reference_image")]),
(inputnode, acc_msk_brain, [("bold_mask", "in_mask")]),
(acc_masks, acc_msk_tfm, [("out_masks", "input_image")]),
(acc_msk_tfm, acc_msk_brain, [("output_image", "in_file")]),
(acc_msk_brain, acc_msk_bin, [("out_file", "in_file")]),
(acc_msk_bin, acompcor, [("out_file", "mask_files")]),
# tCompCor
(inputnode, tcompcor, [("bold", "realigned_file"),
("skip_vols", "ignore_initial_volumes"),
("bold_mask", "mask_files")]),
# Global signals extraction (constrained by anatomy)
(inputnode, signals, [('bold', 'in_file')]),
(inputnode, merge_rois, [('bold_mask', 'in1')]),
(acc_msk_bin, merge_rois, [('out_file', 'in2')]),
(tcompcor, merge_rois, [('high_variance_masks', 'in3')]),
(merge_rois, signals, [('out', 'label_files')]),
# Collate computed confounds together
(inputnode, add_motion_headers, [('movpar_file', 'in_file')]),
(inputnode, add_rmsd_header, [('rmsd_file', 'in_file')]),
(dvars, add_dvars_header, [('out_nstd', 'in_file')]),
(dvars, add_std_dvars_header, [('out_std', 'in_file')]),
(signals, concat, [('out_file', 'signals')]),
(fdisp, concat, [('out_file', 'fd')]),
(tcompcor, concat, [('components_file', 'tcompcor'),
('pre_filter_file', 'cos_basis')]),
(acompcor, concat, [('components_file', 'acompcor')]),
(add_motion_headers, concat, [('out_file', 'motion')]),
(add_rmsd_header, concat, [('out_file', 'rmsd')]),
(add_dvars_header, concat, [('out_file', 'dvars')]),
(add_std_dvars_header, concat, [('out_file', 'std_dvars')]),
# Confounds metadata
(tcompcor, tcc_metadata_fmt, [('metadata_file', 'in_file')]),
(acompcor, acc_metadata_fmt, [('metadata_file', 'in_file')]),
(tcc_metadata_fmt, mrg_conf_metadata, [('output', 'in1')]),
(acc_metadata_fmt, mrg_conf_metadata, [('output', 'in2')]),
(mrg_conf_metadata, mrg_conf_metadata2, [('out', 'in_dicts')]),
# Expand the model with derivatives, quadratics, and spikes
(concat, model_expand, [('confounds_file', 'confounds_file')]),
(model_expand, spike_regress, [('confounds_file', 'confounds_file')]),
# Set outputs
(spike_regress, outputnode, [('confounds_file', 'confounds_file')]),
(mrg_conf_metadata2, outputnode, [('out_dict', 'confounds_metadata')]),
(tcompcor, outputnode, [("high_variance_masks", "tcompcor_mask")]),
(acc_msk_bin, outputnode, [("out_file", "acompcor_masks")]),
(inputnode, rois_plot, [('bold', 'in_file'),
('bold_mask', 'in_mask')]),
(tcompcor, mrg_compcor, [('high_variance_masks', 'in1')]),
(acc_msk_bin, mrg_compcor, [(('out_file', _last), 'in2')]),
(mrg_compcor, rois_plot, [('out', 'in_rois')]),
(rois_plot, ds_report_bold_rois, [('out_report', 'in_file')]),
(tcompcor, mrg_cc_metadata, [('metadata_file', 'in1')]),
(acompcor, mrg_cc_metadata, [('metadata_file', 'in2')]),
(mrg_cc_metadata, compcor_plot, [('out', 'metadata_files')]),
(compcor_plot, ds_report_compcor, [('out_file', 'in_file')]),
(concat, conf_corr_plot, [('confounds_file', 'confounds_file'),
(('confounds_file', _select_cols), 'columns')
]),
(conf_corr_plot, ds_report_conf_corr, [('out_file', 'in_file')]),
])
return workflow
def init_func_preproc_wf(bold_file):
"""
This workflow controls the functional preprocessing stages of *fMRIPrep*.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.tests import mock_config
from fmriprep import config
from fmriprep.workflows.bold.base import init_func_preproc_wf
with mock_config():
bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
/ 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
wf = init_func_preproc_wf(str(bold_file))
Parameters
----------
bold_file
BOLD series NIfTI file
Inputs
------
bold_file
BOLD series NIfTI file
t1w_preproc
Bias-corrected structural template image
t1w_mask
Mask of the skull-stripped template image
t1w_dseg
Segmentation of preprocessed structural image, including
gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)
t1w_asec
Segmentation of structural image, done with FreeSurfer.
t1w_aparc
Parcellation of structural image, done with FreeSurfer.
t1w_tpms
List of tissue probability maps in T1w space
template
List of templates to target
anat2std_xfm
List of transform files, collated with templates
std2anat_xfm
List of inverse transform files, collated with templates
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1w2fsnative_xfm
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
fsnative2t1w_xfm
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
Outputs
-------
bold_t1
BOLD series, resampled to T1w space
bold_mask_t1
BOLD series mask in T1w space
bold_std
BOLD series, resampled to template space
bold_mask_std
BOLD series mask in template space
confounds
TSV of confounds
surfaces
BOLD series, resampled to FreeSurfer surfaces
aroma_noise_ics
Noise components identified by ICA-AROMA
melodic_mix
FSL MELODIC mixing matrix
bold_cifti
BOLD CIFTI image
cifti_variant
combination of target spaces for `bold_cifti`
See Also
--------
* :py:func:`~niworkflows.func.util.init_bold_reference_wf`
* :py:func:`~fmriprep.workflows.bold.stc.init_bold_stc_wf`
* :py:func:`~fmriprep.workflows.bold.hmc.init_bold_hmc_wf`
* :py:func:`~fmriprep.workflows.bold.t2s.init_bold_t2s_wf`
* :py:func:`~fmriprep.workflows.bold.registration.init_bold_t1_trans_wf`
* :py:func:`~fmriprep.workflows.bold.registration.init_bold_reg_wf`
* :py:func:`~fmriprep.workflows.bold.confounds.init_bold_confounds_wf`
* :py:func:`~fmriprep.workflows.bold.confounds.init_ica_aroma_wf`
* :py:func:`~fmriprep.workflows.bold.resampling.init_bold_std_trans_wf`
* :py:func:`~fmriprep.workflows.bold.resampling.init_bold_preproc_trans_wf`
* :py:func:`~fmriprep.workflows.bold.resampling.init_bold_surf_wf`
* :py:func:`~sdcflows.workflows.fmap.init_fmap_wf`
* :py:func:`~sdcflows.workflows.pepolar.init_pepolar_unwarp_wf`
* :py:func:`~sdcflows.workflows.phdiff.init_phdiff_wf`
* :py:func:`~sdcflows.workflows.syn.init_syn_sdc_wf`
* :py:func:`~sdcflows.workflows.unwarp.init_sdc_unwarp_wf`
"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.func.util import init_bold_reference_wf
from niworkflows.interfaces.nibabel import ApplyMask
from niworkflows.interfaces.utility import KeySelect
from niworkflows.interfaces.utils import DictMerge
from sdcflows.workflows.base import init_sdc_estimate_wf, fieldmap_wrangler
ref_file = bold_file
mem_gb = {'filesize': 1, 'resampled': 1, 'largemem': 1}
bold_tlen = 10
multiecho = isinstance(bold_file, list)
# Have some options handy
layout = config.execution.layout
omp_nthreads = config.nipype.omp_nthreads
freesurfer = config.workflow.run_reconall
spaces = config.workflow.spaces
if multiecho:
tes = [layout.get_metadata(echo)['EchoTime'] for echo in bold_file]
ref_file = dict(zip(tes, bold_file))[min(tes)]
if os.path.isfile(ref_file):
bold_tlen, mem_gb = _create_mem_gb(ref_file)
wf_name = _get_wf_name(ref_file)
config.loggers.workflow.debug(
'Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
'Memory resampled/largemem=%.2f/%.2f GB.', ref_file,
mem_gb['filesize'], bold_tlen, mem_gb['resampled'], mem_gb['largemem'])
sbref_file = None
# Find associated sbref, if possible
entities = layout.parse_file_entities(ref_file)
entities['suffix'] = 'sbref'
entities['extension'] = ['nii', 'nii.gz'] # Overwrite extensions
files = layout.get(return_type='file', **entities)
refbase = os.path.basename(ref_file)
if 'sbref' in config.workflow.ignore:
config.loggers.workflow.info("Single-band reference files ignored.")
elif files and multiecho:
config.loggers.workflow.warning(
"Single-band reference found, but not supported in "
"multi-echo workflows at this time. Ignoring.")
elif files:
sbref_file = files[0]
sbbase = os.path.basename(sbref_file)
if len(files) > 1:
config.loggers.workflow.warning(
"Multiple single-band reference files found for {}; using "
"{}".format(refbase, sbbase))
else:
config.loggers.workflow.info(
"Using single-band reference file %s.", sbbase)
else:
config.loggers.workflow.info("No single-band-reference found for %s.",
refbase)
metadata = layout.get_metadata(ref_file)
# Find fieldmaps. Options: (phase1|phase2|phasediff|epi|fieldmap|syn)
fmaps = None
if 'fieldmaps' not in config.workflow.ignore:
fmaps = fieldmap_wrangler(layout,
ref_file,
use_syn=config.workflow.use_syn,
force_syn=config.workflow.force_syn)
elif config.workflow.use_syn or config.workflow.force_syn:
# If fieldmaps are not enabled, activate SyN-SDC in unforced (False) mode
fmaps = {'syn': False}
# Short circuits: (True and True and (False or 'TooShort')) == 'TooShort'
run_stc = (bool(metadata.get("SliceTiming"))
and 'slicetiming' not in config.workflow.ignore
and (_get_series_len(ref_file) > 4 or "TooShort"))
# Check if MEEPI for T2* coregistration target
if config.workflow.t2s_coreg and not multiecho:
config.loggers.workflow.warning(
"No multiecho BOLD images found for T2* coregistration. "
"Using standard EPI-T1 coregistration.")
config.workflow.t2s_coreg = False
# By default, force-bbr for t2s_coreg unless user specifies otherwise
if config.workflow.t2s_coreg and config.workflow.use_bbr is None:
config.workflow.use_bbr = True
# Build workflow
workflow = Workflow(name=wf_name)
workflow.__postdesc__ = """\
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
transform matrices, susceptibility distortion correction when available,
and co-registrations to anatomical and output spaces).
Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
configured with Lanczos interpolation to minimize the smoothing
effects of other kernels [@lanczos].
Non-gridded (surface) resamplings were performed using `mri_vol2surf`
(FreeSurfer).
"""
inputnode = pe.Node(niu.IdentityInterface(fields=[
'bold_file', 'subjects_dir', 'subject_id', 't1w_preproc', 't1w_mask',
't1w_dseg', 't1w_tpms', 't1w_aseg', 't1w_aparc', 'anat2std_xfm',
'std2anat_xfm', 'template', 't1w2fsnative_xfm', 'fsnative2t1w_xfm'
]),
name='inputnode')
inputnode.inputs.bold_file = bold_file
if sbref_file is not None:
from niworkflows.interfaces.images import ValidateImage
val_sbref = pe.Node(ValidateImage(in_file=sbref_file),
name='val_sbref')
outputnode = pe.Node(niu.IdentityInterface(fields=[
'bold_t1', 'bold_t1_ref', 'bold_mask_t1', 'bold_aseg_t1',
'bold_aparc_t1', 'bold_std', 'bold_std_ref', 'bold_mask_std',
'bold_aseg_std', 'bold_aparc_std', 'bold_native', 'bold_cifti',
'cifti_variant', 'cifti_metadata', 'cifti_density', 'surfaces',
'confounds', 'aroma_noise_ics', 'melodic_mix', 'nonaggr_denoised_file',
'confounds_metadata'
]),
name='outputnode')
# Generate a brain-masked conversion of the t1w
t1w_brain = pe.Node(ApplyMask(), name='t1w_brain')
# BOLD buffer: an identity used as a pointer to either the original BOLD
# or the STC'ed one for further use.
boldbuffer = pe.Node(niu.IdentityInterface(fields=['bold_file']),
name='boldbuffer')
summary = pe.Node(FunctionalSummary(
slice_timing=run_stc,
registration=('FSL', 'FreeSurfer')[freesurfer],
registration_dof=config.workflow.bold2t1w_dof,
registration_init=config.workflow.bold2t1w_init,
pe_direction=metadata.get("PhaseEncodingDirection"),
tr=metadata.get("RepetitionTime")),
name='summary',
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
run_without_submitting=True)
summary.inputs.dummy_scans = config.workflow.dummy_scans
func_derivatives_wf = init_func_derivatives_wf(
bids_root=layout.root,
cifti_output=config.workflow.cifti_output,
freesurfer=freesurfer,
metadata=metadata,
output_dir=str(config.execution.output_dir),
spaces=spaces,
use_aroma=config.workflow.use_aroma,
)
workflow.connect([
(outputnode, func_derivatives_wf, [
('bold_t1', 'inputnode.bold_t1'),
('bold_t1_ref', 'inputnode.bold_t1_ref'),
('bold_aseg_t1', 'inputnode.bold_aseg_t1'),
('bold_aparc_t1', 'inputnode.bold_aparc_t1'),
('bold_mask_t1', 'inputnode.bold_mask_t1'),
('bold_native', 'inputnode.bold_native'),
('confounds', 'inputnode.confounds'),
('surfaces', 'inputnode.surf_files'),
('aroma_noise_ics', 'inputnode.aroma_noise_ics'),
('melodic_mix', 'inputnode.melodic_mix'),
('nonaggr_denoised_file', 'inputnode.nonaggr_denoised_file'),
('bold_cifti', 'inputnode.bold_cifti'),
('cifti_variant', 'inputnode.cifti_variant'),
('cifti_metadata', 'inputnode.cifti_metadata'),
('cifti_density', 'inputnode.cifti_density'),
('confounds_metadata', 'inputnode.confounds_metadata'),
]),
])
# Generate a tentative boldref
bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
bold_reference_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
if sbref_file is not None:
workflow.connect([
(val_sbref, bold_reference_wf, [('out_file',
'inputnode.sbref_file')]),
])
# Top-level BOLD splitter
bold_split = pe.Node(FSLSplit(dimension='t'),
name='bold_split',
mem_gb=mem_gb['filesize'] * 3)
# HMC on the BOLD
bold_hmc_wf = init_bold_hmc_wf(name='bold_hmc_wf',
mem_gb=mem_gb['filesize'],
omp_nthreads=omp_nthreads)
# calculate BOLD registration to T1w
bold_reg_wf = init_bold_reg_wf(name='bold_reg_wf',
freesurfer=freesurfer,
use_bbr=config.workflow.use_bbr,
bold2t1w_dof=config.workflow.bold2t1w_dof,
bold2t1w_init=config.workflow.bold2t1w_init,
mem_gb=mem_gb['resampled'],
omp_nthreads=omp_nthreads,
use_compression=False)
# apply BOLD registration to T1w
bold_t1_trans_wf = init_bold_t1_trans_wf(name='bold_t1_trans_wf',
freesurfer=freesurfer,
use_fieldwarp=bool(fmaps),
multiecho=multiecho,
mem_gb=mem_gb['resampled'],
omp_nthreads=omp_nthreads,
use_compression=False)
# get confounds
bold_confounds_wf = init_bold_confs_wf(
mem_gb=mem_gb['largemem'],
metadata=metadata,
regressors_all_comps=config.workflow.regressors_all_comps,
regressors_fd_th=config.workflow.regressors_fd_th,
regressors_dvars_th=config.workflow.regressors_dvars_th,
name='bold_confounds_wf')
bold_confounds_wf.get_node('inputnode').inputs.t1_transform_flags = [False]
# Apply transforms in 1 shot
# Only use uncompressed output if AROMA is to be run
bold_bold_trans_wf = init_bold_preproc_trans_wf(
mem_gb=mem_gb['resampled'],
omp_nthreads=omp_nthreads,
use_compression=not config.execution.low_mem,
use_fieldwarp=bool(fmaps),
name='bold_bold_trans_wf')
bold_bold_trans_wf.inputs.inputnode.name_source = ref_file
# SLICE-TIME CORRECTION (or bypass) #############################################
if run_stc is True: # bool('TooShort') == True, so check True explicitly
bold_stc_wf = init_bold_stc_wf(name='bold_stc_wf', metadata=metadata)
workflow.connect([
(bold_reference_wf, bold_stc_wf, [('outputnode.skip_vols',
'inputnode.skip_vols')]),
(bold_stc_wf, boldbuffer, [('outputnode.stc_file', 'bold_file')]),
])
if not multiecho:
workflow.connect([(bold_reference_wf, bold_stc_wf, [
('outputnode.bold_file', 'inputnode.bold_file')
])])
else: # for meepi, iterate through stc_wf for all workflows
meepi_echos = boldbuffer.clone(name='meepi_echos')
meepi_echos.iterables = ('bold_file', bold_file)
workflow.connect([(meepi_echos, bold_stc_wf,
[('bold_file', 'inputnode.bold_file')])])
elif not multiecho: # STC is too short or False
# bypass STC from original BOLD to the splitter through boldbuffer
workflow.connect([(bold_reference_wf, boldbuffer,
[('outputnode.bold_file', 'bold_file')])])
else:
# for meepi, iterate over all meepi echos to boldbuffer
boldbuffer.iterables = ('bold_file', bold_file)
# SDC (SUSCEPTIBILITY DISTORTION CORRECTION) or bypass ##########################
bold_sdc_wf = init_sdc_estimate_wf(fmaps,
metadata,
omp_nthreads=omp_nthreads,
debug=config.execution.debug)
# MULTI-ECHO EPI DATA #############################################
if multiecho:
from niworkflows.func.util import init_skullstrip_bold_wf
skullstrip_bold_wf = init_skullstrip_bold_wf(name='skullstrip_bold_wf')
inputnode.inputs.bold_file = ref_file # Replace reference w first echo
join_echos = pe.JoinNode(
niu.IdentityInterface(fields=['bold_files']),
joinsource=('meepi_echos' if run_stc is True else 'boldbuffer'),
joinfield=['bold_files'],
name='join_echos')
# create optimal combination, adaptive T2* map
bold_t2s_wf = init_bold_t2s_wf(echo_times=tes,
mem_gb=mem_gb['resampled'],
omp_nthreads=omp_nthreads,
t2s_coreg=config.workflow.t2s_coreg,
name='bold_t2smap_wf')
workflow.connect([
(skullstrip_bold_wf, join_echos,
[('outputnode.skull_stripped_file', 'bold_files')]),
(join_echos, bold_t2s_wf, [('bold_files', 'inputnode.bold_file')]),
])
# MAIN WORKFLOW STRUCTURE #######################################################
workflow.connect([
(inputnode, t1w_brain, [('t1w_preproc', 'in_file'),
('t1w_mask', 'in_mask')]),
# Generate early reference
(inputnode, bold_reference_wf, [('bold_file', 'inputnode.bold_file')]),
# BOLD buffer has slice-time corrected if it was run, original otherwise
(boldbuffer, bold_split, [('bold_file', 'in_file')]),
# HMC
(bold_reference_wf, bold_hmc_wf,
[('outputnode.raw_ref_image', 'inputnode.raw_ref_image'),
('outputnode.bold_file', 'inputnode.bold_file')]),
(bold_reference_wf, summary, [('outputnode.algo_dummy_scans',
'algo_dummy_scans')]),
# EPI-T1 registration workflow
(
inputnode,
bold_reg_wf,
[
('t1w_dseg', 'inputnode.t1w_dseg'),
# Undefined if --fs-no-reconall, but this is safe
('subjects_dir', 'inputnode.subjects_dir'),
('subject_id', 'inputnode.subject_id'),
('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')
]),
(t1w_brain, bold_reg_wf, [('out_file', 'inputnode.t1w_brain')]),
(inputnode, bold_t1_trans_wf, [('bold_file', 'inputnode.name_source'),
('t1w_mask', 'inputnode.t1w_mask'),
('t1w_aseg', 'inputnode.t1w_aseg'),
('t1w_aparc', 'inputnode.t1w_aparc')]),
(t1w_brain, bold_t1_trans_wf, [('out_file', 'inputnode.t1w_brain')]),
# unused if multiecho, but this is safe
(bold_hmc_wf, bold_t1_trans_wf, [('outputnode.xforms',
'inputnode.hmc_xforms')]),
(bold_reg_wf, bold_t1_trans_wf, [('outputnode.itk_bold_to_t1',
'inputnode.itk_bold_to_t1')]),
(bold_t1_trans_wf, outputnode,
[('outputnode.bold_t1', 'bold_t1'),
('outputnode.bold_t1_ref', 'bold_t1_ref'),
('outputnode.bold_aseg_t1', 'bold_aseg_t1'),
('outputnode.bold_aparc_t1', 'bold_aparc_t1')]),
(bold_reg_wf, summary, [('outputnode.fallback', 'fallback')]),
# SDC (or pass-through workflow)
(t1w_brain, bold_sdc_wf, [('out_file', 'inputnode.t1w_brain')]),
(bold_reference_wf, bold_sdc_wf,
[('outputnode.ref_image', 'inputnode.epi_file'),
('outputnode.ref_image_brain', 'inputnode.epi_brain'),
('outputnode.bold_mask', 'inputnode.epi_mask')]),
(bold_sdc_wf, bold_t1_trans_wf, [('outputnode.out_warp',
'inputnode.fieldwarp')]),
(bold_sdc_wf, bold_bold_trans_wf,
[('outputnode.out_warp', 'inputnode.fieldwarp'),
('outputnode.epi_mask', 'inputnode.bold_mask')]),
(bold_sdc_wf, summary, [('outputnode.method', 'distortion_correction')
]),
# Connect bold_confounds_wf
(inputnode, bold_confounds_wf, [('t1w_tpms', 'inputnode.t1w_tpms'),
('t1w_mask', 'inputnode.t1w_mask')]),
(bold_hmc_wf, bold_confounds_wf, [('outputnode.movpar_file',
'inputnode.movpar_file')]),
(bold_reg_wf, bold_confounds_wf, [('outputnode.itk_t1_to_bold',
'inputnode.t1_bold_xform')]),
(bold_reference_wf, bold_confounds_wf, [('outputnode.skip_vols',
'inputnode.skip_vols')]),
(bold_confounds_wf, outputnode, [
('outputnode.confounds_file', 'confounds'),
]),
(bold_confounds_wf, outputnode, [
('outputnode.confounds_metadata', 'confounds_metadata'),
]),
# Connect bold_bold_trans_wf
(bold_split, bold_bold_trans_wf, [('out_files', 'inputnode.bold_file')]
),
(bold_hmc_wf, bold_bold_trans_wf, [('outputnode.xforms',
'inputnode.hmc_xforms')]),
# Summary
(outputnode, summary, [('confounds', 'confounds_file')]),
])
if not config.workflow.t2s_coreg:
workflow.connect([
(bold_sdc_wf, bold_reg_wf, [('outputnode.epi_brain',
'inputnode.ref_bold_brain')]),
(bold_sdc_wf, bold_t1_trans_wf,
[('outputnode.epi_brain', 'inputnode.ref_bold_brain'),
('outputnode.epi_mask', 'inputnode.ref_bold_mask')]),
])
else:
workflow.connect([
# For t2s_coreg, replace EPI-to-T1w registration inputs
(bold_t2s_wf, bold_reg_wf, [('outputnode.bold_ref_brain',
'inputnode.ref_bold_brain')]),
(bold_t2s_wf, bold_t1_trans_wf,
[('outputnode.bold_ref_brain', 'inputnode.ref_bold_brain'),
('outputnode.bold_mask', 'inputnode.ref_bold_mask')]),
])
# for standard EPI data, pass along correct file
if not multiecho:
workflow.connect([
(inputnode, func_derivatives_wf, [('bold_file',
'inputnode.source_file')]),
(bold_bold_trans_wf, bold_confounds_wf,
[('outputnode.bold', 'inputnode.bold'),
('outputnode.bold_mask', 'inputnode.bold_mask')]),
(bold_split, bold_t1_trans_wf, [('out_files',
'inputnode.bold_split')]),
])
else: # for meepi, create and use optimal combination
workflow.connect([
# update name source for optimal combination
(inputnode, func_derivatives_wf,
[(('bold_file', combine_meepi_source), 'inputnode.source_file')]),
(bold_bold_trans_wf, skullstrip_bold_wf, [('outputnode.bold',
'inputnode.in_file')]),
(bold_t2s_wf, bold_confounds_wf,
[('outputnode.bold', 'inputnode.bold'),
('outputnode.bold_mask', 'inputnode.bold_mask')]),
(bold_t2s_wf, bold_t1_trans_wf, [('outputnode.bold',
'inputnode.bold_split')]),
])
if fmaps:
from sdcflows.workflows.outputs import init_sdc_unwarp_report_wf
# Report on BOLD correction
fmap_unwarp_report_wf = init_sdc_unwarp_report_wf()
workflow.connect([
(inputnode, fmap_unwarp_report_wf, [('t1w_dseg',
'inputnode.in_seg')]),
(bold_reference_wf, fmap_unwarp_report_wf,
[('outputnode.ref_image', 'inputnode.in_pre')]),
(bold_reg_wf, fmap_unwarp_report_wf, [('outputnode.itk_t1_to_bold',
'inputnode.in_xfm')]),
(bold_sdc_wf, fmap_unwarp_report_wf, [('outputnode.epi_corrected',
'inputnode.in_post')]),
])
# Overwrite ``out_path_base`` of unwarping DataSinks
for node in fmap_unwarp_report_wf.list_node_names():
if node.split('.')[-1].startswith('ds_'):
fmap_unwarp_report_wf.get_node(
node).interface.out_path_base = 'fmriprep'
for node in bold_sdc_wf.list_node_names():
if node.split('.')[-1].startswith('ds_'):
bold_sdc_wf.get_node(node).interface.out_path_base = 'fmriprep'
if 'syn' in fmaps:
sdc_select_std = pe.Node(KeySelect(fields=['std2anat_xfm']),
name='sdc_select_std',
run_without_submitting=True)
sdc_select_std.inputs.key = 'MNI152NLin2009cAsym'
workflow.connect([
(inputnode, sdc_select_std, [('std2anat_xfm', 'std2anat_xfm'),
('template', 'keys')]),
(sdc_select_std, bold_sdc_wf, [('std2anat_xfm',
'inputnode.std2anat_xfm')]),
])
if fmaps.get('syn') is True: # SyN forced
syn_unwarp_report_wf = init_sdc_unwarp_report_wf(
name='syn_unwarp_report_wf', forcedsyn=True)
workflow.connect([
(inputnode, syn_unwarp_report_wf, [('t1w_dseg',
'inputnode.in_seg')]),
(bold_reference_wf, syn_unwarp_report_wf,
[('outputnode.ref_image', 'inputnode.in_pre')]),
(bold_reg_wf, syn_unwarp_report_wf,
[('outputnode.itk_t1_to_bold', 'inputnode.in_xfm')]),
(bold_sdc_wf, syn_unwarp_report_wf, [('outputnode.syn_ref',
'inputnode.in_post')]),
])
# Overwrite ``out_path_base`` of unwarping DataSinks
for node in syn_unwarp_report_wf.list_node_names():
if node.split('.')[-1].startswith('ds_'):
syn_unwarp_report_wf.get_node(
node).interface.out_path_base = 'fmriprep'
# Map final BOLD mask into T1w space (if required)
nonstd_spaces = set(spaces.get_nonstandard())
if nonstd_spaces.intersection(('T1w', 'anat')):
from niworkflows.interfaces.fixes import (FixHeaderApplyTransforms as
ApplyTransforms)
boldmask_to_t1w = pe.Node(ApplyTransforms(interpolation='MultiLabel',
float=True),
name='boldmask_to_t1w',
mem_gb=0.1)
workflow.connect([
(bold_reg_wf, boldmask_to_t1w, [('outputnode.itk_bold_to_t1',
'transforms')]),
(bold_t1_trans_wf, boldmask_to_t1w, [('outputnode.bold_mask_t1',
'reference_image')]),
(bold_bold_trans_wf if not multiecho else bold_t2s_wf,
boldmask_to_t1w, [('outputnode.bold_mask', 'input_image')]),
(boldmask_to_t1w, outputnode, [('output_image', 'bold_mask_t1')]),
])
if nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref')):
workflow.connect([
(bold_bold_trans_wf, outputnode, [('outputnode.bold',
'bold_native')]),
(bold_bold_trans_wf, func_derivatives_wf,
[('outputnode.bold_ref', 'inputnode.bold_native_ref'),
('outputnode.bold_mask', 'inputnode.bold_mask_native')]),
])
if spaces.get_spaces(nonstandard=False, dim=(3, )):
# Apply transforms in 1 shot
# Only use uncompressed output if AROMA is to be run
bold_std_trans_wf = init_bold_std_trans_wf(
freesurfer=freesurfer,
mem_gb=mem_gb['resampled'],
omp_nthreads=omp_nthreads,
spaces=spaces,
name='bold_std_trans_wf',
use_compression=not config.execution.low_mem,
use_fieldwarp=bool(fmaps),
)
workflow.connect([
(inputnode, bold_std_trans_wf,
[('template', 'inputnode.templates'),
('anat2std_xfm', 'inputnode.anat2std_xfm'),
('bold_file', 'inputnode.name_source'),
('t1w_aseg', 'inputnode.bold_aseg'),
('t1w_aparc', 'inputnode.bold_aparc')]),
(bold_hmc_wf, bold_std_trans_wf, [('outputnode.xforms',
'inputnode.hmc_xforms')]),
(bold_reg_wf, bold_std_trans_wf, [('outputnode.itk_bold_to_t1',
'inputnode.itk_bold_to_t1')]),
(bold_bold_trans_wf if not multiecho else bold_t2s_wf,
bold_std_trans_wf, [('outputnode.bold_mask',
'inputnode.bold_mask')]),
(bold_sdc_wf, bold_std_trans_wf, [('outputnode.out_warp',
'inputnode.fieldwarp')]),
(bold_std_trans_wf, outputnode,
[('outputnode.bold_std', 'bold_std'),
('outputnode.bold_std_ref', 'bold_std_ref'),
('outputnode.bold_mask_std', 'bold_mask_std')]),
])
if freesurfer:
workflow.connect([
(bold_std_trans_wf, func_derivatives_wf, [
('outputnode.bold_aseg_std', 'inputnode.bold_aseg_std'),
('outputnode.bold_aparc_std', 'inputnode.bold_aparc_std'),
]),
(bold_std_trans_wf, outputnode,
[('outputnode.bold_aseg_std', 'bold_aseg_std'),
('outputnode.bold_aparc_std', 'bold_aparc_std')]),
])
if not multiecho:
workflow.connect([(bold_split, bold_std_trans_wf,
[('out_files', 'inputnode.bold_split')])])
else:
split_opt_comb = bold_split.clone(name='split_opt_comb')
workflow.connect([(bold_t2s_wf, split_opt_comb,
[('outputnode.bold', 'in_file')]),
(split_opt_comb, bold_std_trans_wf,
[('out_files', 'inputnode.bold_split')])])
# func_derivatives_wf internally parametrizes over snapshotted spaces.
workflow.connect([
(bold_std_trans_wf, func_derivatives_wf, [
('outputnode.template', 'inputnode.template'),
('outputnode.spatial_reference',
'inputnode.spatial_reference'),
('outputnode.bold_std_ref', 'inputnode.bold_std_ref'),
('outputnode.bold_std', 'inputnode.bold_std'),
('outputnode.bold_mask_std', 'inputnode.bold_mask_std'),
]),
])
if config.workflow.use_aroma: # ICA-AROMA workflow
from .confounds import init_ica_aroma_wf
ica_aroma_wf = init_ica_aroma_wf(
mem_gb=mem_gb['resampled'],
metadata=metadata,
omp_nthreads=omp_nthreads,
use_fieldwarp=bool(fmaps),
err_on_aroma_warn=config.workflow.aroma_err_on_warn,
aroma_melodic_dim=config.workflow.aroma_melodic_dim,
name='ica_aroma_wf')
join = pe.Node(niu.Function(output_names=["out_file"],
function=_to_join),
name='aroma_confounds')
mrg_conf_metadata = pe.Node(niu.Merge(2),
name='merge_confound_metadata',
run_without_submitting=True)
mrg_conf_metadata2 = pe.Node(DictMerge(),
name='merge_confound_metadata2',
run_without_submitting=True)
workflow.disconnect([
(bold_confounds_wf, outputnode, [
('outputnode.confounds_file', 'confounds'),
]),
(bold_confounds_wf, outputnode, [
('outputnode.confounds_metadata', 'confounds_metadata'),
]),
])
workflow.connect([
(inputnode, ica_aroma_wf, [('bold_file',
'inputnode.name_source')]),
(bold_hmc_wf, ica_aroma_wf, [('outputnode.movpar_file',
'inputnode.movpar_file')]),
(bold_reference_wf, ica_aroma_wf, [('outputnode.skip_vols',
'inputnode.skip_vols')]),
(bold_confounds_wf, join, [('outputnode.confounds_file',
'in_file')]),
(bold_confounds_wf, mrg_conf_metadata,
[('outputnode.confounds_metadata', 'in1')]),
(ica_aroma_wf, join, [('outputnode.aroma_confounds',
'join_file')]),
(ica_aroma_wf, mrg_conf_metadata,
[('outputnode.aroma_metadata', 'in2')]),
(mrg_conf_metadata, mrg_conf_metadata2, [('out', 'in_dicts')]),
(ica_aroma_wf, outputnode,
[('outputnode.aroma_noise_ics', 'aroma_noise_ics'),
('outputnode.melodic_mix', 'melodic_mix'),
('outputnode.nonaggr_denoised_file', 'nonaggr_denoised_file')
]),
(join, outputnode, [('out_file', 'confounds')]),
(mrg_conf_metadata2, outputnode, [('out_dict',
'confounds_metadata')]),
(bold_std_trans_wf, ica_aroma_wf,
[('outputnode.bold_std', 'inputnode.bold_std'),
('outputnode.bold_mask_std', 'inputnode.bold_mask_std'),
('outputnode.spatial_reference',
'inputnode.spatial_reference')]),
])
# SURFACES ##################################################################################
# Freesurfer
freesurfer_spaces = spaces.get_fs_spaces()
if freesurfer and freesurfer_spaces:
config.loggers.workflow.debug(
'Creating BOLD surface-sampling workflow.')
bold_surf_wf = init_bold_surf_wf(
mem_gb=mem_gb['resampled'],
surface_spaces=freesurfer_spaces,
medial_surface_nan=config.workflow.medial_surface_nan,
name='bold_surf_wf')
workflow.connect([
(inputnode, bold_surf_wf,
[('t1w_preproc', 'inputnode.t1w_preproc'),
('subjects_dir', 'inputnode.subjects_dir'),
('subject_id', 'inputnode.subject_id'),
('t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm')]),
(bold_t1_trans_wf, bold_surf_wf, [('outputnode.bold_t1',
'inputnode.source_file')]),
(bold_surf_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
(bold_surf_wf, func_derivatives_wf, [('outputnode.target',
'inputnode.surf_refs')]),
])
# CIFTI output
if config.workflow.cifti_output:
from .resampling import init_bold_grayords_wf
bold_grayords_wf = init_bold_grayords_wf(
grayord_density=config.workflow.cifti_output,
mem_gb=mem_gb['resampled'],
repetition_time=metadata['RepetitionTime'])
workflow.connect([
(inputnode, bold_grayords_wf, [('subjects_dir',
'inputnode.subjects_dir')]),
(bold_std_trans_wf, bold_grayords_wf,
[('outputnode.bold_std', 'inputnode.bold_std'),
('outputnode.spatial_reference',
'inputnode.spatial_reference')]),
(bold_surf_wf, bold_grayords_wf, [
('outputnode.surfaces', 'inputnode.surf_files'),
('outputnode.target', 'inputnode.surf_refs'),
]),
(bold_grayords_wf, outputnode,
[('outputnode.cifti_bold', 'bold_cifti'),
('outputnode.cifti_variant', 'cifti_variant'),
('outputnode.cifti_metadata', 'cifti_metadata'),
('outputnode.cifti_density', 'cifti_density')]),
])
if spaces.get_spaces(nonstandard=False, dim=(3, )):
carpetplot_wf = init_carpetplot_wf(
mem_gb=mem_gb['resampled'],
metadata=metadata,
cifti_output=config.workflow.cifti_output,
name='carpetplot_wf')
if config.workflow.cifti_output:
workflow.connect(bold_grayords_wf, 'outputnode.cifti_bold',
carpetplot_wf, 'inputnode.cifti_bold')
else:
# Xform to 'MNI152NLin2009cAsym' is always computed.
carpetplot_select_std = pe.Node(KeySelect(
fields=['std2anat_xfm'], key='MNI152NLin2009cAsym'),
name='carpetplot_select_std',
run_without_submitting=True)
workflow.connect([
(inputnode, carpetplot_select_std, [('std2anat_xfm',
'std2anat_xfm'),
('template', 'keys')]),
(carpetplot_select_std, carpetplot_wf,
[('std2anat_xfm', 'inputnode.std2anat_xfm')]),
(bold_bold_trans_wf if not multiecho else bold_t2s_wf,
carpetplot_wf, [('outputnode.bold', 'inputnode.bold'),
('outputnode.bold_mask',
'inputnode.bold_mask')]),
(bold_reg_wf, carpetplot_wf, [('outputnode.itk_t1_to_bold',
'inputnode.t1_bold_xform')]),
])
workflow.connect([(bold_confounds_wf, carpetplot_wf, [
('outputnode.confounds_file', 'inputnode.confounds_file')
])])
# REPORTING ############################################################
reportlets_dir = str(config.execution.work_dir / 'reportlets')
ds_report_summary = pe.Node(DerivativesDataSink(desc='summary',
keep_dtype=True),
name='ds_report_summary',
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB)
ds_report_validation = pe.Node(DerivativesDataSink(
base_directory=reportlets_dir, desc='validation', keep_dtype=True),
name='ds_report_validation',
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB)
workflow.connect([
(summary, ds_report_summary, [('out_report', 'in_file')]),
(bold_reference_wf, ds_report_validation,
[('outputnode.validation_report', 'in_file')]),
])
# Fill-in datasinks of reportlets seen so far
for node in workflow.list_node_names():
if node.split('.')[-1].startswith('ds_report'):
workflow.get_node(node).inputs.base_directory = reportlets_dir
workflow.get_node(node).inputs.source_file = ref_file
return workflow
def init_syn_preprocessing_wf(
*,
debug=False,
name="syn_preprocessing_wf",
omp_nthreads=1,
auto_bold_nss=False,
t1w_inversion=False,
):
"""
Prepare EPI references and co-registration to anatomical for SyN.
Workflow Graph
.. workflow ::
:graph2use: orig
:simple_form: yes
from sdcflows.workflows.fit.syn import init_syn_sdc_wf
wf = init_syn_sdc_wf(omp_nthreads=8)
Parameters
----------
debug : :obj:`bool`
Whether a fast (less accurate) configuration of the workflow should be applied.
name : :obj:`str`
Name for this workflow
omp_nthreads : :obj:`int`
Parallelize internal tasks across the number of CPUs given by this option.
auto_bold_nss : :obj:`bool`
Set up the reference workflow to automatically execute nonsteady states detection
of BOLD images.
t1w_inversion : :obj:`bool`
Run T1w intensity inversion so that it looks more like a T2 contrast.
Inputs
------
in_epis : :obj:`list` of :obj:`str`
Distorted EPI images that will be merged together to create the
EPI reference file.
t_masks : :obj:`list` of :obj:`bool`
(optional) mask of timepoints for calculating an EPI reference.
Not used if ``auto_bold_nss=True``.
in_meta : :obj:`list` of :obj:`dict`
Metadata dictionaries corresponding to the ``in_epis`` input.
in_anat : :obj:`str`
A preprocessed anatomical (T1w or T2w) image.
mask_anat : :obj:`str`
A brainmask corresponding to the anatomical (T1w or T2w) image.
std2anat_xfm : :obj:`str`
inverse registration transform of T1w image to MNI template.
Outputs
-------
epi_ref : :obj:`tuple` (:obj:`str`, :obj:`dict`)
A tuple, where the first element is the path of the distorted EPI
reference map (e.g., an average of *b=0* volumes), and the second
element is a dictionary of associated metadata.
anat_ref : :obj:`str`
Path to the anatomical, skull-stripped reference in EPI space.
anat_mask : :obj:`str`
Path to the brain mask corresponding to ``anat_ref`` in EPI space.
sd_prior : :obj:`str`
A template map of areas with strong susceptibility distortions (SD) to regularize
the cost function of SyN.
"""
from pkg_resources import resource_filename as pkgrf
from niworkflows.interfaces.nibabel import (
IntensityClip,
ApplyMask,
GenerateSamplingReference,
)
from niworkflows.interfaces.fixes import (
FixHeaderApplyTransforms as ApplyTransforms,
FixHeaderRegistration as Registration,
)
from niworkflows.workflows.epi.refmap import init_epi_reference_wf
from ...interfaces.utils import Deoblique, DenoiseImage
from ...interfaces.brainmask import BrainExtraction, BinaryDilation
workflow = Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(
fields=[
"in_epis",
"t_masks",
"in_meta",
"in_anat",
"mask_anat",
"std2anat_xfm",
]
),
name="inputnode",
)
outputnode = pe.Node(
niu.IdentityInterface(
fields=["epi_ref", "epi_mask", "anat_ref", "anat_mask", "sd_prior"]
),
name="outputnode",
)
deob_epi = pe.Node(Deoblique(), name="deob_epi")
# Mapping & preparing prior knowledge
# Concatenate transform files:
# 1) MNI -> anat; 2) ATLAS -> MNI
transform_list = pe.Node(
niu.Merge(3),
name="transform_list",
mem_gb=DEFAULT_MEMORY_MIN_GB,
run_without_submitting=True,
)
transform_list.inputs.in3 = pkgrf(
"sdcflows", "data/fmap_atlas_2_MNI152NLin2009cAsym_affine.mat"
)
prior2epi = pe.Node(
ApplyTransforms(
invert_transform_flags=[True, False, False],
input_image=pkgrf("sdcflows", "data/fmap_atlas.nii.gz"),
),
name="prior2epi",
n_procs=omp_nthreads,
mem_gb=0.3,
)
anat2epi = pe.Node(
ApplyTransforms(invert_transform_flags=[True]),
name="anat2epi",
n_procs=omp_nthreads,
mem_gb=0.3,
)
mask2epi = pe.Node(
ApplyTransforms(invert_transform_flags=[True], interpolation="MultiLabel"),
name="mask2epi",
n_procs=omp_nthreads,
mem_gb=0.3,
)
mask_dtype = pe.Node(
niu.Function(function=_set_dtype, input_names=["in_file", "dtype"]),
name="mask_dtype",
)
mask_dtype.inputs.dtype = "uint8"
epi_reference_wf = init_epi_reference_wf(
omp_nthreads=omp_nthreads,
auto_bold_nss=auto_bold_nss,
)
epi_brain = pe.Node(BrainExtraction(), name="epi_brain")
merge_output = pe.Node(
niu.Function(function=_merge_meta),
name="merge_output",
run_without_submitting=True,
)
mask_anat = pe.Node(ApplyMask(), name="mask_anat")
clip_anat = pe.Node(IntensityClip(p_min=0.0, p_max=99.8), name="clip_anat")
ref_anat = pe.Node(
DenoiseImage(copy_header=True), name="ref_anat", n_procs=omp_nthreads
)
epi2anat = pe.Node(
Registration(from_file=resource_filename("sdcflows", "data/affine.json")),
name="epi2anat",
n_procs=omp_nthreads,
)
epi2anat.inputs.output_warped_image = debug
epi2anat.inputs.output_inverse_warped_image = debug
if debug:
epi2anat.inputs.args = "--write-interval-volumes 5"
def _remove_first_mask(in_file):
if not isinstance(in_file, list):
in_file = [in_file]
in_file.insert(0, "NULL")
return in_file
anat_dilmsk = pe.Node(BinaryDilation(), name="anat_dilmsk")
epi_dilmsk = pe.Node(BinaryDilation(), name="epi_dilmsk")
sampling_ref = pe.Node(GenerateSamplingReference(), name="sampling_ref")
# fmt:off
workflow.connect([
(inputnode, transform_list, [("std2anat_xfm", "in2")]),
(inputnode, epi_reference_wf, [("in_epis", "inputnode.in_files")]),
(inputnode, merge_output, [("in_meta", "meta_list")]),
(inputnode, anat_dilmsk, [("mask_anat", "in_file")]),
(inputnode, mask_anat, [("in_anat", "in_file"),
("mask_anat", "in_mask")]),
(inputnode, mask2epi, [("mask_anat", "input_image")]),
(epi_reference_wf, deob_epi, [("outputnode.epi_ref_file", "in_file")]),
(deob_epi, merge_output, [("out_file", "epi_ref")]),
(mask_anat, clip_anat, [("out_file", "in_file")]),
(clip_anat, ref_anat, [("out_file", "input_image")]),
(deob_epi, epi_brain, [("out_file", "in_file")]),
(epi_brain, epi_dilmsk, [("out_mask", "in_file")]),
(ref_anat, epi2anat, [("output_image", "fixed_image")]),
(anat_dilmsk, epi2anat, [("out_file", "fixed_image_masks")]),
(deob_epi, epi2anat, [("out_file", "moving_image")]),
(epi_dilmsk, epi2anat, [
(("out_file", _remove_first_mask), "moving_image_masks")]),
(deob_epi, sampling_ref, [("out_file", "fixed_image")]),
(epi2anat, transform_list, [("forward_transforms", "in1")]),
(transform_list, prior2epi, [("out", "transforms")]),
(sampling_ref, prior2epi, [("out_file", "reference_image")]),
(ref_anat, anat2epi, [("output_image", "input_image")]),
(epi2anat, anat2epi, [("forward_transforms", "transforms")]),
(sampling_ref, anat2epi, [("out_file", "reference_image")]),
(epi2anat, mask2epi, [("forward_transforms", "transforms")]),
(sampling_ref, mask2epi, [("out_file", "reference_image")]),
(mask2epi, mask_dtype, [("output_image", "in_file")]),
(anat2epi, outputnode, [("output_image", "anat_ref")]),
(mask_dtype, outputnode, [("out", "anat_mask")]),
(merge_output, outputnode, [("out", "epi_ref")]),
(epi_brain, outputnode, [("out_mask", "epi_mask")]),
(prior2epi, outputnode, [("output_image", "sd_prior")]),
])
# fmt:on
if debug:
from niworkflows.interfaces.nibabel import RegridToZooms
regrid_anat = pe.Node(
RegridToZooms(zooms=(2.0, 2.0, 2.0), smooth=True), name="regrid_anat"
)
# fmt:off
workflow.connect([
(inputnode, regrid_anat, [("in_anat", "in_file")]),
(regrid_anat, sampling_ref, [("out_file", "moving_image")]),
])
# fmt:on
else:
# fmt:off
workflow.connect([
(inputnode, sampling_ref, [("in_anat", "moving_image")]),
])
# fmt:on
if not auto_bold_nss:
workflow.connect(inputnode, "t_masks", epi_reference_wf, "inputnode.t_masks")
return workflow
def init_anat_derivatives_wf(
*,
bids_root,
freesurfer,
num_t1w,
output_dir,
spaces,
name="anat_derivatives_wf",
tpm_labels=BIDS_TISSUE_ORDER,
):
"""
Set up a battery of datasinks to store derivatives in the right location.
Parameters
----------
bids_root : :obj:`str`
Root path of BIDS dataset
freesurfer : :obj:`bool`
FreeSurfer was enabled
num_t1w : :obj:`int`
Number of T1w images
output_dir : :obj:`str`
Directory in which to save derivatives
name : :obj:`str`
Workflow name (default: anat_derivatives_wf)
tpm_labels : :obj:`tuple`
Tissue probability maps in order
Inputs
------
template
Template space and specifications
source_files
List of input T1w images
t1w_ref_xfms
List of affine transforms to realign input T1w images
t1w_preproc
The T1w reference map, which is calculated as the average of bias-corrected
and preprocessed T1w images, defining the anatomical space.
t1w_mask
Mask of the ``t1w_preproc``
t1w_dseg
Segmentation in T1w space
t1w_tpms
Tissue probability maps in T1w space
anat2std_xfm
Nonlinear spatial transform to resample imaging data given in anatomical space
into standard space.
std2anat_xfm
Inverse transform of ``anat2std_xfm``
std_t1w
T1w reference resampled in one or more standard spaces.
std_mask
Mask of skull-stripped template, in standard space
std_dseg
Segmentation, resampled into standard space
std_tpms
Tissue probability maps in standard space
t1w2fsnative_xfm
LTA-style affine matrix translating from T1w to
FreeSurfer-conformed subject space
fsnative2t1w_xfm
LTA-style affine matrix translating from FreeSurfer-conformed
subject space to T1w
surfaces
GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)
t1w_fs_aseg
FreeSurfer's aseg segmentation, in native T1w space
t1w_fs_aparc
FreeSurfer's aparc+aseg segmentation, in native T1w space
"""
from niworkflows.interfaces.utility import KeySelect
workflow = Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"template",
"source_files",
"t1w_ref_xfms",
"t1w_preproc",
"t1w_mask",
"t1w_dseg",
"t1w_tpms",
"anat2std_xfm",
"std2anat_xfm",
"t1w2fsnative_xfm",
"fsnative2t1w_xfm",
"surfaces",
"t1w_fs_aseg",
"t1w_fs_aparc",
]),
name="inputnode",
)
raw_sources = pe.Node(niu.Function(function=_bids_relative),
name="raw_sources")
raw_sources.inputs.bids_root = bids_root
ds_t1w_preproc = pe.Node(
DerivativesDataSink(base_directory=output_dir,
desc="preproc",
compress=True),
name="ds_t1w_preproc",
run_without_submitting=True,
)
ds_t1w_preproc.inputs.SkullStripped = False
ds_t1w_mask = pe.Node(
DerivativesDataSink(base_directory=output_dir,
desc="brain",
suffix="mask",
compress=True),
name="ds_t1w_mask",
run_without_submitting=True,
)
ds_t1w_mask.inputs.Type = "Brain"
ds_t1w_dseg = pe.Node(
DerivativesDataSink(base_directory=output_dir,
suffix="dseg",
compress=True),
name="ds_t1w_dseg",
run_without_submitting=True,
)
ds_t1w_tpms = pe.Node(
DerivativesDataSink(base_directory=output_dir,
suffix="probseg",
compress=True),
name="ds_t1w_tpms",
run_without_submitting=True,
)
ds_t1w_tpms.inputs.label = tpm_labels
# fmt:off
workflow.connect([
(inputnode, raw_sources, [('source_files', 'in_files')]),
(inputnode, ds_t1w_preproc, [('t1w_preproc', 'in_file'),
('source_files', 'source_file')]),
(inputnode, ds_t1w_mask, [('t1w_mask', 'in_file'),
('source_files', 'source_file')]),
(inputnode, ds_t1w_tpms, [('t1w_tpms', 'in_file'),
('source_files', 'source_file')]),
(inputnode, ds_t1w_dseg, [('t1w_dseg', 'in_file'),
('source_files', 'source_file')]),
(raw_sources, ds_t1w_mask, [('out', 'RawSources')]),
])
# fmt:on
# Transforms
if spaces.get_spaces(nonstandard=False, dim=(3, )):
ds_std2t1w_xfm = pe.MapNode(
DerivativesDataSink(base_directory=output_dir,
to="T1w",
mode="image",
suffix="xfm"),
iterfield=("in_file", "from"),
name="ds_std2t1w_xfm",
run_without_submitting=True,
)
ds_t1w2std_xfm = pe.MapNode(
DerivativesDataSink(base_directory=output_dir,
mode="image",
suffix="xfm",
**{"from": "T1w"}),
iterfield=("in_file", "to"),
name="ds_t1w2std_xfm",
run_without_submitting=True,
)
# fmt:off
workflow.connect([
(inputnode, ds_t1w2std_xfm, [('anat2std_xfm', 'in_file'),
(('template', _combine_cohort), 'to'),
('source_files', 'source_file')]),
(inputnode, ds_std2t1w_xfm, [('std2anat_xfm', 'in_file'),
(('template', _combine_cohort),
'from'),
('source_files', 'source_file')]),
])
# fmt:on
if num_t1w > 1:
# Please note the dictionary unpacking to provide the from argument.
# It is necessary because from is a protected keyword (not allowed as argument name).
ds_t1w_ref_xfms = pe.MapNode(
DerivativesDataSink(
base_directory=output_dir,
to="T1w",
mode="image",
suffix="xfm",
extension="txt",
**{"from": "orig"},
),
iterfield=["source_file", "in_file"],
name="ds_t1w_ref_xfms",
run_without_submitting=True,
)
# fmt:off
workflow.connect([
(inputnode, ds_t1w_ref_xfms, [('source_files', 'source_file'),
('t1w_ref_xfms', 'in_file')]),
])
# fmt:on
# Write derivatives in standard spaces specified by --output-spaces
if getattr(spaces, "_cached") is not None and spaces.cached.references:
from niworkflows.interfaces.space import SpaceDataSource
from niworkflows.interfaces.nibabel import GenerateSamplingReference
from niworkflows.interfaces.fixes import (
FixHeaderApplyTransforms as ApplyTransforms, )
from ..interfaces.templateflow import TemplateFlowSelect
spacesource = pe.Node(SpaceDataSource(),
name="spacesource",
run_without_submitting=True)
spacesource.iterables = (
"in_tuple",
[(s.fullname, s.spec)
for s in spaces.cached.get_standard(dim=(3, ))],
)
gen_tplid = pe.Node(
niu.Function(function=_fmt_cohort),
name="gen_tplid",
run_without_submitting=True,
)
select_xfm = pe.Node(
KeySelect(fields=["anat2std_xfm"]),
name="select_xfm",
run_without_submitting=True,
)
select_tpl = pe.Node(TemplateFlowSelect(),
name="select_tpl",
run_without_submitting=True)
gen_ref = pe.Node(GenerateSamplingReference(),
name="gen_ref",
mem_gb=0.01)
# Mask T1w preproc images
mask_t1w = pe.Node(ApplyMask(), name='mask_t1w')
# Resample T1w-space inputs
anat2std_t1w = pe.Node(
ApplyTransforms(
dimension=3,
default_value=0,
float=True,
interpolation="LanczosWindowedSinc",
),
name="anat2std_t1w",
)
anat2std_mask = pe.Node(ApplyTransforms(interpolation="MultiLabel"),
name="anat2std_mask")
anat2std_dseg = pe.Node(ApplyTransforms(interpolation="MultiLabel"),
name="anat2std_dseg")
anat2std_tpms = pe.MapNode(
ApplyTransforms(dimension=3,
default_value=0,
float=True,
interpolation="Gaussian"),
iterfield=["input_image"],
name="anat2std_tpms",
)
ds_std_t1w = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
desc="preproc",
compress=True,
),
name="ds_std_t1w",
run_without_submitting=True,
)
ds_std_t1w.inputs.SkullStripped = True
ds_std_mask = pe.Node(
DerivativesDataSink(base_directory=output_dir,
desc="brain",
suffix="mask",
compress=True),
name="ds_std_mask",
run_without_submitting=True,
)
ds_std_mask.inputs.Type = "Brain"
ds_std_dseg = pe.Node(
DerivativesDataSink(base_directory=output_dir,
suffix="dseg",
compress=True),
name="ds_std_dseg",
run_without_submitting=True,
)
ds_std_tpms = pe.Node(
DerivativesDataSink(base_directory=output_dir,
suffix="probseg",
compress=True),
name="ds_std_tpms",
run_without_submitting=True,
)
# CRITICAL: the sequence of labels here (CSF-GM-WM) is that of the output of FSL-FAST
# (intensity mean, per tissue). This order HAS to be matched also by the ``tpms``
# output in the data/io_spec.json file.
ds_std_tpms.inputs.label = tpm_labels
# fmt:off
workflow.connect([
(inputnode, mask_t1w, [('t1w_preproc', 'in_file'),
('t1w_mask', 'in_mask')]),
(mask_t1w, anat2std_t1w, [('out_file', 'input_image')]),
(inputnode, anat2std_mask, [('t1w_mask', 'input_image')]),
(inputnode, anat2std_dseg, [('t1w_dseg', 'input_image')]),
(inputnode, anat2std_tpms, [('t1w_tpms', 'input_image')]),
(inputnode, gen_ref, [('t1w_preproc', 'moving_image')]),
(inputnode, select_xfm, [('anat2std_xfm', 'anat2std_xfm'),
('template', 'keys')]),
(spacesource, gen_tplid, [('space', 'template'),
('cohort', 'cohort')]),
(gen_tplid, select_xfm, [('out', 'key')]),
(spacesource, select_tpl, [('space', 'template'),
('cohort', 'cohort'),
(('resolution', _no_native),
'resolution')]),
(spacesource, gen_ref, [(('resolution', _is_native), 'keep_native')
]),
(select_tpl, gen_ref, [('t1w_file', 'fixed_image')]),
(anat2std_t1w, ds_std_t1w, [('output_image', 'in_file')]),
(anat2std_mask, ds_std_mask, [('output_image', 'in_file')]),
(anat2std_dseg, ds_std_dseg, [('output_image', 'in_file')]),
(anat2std_tpms, ds_std_tpms, [('output_image', 'in_file')]),
(select_tpl, ds_std_mask, [(('brain_mask', _drop_path),
'RawSources')]),
])
workflow.connect(
# Connect apply transforms nodes
[(gen_ref, n, [('out_file', 'reference_image')])
for n in (anat2std_t1w, anat2std_mask, anat2std_dseg,
anat2std_tpms)] +
[(select_xfm, n, [('anat2std_xfm', 'transforms')])
for n in (anat2std_t1w, anat2std_mask, anat2std_dseg,
anat2std_tpms)]
# Connect the source_file input of these datasinks
+ [(inputnode, n, [('source_files', 'source_file')])
for n in (ds_std_t1w, ds_std_mask, ds_std_dseg, ds_std_tpms)]
# Connect the space input of these datasinks
+ [(spacesource, n, [('space', 'space'), ('cohort', 'cohort'),
('resolution', 'resolution')])
for n in (ds_std_t1w, ds_std_mask, ds_std_dseg, ds_std_tpms)])
# fmt:on
if not freesurfer:
return workflow
from niworkflows.interfaces.nitransforms import ConcatenateXFMs
from niworkflows.interfaces.surf import Path2BIDS
# FS native space transforms
lta2itk_fwd = pe.Node(ConcatenateXFMs(),
name="lta2itk_fwd",
run_without_submitting=True)
lta2itk_inv = pe.Node(ConcatenateXFMs(),
name="lta2itk_inv",
run_without_submitting=True)
ds_t1w_fsnative = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
mode="image",
to="fsnative",
suffix="xfm",
extension="txt",
**{"from": "T1w"},
),
name="ds_t1w_fsnative",
run_without_submitting=True,
)
ds_fsnative_t1w = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
mode="image",
to="T1w",
suffix="xfm",
extension="txt",
**{"from": "fsnative"},
),
name="ds_fsnative_t1w",
run_without_submitting=True,
)
# Surfaces
name_surfs = pe.MapNode(Path2BIDS(),
iterfield="in_file",
name="name_surfs",
run_without_submitting=True)
ds_surfs = pe.MapNode(
DerivativesDataSink(base_directory=output_dir, extension=".surf.gii"),
iterfield=["in_file", "hemi", "suffix"],
name="ds_surfs",
run_without_submitting=True,
)
# Parcellations
ds_t1w_fsaseg = pe.Node(
DerivativesDataSink(base_directory=output_dir,
desc="aseg",
suffix="dseg",
compress=True),
name="ds_t1w_fsaseg",
run_without_submitting=True,
)
ds_t1w_fsparc = pe.Node(
DerivativesDataSink(base_directory=output_dir,
desc="aparcaseg",
suffix="dseg",
compress=True),
name="ds_t1w_fsparc",
run_without_submitting=True,
)
# fmt:off
workflow.connect([
(inputnode, lta2itk_fwd, [('t1w2fsnative_xfm', 'in_xfms')]),
(inputnode, lta2itk_inv, [('fsnative2t1w_xfm', 'in_xfms')]),
(inputnode, ds_t1w_fsnative, [('source_files', 'source_file')]),
(lta2itk_fwd, ds_t1w_fsnative, [('out_xfm', 'in_file')]),
(inputnode, ds_fsnative_t1w, [('source_files', 'source_file')]),
(lta2itk_inv, ds_fsnative_t1w, [('out_xfm', 'in_file')]),
(inputnode, name_surfs, [('surfaces', 'in_file')]),
(inputnode, ds_surfs, [('surfaces', 'in_file'),
('source_files', 'source_file')]),
(name_surfs, ds_surfs, [('hemi', 'hemi'), ('suffix', 'suffix')]),
(inputnode, ds_t1w_fsaseg, [('t1w_fs_aseg', 'in_file'),
('source_files', 'source_file')]),
(inputnode, ds_t1w_fsparc, [('t1w_fs_aparc', 'in_file'),
('source_files', 'source_file')]),
])
# fmt:on
return workflow
def init_dwi_preproc_wf(dwi_file, has_fieldmap=False):
"""
Build a preprocessing workflow for one DWI run.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from dmriprep.config.testing import mock_config
from dmriprep import config
from dmriprep.workflows.dwi.base import init_dwi_preproc_wf
with mock_config():
wf = init_dwi_preproc_wf(
f"{config.execution.layout.root}/"
"sub-THP0005/dwi/sub-THP0005_dwi.nii.gz"
)
Parameters
----------
dwi_file : :obj:`os.PathLike`
One diffusion MRI dataset to be processed.
has_fieldmap : :obj:`bool`
Build the workflow with a path to register a fieldmap to the DWI.
Inputs
------
dwi_file
dwi NIfTI file
in_bvec
File path of the b-vectors
in_bval
File path of the b-values
fmap
File path of the fieldmap
fmap_ref
File path of the fieldmap reference
fmap_coeff
File path of the fieldmap coefficients
fmap_mask
File path of the fieldmap mask
fmap_id
The BIDS modality label of the fieldmap being used
Outputs
-------
dwi_reference
A 3D :math:`b = 0` reference, before susceptibility distortion correction.
dwi_mask
A 3D, binary mask of the ``dwi_reference`` above.
gradients_rasb
A *RASb* (RAS+ coordinates, scaled b-values, normalized b-vectors, BIDS-compatible)
gradient table.
See Also
--------
* :py:func:`~dmriprep.workflows.dwi.util.init_dwi_reference_wf`
* :py:func:`~dmriprep.workflows.dwi.outputs.init_dwi_derivatives_wf`
* :py:func:`~dmriprep.workflows.dwi.outputs.init_reportlets_wf`
"""
from niworkflows.interfaces.reportlets.registration import (
SimpleBeforeAfterRPT as SimpleBeforeAfter, )
from ...interfaces.vectors import CheckGradientTable
from .util import init_dwi_reference_wf
from .outputs import init_dwi_derivatives_wf, init_reportlets_wf
from .eddy import init_eddy_wf
layout = config.execution.layout
dwi_file = Path(dwi_file)
config.loggers.workflow.debug(
f"Creating DWI preprocessing workflow for <{dwi_file.name}>")
if has_fieldmap:
import re
from sdcflows.fieldmaps import get_identifier
dwi_rel = re.sub(r"^sub-[a-zA-Z0-9]*/", "",
str(dwi_file.relative_to(layout.root)))
estimator_key = get_identifier(dwi_rel)
if not estimator_key:
has_fieldmap = False
config.loggers.workflow.critical(
f"None of the available B0 fieldmaps are associated to <{dwi_rel}>"
)
# Build workflow
workflow = Workflow(name=_get_wf_name(dwi_file.name))
inputnode = pe.Node(
niu.IdentityInterface(fields=[
# DWI
"dwi_file",
"in_bvec",
"in_bval",
# From SDCFlows
"fmap",
"fmap_ref",
"fmap_coeff",
"fmap_mask",
"fmap_id",
# From anatomical
"t1w_preproc",
"t1w_mask",
"t1w_dseg",
"t1w_aseg",
"t1w_aparc",
"t1w_tpms",
"template",
"anat2std_xfm",
"std2anat_xfm",
"subjects_dir",
"subject_id",
"t1w2fsnative_xfm",
"fsnative2t1w_xfm",
]),
name="inputnode",
)
inputnode.inputs.dwi_file = str(dwi_file.absolute())
inputnode.inputs.in_bvec = str(layout.get_bvec(dwi_file))
inputnode.inputs.in_bval = str(layout.get_bval(dwi_file))
outputnode = pe.Node(
niu.IdentityInterface(
fields=["dwi_reference", "dwi_mask", "gradients_rasb"]),
name="outputnode",
)
gradient_table = pe.Node(CheckGradientTable(), name="gradient_table")
dwi_reference_wf = init_dwi_reference_wf(
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
omp_nthreads=config.nipype.omp_nthreads)
dwi_derivatives_wf = init_dwi_derivatives_wf(
output_dir=str(config.execution.output_dir))
# MAIN WORKFLOW STRUCTURE
# fmt: off
workflow.connect([
(inputnode, gradient_table, [("dwi_file", "dwi_file"),
("in_bvec", "in_bvec"),
("in_bval", "in_bval")]),
(inputnode, dwi_reference_wf, [("dwi_file", "inputnode.dwi_file")]),
(inputnode, dwi_derivatives_wf, [("dwi_file", "inputnode.source_file")
]),
(gradient_table, dwi_reference_wf, [("b0_ixs", "inputnode.b0_ixs")]),
(gradient_table, outputnode, [("out_rasb", "gradients_rasb")]),
(outputnode, dwi_derivatives_wf, [
("dwi_reference", "inputnode.dwi_ref"),
("dwi_mask", "inputnode.dwi_mask"),
]),
])
# fmt: on
if config.workflow.run_reconall:
from niworkflows.interfaces.nibabel import ApplyMask
from niworkflows.anat.coregistration import init_bbreg_wf
from ...utils.misc import sub_prefix as _prefix
# Mask the T1w
t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")
bbr_wf = init_bbreg_wf(
debug=config.execution.debug,
epi2t1w_init=config.workflow.dwi2t1w_init,
omp_nthreads=config.nipype.omp_nthreads,
)
ds_report_reg = pe.Node(
DerivativesDataSink(
base_directory=str(config.execution.output_dir),
datatype="figures",
),
name="ds_report_reg",
run_without_submitting=True,
)
def _bold_reg_suffix(fallback):
return "coreg" if fallback else "bbregister"
# fmt: off
workflow.connect([
(inputnode, bbr_wf, [
("fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
(("subject_id", _prefix), "inputnode.subject_id"),
("subjects_dir", "inputnode.subjects_dir"),
]),
# T1w Mask
(inputnode, t1w_brain, [("t1w_preproc", "in_file"),
("t1w_mask", "in_mask")]),
(inputnode, ds_report_reg, [("dwi_file", "source_file")]),
# BBRegister
(dwi_reference_wf, bbr_wf, [("outputnode.ref_image",
"inputnode.in_file")]),
(bbr_wf, ds_report_reg, [('outputnode.out_report', 'in_file'),
(('outputnode.fallback',
_bold_reg_suffix), 'desc')]),
])
# fmt: on
if "eddy" not in config.workflow.ignore:
# Eddy distortion correction
eddy_wf = init_eddy_wf(debug=config.execution.debug)
eddy_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
ds_report_eddy = pe.Node(
DerivativesDataSink(
base_directory=str(config.execution.output_dir),
desc="eddy",
datatype="figures",
),
name="ds_report_eddy",
run_without_submitting=True,
)
eddy_report = pe.Node(
SimpleBeforeAfter(
before_label="Distorted",
after_label="Eddy Corrected",
),
name="eddy_report",
mem_gb=0.1,
)
# fmt:off
workflow.connect([
(dwi_reference_wf, eddy_wf, [
("outputnode.dwi_file", "inputnode.dwi_file"),
("outputnode.dwi_mask", "inputnode.dwi_mask"),
]),
(inputnode, eddy_wf, [("in_bvec", "inputnode.in_bvec"),
("in_bval", "inputnode.in_bval")]),
(dwi_reference_wf, eddy_report, [("outputnode.ref_image", "before")
]),
(eddy_wf, eddy_report, [('outputnode.eddy_ref_image', 'after')]),
(dwi_reference_wf, ds_report_eddy, [("outputnode.dwi_file",
"source_file")]),
(eddy_report, ds_report_eddy, [("out_report", "in_file")]),
])
# fmt:on
# REPORTING ############################################################
reportlets_wf = init_reportlets_wf(
str(config.execution.output_dir),
sdc_report=has_fieldmap,
)
# fmt: off
workflow.connect([
(inputnode, reportlets_wf, [("dwi_file", "inputnode.source_file")]),
(dwi_reference_wf, reportlets_wf, [
("outputnode.validation_report", "inputnode.validation_report"),
]),
(outputnode, reportlets_wf, [
("dwi_reference", "inputnode.dwi_ref"),
("dwi_mask", "inputnode.dwi_mask"),
]),
])
# fmt: on
if not has_fieldmap:
# fmt: off
workflow.connect([
(dwi_reference_wf, outputnode,
[("outputnode.ref_image", "dwi_reference"),
("outputnode.dwi_mask", "dwi_mask")]),
])
# fmt: on
return workflow
from niworkflows.interfaces.utility import KeySelect
from sdcflows.workflows.apply.registration import init_coeff2epi_wf
from sdcflows.workflows.apply.correction import init_unwarp_wf
coeff2epi_wf = init_coeff2epi_wf(
debug=config.execution.debug,
omp_nthreads=config.nipype.omp_nthreads,
write_coeff=True,
)
unwarp_wf = init_unwarp_wf(debug=config.execution.debug,
omp_nthreads=config.nipype.omp_nthreads)
unwarp_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
output_select = pe.Node(
KeySelect(fields=["fmap", "fmap_ref", "fmap_coeff", "fmap_mask"]),
name="output_select",
run_without_submitting=True,
)
output_select.inputs.key = estimator_key[0]
if len(estimator_key) > 1:
config.loggers.workflow.warning(
f"Several fieldmaps <{', '.join(estimator_key)}> are "
f"'IntendedFor' <{dwi_file}>, using {estimator_key[0]}")
sdc_report = pe.Node(
SimpleBeforeAfter(
before_label="Distorted",
after_label="Corrected",
),
name="sdc_report",
mem_gb=0.1,
)
# fmt: off
workflow.connect([
(inputnode, output_select, [("fmap", "fmap"), ("fmap_ref", "fmap_ref"),
("fmap_coeff", "fmap_coeff"),
("fmap_mask", "fmap_mask"),
("fmap_id", "keys")]),
(output_select, coeff2epi_wf, [("fmap_ref", "inputnode.fmap_ref"),
("fmap_coeff", "inputnode.fmap_coeff"),
("fmap_mask", "inputnode.fmap_mask")]),
(dwi_reference_wf, coeff2epi_wf,
[("outputnode.ref_image", "inputnode.target_ref"),
("outputnode.dwi_mask", "inputnode.target_mask")]),
(dwi_reference_wf, unwarp_wf, [("outputnode.ref_image",
"inputnode.distorted")]),
(coeff2epi_wf, unwarp_wf, [("outputnode.fmap_coeff",
"inputnode.fmap_coeff")]),
(dwi_reference_wf, sdc_report, [("outputnode.ref_image", "before")]),
(unwarp_wf, sdc_report, [("outputnode.corrected", "after"),
("outputnode.corrected_mask", "wm_seg")]),
(sdc_report, reportlets_wf, [("out_report", "inputnode.sdc_report")]),
(unwarp_wf, outputnode, [("outputnode.corrected", "dwi_reference"),
("outputnode.corrected_mask", "dwi_mask")]),
])
# fmt: on
return workflow
def init_infant_brain_extraction_wf(
age_months=None,
ants_affine_init=False,
bspline_fitting_distance=200,
sloppy=False,
skull_strip_template="UNCInfant",
template_specs=None,
mem_gb=3.0,
debug=False,
name="infant_brain_extraction_wf",
omp_nthreads=None,
):
"""
Build an atlas-based brain extraction pipeline for infant T2w MRI data.
Pros/Cons of available templates
--------------------------------
* MNIInfant
+ More cohorts available for finer-grain control
+ T1w/T2w images available
- Template masks are poor
* UNCInfant
+ Accurate masks
- No T2w image available
Parameters
----------
age_months : :obj:`int`
Age of this participant, in months.
ants_affine_init : :obj:`bool`, optional
Set-up a pre-initialization step with ``antsAI`` to account for mis-oriented images.
bspline_fitting_distance : :obj:`float`
Distance in mm between B-Spline control points for N4 INU estimation.
sloppy : :obj:`bool`
Run in *sloppy* mode.
skull_strip_template : :obj:`str`
A TemplateFlow ID indicating which template will be used as target for atlas-based
segmentation.
template_specs : :obj:`dict`
Additional template specifications (e.g., resolution or cohort) to correctly select
the adequate template instance.
mem_gb : :obj:`float`
Base memory fingerprint unit.
name : :obj:`str`
This particular workflow's unique name (Nipype requirement).
omp_nthreads : :obj:`int`
The number of threads for individual processes in this workflow.
debug : :obj:`bool`
Produce intermediate registration files
Inputs
------
in_t2w : :obj:`str`
The unprocessed input T2w image.
Outputs
-------
t2w_preproc : :obj:`str`
The preprocessed T2w image (INU and clipping).
t2w_brain : :obj:`str`
The preprocessed, brain-extracted T2w image.
out_mask : :obj:`str`
The brainmask projected from the template into the T2w, after
binarization.
out_probmap : :obj:`str`
The same as above, before binarization.
"""
from nipype.interfaces.ants import N4BiasFieldCorrection, ImageMath
# niworkflows
from niworkflows.interfaces.nibabel import ApplyMask, Binarize, IntensityClip
from niworkflows.interfaces.fixes import (
FixHeaderRegistration as Registration,
FixHeaderApplyTransforms as ApplyTransforms,
)
from templateflow.api import get as get_template
from ...interfaces.nibabel import BinaryDilation
from ...utils.misc import cohort_by_months
# handle template specifics
template_specs = template_specs or {}
if skull_strip_template == "MNIInfant":
template_specs["resolution"] = 2 if sloppy else 1
if not template_specs.get("cohort"):
if age_months is None:
raise KeyError(
f"Age or cohort for {skull_strip_template} must be provided!")
template_specs["cohort"] = cohort_by_months(skull_strip_template,
age_months)
tpl_target_path = get_template(
skull_strip_template,
suffix="T1w", # no T2w template
desc=None,
**template_specs,
)
if not tpl_target_path:
raise RuntimeError(
f"An instance of template <tpl-{skull_strip_template}> with T1w suffix "
"could not be found.")
tpl_brainmask_path = get_template(skull_strip_template,
label="brain",
suffix="probseg",
**template_specs) or get_template(
skull_strip_template,
desc="brain",
suffix="mask",
**template_specs)
tpl_regmask_path = get_template(
skull_strip_template,
label="BrainCerebellumExtraction",
suffix="mask",
**template_specs,
)
# main workflow
workflow = pe.Workflow(name)
inputnode = pe.Node(niu.IdentityInterface(fields=["in_t2w"]),
name="inputnode")
outputnode = pe.Node(
niu.IdentityInterface(
fields=["t2w_preproc", "t2w_brain", "out_mask", "out_probmap"]),
name="outputnode",
)
# Ensure template comes with a range of intensities ANTs will like
clip_tmpl = pe.Node(IntensityClip(p_max=99), name="clip_tmpl")
clip_tmpl.inputs.in_file = _pop(tpl_target_path)
# Generate laplacian registration targets
lap_tmpl = pe.Node(ImageMath(operation="Laplacian", op2="0.4 1"),
name="lap_tmpl")
lap_t2w = pe.Node(ImageMath(operation="Laplacian", op2="0.4 1"),
name="lap_t2w")
norm_lap_tmpl = pe.Node(niu.Function(function=_norm_lap),
name="norm_lap_tmpl")
norm_lap_t2w = pe.Node(niu.Function(function=_norm_lap),
name="norm_lap_t2w")
# Merge image nodes
mrg_tmpl = pe.Node(niu.Merge(2),
name="mrg_tmpl",
run_without_submitting=True)
mrg_t2w = pe.Node(niu.Merge(2),
name="mrg_t2w",
run_without_submitting=True)
bin_regmask = pe.Node(Binarize(thresh_low=0.20), name="bin_regmask")
bin_regmask.inputs.in_file = str(tpl_brainmask_path)
refine_mask = pe.Node(BinaryDilation(radius=3, iterations=2),
name="refine_mask")
fixed_masks = pe.Node(niu.Merge(4),
name="fixed_masks",
run_without_submitting=True)
fixed_masks.inputs.in1 = "NULL"
fixed_masks.inputs.in2 = "NULL"
fixed_masks.inputs.in3 = "NULL" if not tpl_regmask_path else _pop(
tpl_regmask_path)
# Set up initial spatial normalization
ants_params = "testing" if sloppy else "precise"
norm = pe.Node(
Registration(from_file=pkgr_fn(
"nibabies.data", f"antsBrainExtraction_{ants_params}.json")),
name="norm",
n_procs=omp_nthreads,
mem_gb=mem_gb,
)
norm.inputs.float = sloppy
if debug:
norm.inputs.args = "--write-interval-volumes 5"
map_mask_t2w = pe.Node(
ApplyTransforms(interpolation="Gaussian", float=True),
name="map_mask_t2w",
mem_gb=1,
)
# map template brainmask to t2w space
map_mask_t2w.inputs.input_image = str(tpl_brainmask_path)
thr_t2w_mask = pe.Node(Binarize(thresh_low=0.80), name="thr_t2w_mask")
# Refine INU correction
final_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
bspline_fitting_distance=bspline_fitting_distance,
save_bias=True,
copy_header=True,
n_iterations=[50] * 5,
convergence_threshold=1e-7,
rescale_intensities=True,
shrink_factor=4,
),
n_procs=omp_nthreads,
name="final_n4",
)
final_clip = pe.Node(IntensityClip(p_min=5.0, p_max=99.5),
name="final_clip")
apply_mask = pe.Node(ApplyMask(), name="apply_mask")
# fmt:off
workflow.connect([
(inputnode, final_n4, [("in_t2w", "input_image")]),
# 1. Massage T2w
(inputnode, mrg_t2w, [("in_t2w", "in1")]),
(inputnode, lap_t2w, [("in_t2w", "op1")]),
(inputnode, map_mask_t2w, [("in_t2w", "reference_image")]),
(bin_regmask, refine_mask, [("out_file", "in_file")]),
(refine_mask, fixed_masks, [("out_file", "in4")]),
(lap_t2w, norm_lap_t2w, [("output_image", "in_file")]),
(norm_lap_t2w, mrg_t2w, [("out", "in2")]),
# 2. Prepare template
(clip_tmpl, lap_tmpl, [("out_file", "op1")]),
(lap_tmpl, norm_lap_tmpl, [("output_image", "in_file")]),
(clip_tmpl, mrg_tmpl, [("out_file", "in1")]),
(norm_lap_tmpl, mrg_tmpl, [("out", "in2")]),
# 3. Set normalization node inputs
(mrg_tmpl, norm, [("out", "fixed_image")]),
(mrg_t2w, norm, [("out", "moving_image")]),
(fixed_masks, norm, [("out", "fixed_image_masks")]),
# 4. Map template brainmask into T2w space
(norm, map_mask_t2w, [("reverse_transforms", "transforms"),
("reverse_invert_flags",
"invert_transform_flags")]),
(map_mask_t2w, thr_t2w_mask, [("output_image", "in_file")]),
(thr_t2w_mask, apply_mask, [("out_mask", "in_mask")]),
(final_n4, apply_mask, [("output_image", "in_file")]),
# 5. Refine T2w INU correction with brain mask
(map_mask_t2w, final_n4, [("output_image", "weight_image")]),
(final_n4, final_clip, [("output_image", "in_file")]),
# 9. Outputs
(final_clip, outputnode, [("out_file", "t2w_preproc")]),
(map_mask_t2w, outputnode, [("output_image", "out_probmap")]),
(thr_t2w_mask, outputnode, [("out_mask", "out_mask")]),
(apply_mask, outputnode, [("out_file", "t2w_brain")]),
])
# fmt:on
if ants_affine_init:
from nipype.interfaces.ants.utils import AI
ants_kwargs = dict(
metric=("Mattes", 32, "Regular", 0.2),
transform=("Affine", 0.1),
search_factor=(20, 0.12),
principal_axes=False,
convergence=(10, 1e-6, 10),
search_grid=(40, (0, 40, 40)),
verbose=True,
)
if ants_affine_init == "random":
ants_kwargs["metric"] = ("Mattes", 32, "Random", 0.2)
if ants_affine_init == "search":
ants_kwargs["search_grid"] = (20, (20, 40, 40))
init_aff = pe.Node(
AI(**ants_kwargs),
name="init_aff",
n_procs=omp_nthreads,
)
if tpl_regmask_path:
init_aff.inputs.fixed_image_mask = _pop(tpl_regmask_path)
# fmt:off
workflow.connect([
(clip_tmpl, init_aff, [("out_file", "fixed_image")]),
(inputnode, init_aff, [("in_t2w", "moving_image")]),
(init_aff, norm, [("output_transform", "initial_moving_transform")
]),
])
# fmt:on
return workflow
def init_coregistration_wf(
*,
bspline_fitting_distance=200,
mem_gb=3.0,
name="coregistration_wf",
omp_nthreads=None,
sloppy=False,
debug=False,
):
"""
Set-up a T2w-to-T1w within-baby co-registration framework.
See the ANTs' registration config file (under ``nibabies/data``) for further
details.
The main surprise in it is that, for some participants, accurate registration
requires extra degrees of freedom (one affine level and one SyN level) to ensure
that the T1w and T2w images align well.
I attribute this requirement to the following potential reasons:
* The T1w image and the T2w image were acquired in different sessions, apart in
time enough for growth to happen.
Although this is, in theory possible, it doesn't seem the images we have tested
on are acquired on different sessions.
* The skull is still so malleable that a change of position of the baby inside the
coil made an actual change on the overall shape of their head.
* Nonlinear distortions of the T1w and T2w images are, for some reason, more notorious
for babies than they are for adults.
We would need to look into each sequence's details to confirm this.
Parameters
----------
bspline_fitting_distance : :obj:`float`
Distance in mm between B-Spline control points for N4 INU estimation.
mem_gb : :obj:`float`
Base memory fingerprint unit.
name : :obj:`str`
This particular workflow's unique name (Nipype requirement).
omp_nthreads : :obj:`int`
The number of threads for individual processes in this workflow.
sloppy : :obj:`bool`
Run in *sloppy* mode.
debug : :obj:`bool`
Produce intermediate registration files
Inputs
------
in_t1w : :obj:`str`
The unprocessed input T1w image.
in_t2w_preproc : :obj:`str`
The preprocessed input T2w image, from the brain extraction workflow.
in_mask : :obj:`str`
The brainmask, as obtained in T2w space.
in_probmap : :obj:`str`
The probabilistic brainmask, as obtained in T2w space.
Outputs
-------
t1w_preproc : :obj:`str`
The preprocessed T1w image (INU and clipping).
t2w_preproc : :obj:`str`
The preprocessed T2w image (INU and clipping), aligned into the T1w's space.
t1w_brain : :obj:`str`
The preprocessed, brain-extracted T1w image.
t1w_mask : :obj:`str`
The binary brainmask projected from the T2w.
t1w2t2w_xfm : :obj:`str`
The T1w-to-T2w mapping.
"""
from nipype.interfaces.ants import N4BiasFieldCorrection
from niworkflows.interfaces.fixes import (
FixHeaderRegistration as Registration,
FixHeaderApplyTransforms as ApplyTransforms,
)
from niworkflows.interfaces.nibabel import ApplyMask, Binarize
from ...interfaces.nibabel import BinaryDilation
workflow = pe.Workflow(name)
inputnode = pe.Node(
niu.IdentityInterface(
fields=["in_t1w", "in_t2w_preproc", "in_mask", "in_probmap"]),
name="inputnode",
)
outputnode = pe.Node(
niu.IdentityInterface(fields=[
"t1w_preproc",
"t1w_brain",
"t1w_mask",
"t1w2t2w_xfm",
"t2w_preproc",
]),
name="outputnode",
)
fixed_masks_arg = pe.Node(niu.Merge(3),
name="fixed_masks_arg",
run_without_submitting=True)
# Dilate t2w mask for easier t1->t2 registration
reg_mask = pe.Node(BinaryDilation(radius=8, iterations=3), name="reg_mask")
refine_mask = pe.Node(BinaryDilation(radius=8, iterations=1),
name="refine_mask")
# Set up T2w -> T1w within-subject registration
coreg = pe.Node(
Registration(
from_file=pkgr_fn("nibabies.data", "within_subject_t1t2.json")),
name="coreg",
n_procs=omp_nthreads,
mem_gb=mem_gb,
)
coreg.inputs.float = sloppy
if debug:
coreg.inputs.args = "--write-interval-volumes 5"
coreg.inputs.output_inverse_warped_image = sloppy
coreg.inputs.output_warped_image = sloppy
map_mask = pe.Node(ApplyTransforms(interpolation="Gaussian"),
name="map_mask",
mem_gb=1)
map_t2w = pe.Node(ApplyTransforms(interpolation="BSpline"),
name="map_t2w",
mem_gb=1)
thr_mask = pe.Node(Binarize(thresh_low=0.80), name="thr_mask")
final_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
bspline_fitting_distance=bspline_fitting_distance,
save_bias=True,
copy_header=True,
n_iterations=[50] * 5,
convergence_threshold=1e-7,
rescale_intensities=True,
shrink_factor=4,
),
n_procs=omp_nthreads,
name="final_n4",
)
apply_mask = pe.Node(ApplyMask(), name="apply_mask")
# fmt:off
workflow.connect([
(inputnode, map_mask, [("in_t1w", "reference_image")]),
(inputnode, final_n4, [("in_t1w", "input_image")]),
(inputnode, coreg, [("in_t1w", "moving_image"),
("in_t2w_preproc", "fixed_image")]),
(inputnode, map_mask, [("in_probmap", "input_image")]),
(inputnode, reg_mask, [("in_mask", "in_file")]),
(inputnode, refine_mask, [("in_mask", "in_file")]),
(reg_mask, fixed_masks_arg, [("out_file", "in1")]),
(reg_mask, fixed_masks_arg, [("out_file", "in2")]),
(refine_mask, fixed_masks_arg, [("out_file", "in3")]),
(inputnode, map_t2w, [("in_t1w", "reference_image")]),
(inputnode, map_t2w, [("in_t2w_preproc", "input_image")]),
(fixed_masks_arg, coreg, [("out", "fixed_image_masks")]),
(coreg, map_mask, [
("reverse_transforms", "transforms"),
("reverse_invert_flags", "invert_transform_flags"),
]),
(coreg, map_t2w, [
("reverse_transforms", "transforms"),
("reverse_invert_flags", "invert_transform_flags"),
]),
(map_mask, thr_mask, [("output_image", "in_file")]),
(map_mask, final_n4, [("output_image", "weight_image")]),
(final_n4, apply_mask, [("output_image", "in_file")]),
(thr_mask, apply_mask, [("out_mask", "in_mask")]),
(final_n4, outputnode, [("output_image", "t1w_preproc")]),
(map_t2w, outputnode, [("output_image", "t2w_preproc")]),
(thr_mask, outputnode, [("out_mask", "t1w_mask")]),
(apply_mask, outputnode, [("out_file", "t1w_brain")]),
(coreg, outputnode, [("forward_transforms", "t1w2t2w_xfm")]),
])
# fmt:on
return workflow
def init_enhance_and_skullstrip_dwi_wf(
name="enhance_and_skullstrip_dwi_wf", omp_nthreads=1
):
"""
Enhance a *b0* reference and perform brain extraction.
This workflow takes in a *b0* reference image and sharpens the histogram
with the application of the N4 algorithm for removing the
:abbr:`INU (intensity non-uniformity)` bias field and calculates a signal
mask.
Steps of this workflow are:
1. Run ANTs' ``N4BiasFieldCorrection`` on the input
dwi reference image and mask.
2. Calculate a loose mask using FSL's ``bet``, with one mathematical morphology
dilation of one iteration and a sphere of 6mm as structuring element.
3. Mask the :abbr:`INU (intensity non-uniformity)`-corrected image
with the latest mask calculated in 3), then use AFNI's ``3dUnifize``
to *standardize* the T2* contrast distribution.
4. Calculate a mask using AFNI's ``3dAutomask`` after the contrast
enhancement of 4).
5. Calculate a final mask as the intersection of 2) and 4).
6. Apply final mask on the enhanced reference.
Workflow Graph:
.. workflow ::
:graph2use: orig
:simple_form: yes
from dmriprep.workflows.dwi.util import init_enhance_and_skullstrip_dwi_wf
wf = init_enhance_and_skullstrip_dwi_wf(omp_nthreads=1)
.. _N4BiasFieldCorrection: https://hdl.handle.net/10380/3053
Parameters
----------
name : str
Name of workflow (default: ``enhance_and_skullstrip_dwi_wf``)
omp_nthreads : int
number of threads available to parallel nodes
Inputs
------
in_file
The *b0* reference (single volume)
pre_mask
initial mask
Outputs
-------
bias_corrected_file
the ``in_file`` after `N4BiasFieldCorrection`_
skull_stripped_file
the ``bias_corrected_file`` after skull-stripping
mask_file
mask of the skull-stripped input file
out_report
reportlet for the skull-stripping
"""
from niworkflows.interfaces.header import CopyXForm
from niworkflows.interfaces.fixes import (
FixN4BiasFieldCorrection as N4BiasFieldCorrection,
)
from niworkflows.interfaces.nibabel import ApplyMask
workflow = Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=["in_file", "pre_mask"]), name="inputnode"
)
outputnode = pe.Node(
niu.IdentityInterface(
fields=["mask_file", "skull_stripped_file", "bias_corrected_file"]
),
name="outputnode",
)
# Run N4 normally, force num_threads=1 for stability (images are small, no need for >1)
n4_correct = pe.Node(
N4BiasFieldCorrection(
dimension=3, copy_header=True, bspline_fitting_distance=200
),
shrink_factor=2,
name="n4_correct",
n_procs=1,
)
n4_correct.inputs.rescale_intensities = True
# Create a generous BET mask out of the bias-corrected EPI
skullstrip_first_pass = pe.Node(
fsl.BET(frac=0.2, mask=True), name="skullstrip_first_pass"
)
bet_dilate = pe.Node(
fsl.DilateImage(
operation="max",
kernel_shape="sphere",
kernel_size=6.0,
internal_datatype="char",
),
name="skullstrip_first_dilate",
)
bet_mask = pe.Node(fsl.ApplyMask(), name="skullstrip_first_mask")
# Use AFNI's unifize for T2 contrast & fix header
unifize = pe.Node(
afni.Unifize(
t2=True,
outputtype="NIFTI_GZ",
args="-clfrac 0.2 -rbt 18.3 65.0 90.0",
out_file="uni.nii.gz",
),
name="unifize",
)
fixhdr_unifize = pe.Node(CopyXForm(), name="fixhdr_unifize", mem_gb=0.1)
# Run AFNI's 3dAutomask to extract a refined brain mask
skullstrip_second_pass = pe.Node(
afni.Automask(dilate=1, outputtype="NIFTI_GZ"), name="skullstrip_second_pass"
)
fixhdr_skullstrip2 = pe.Node(CopyXForm(), name="fixhdr_skullstrip2", mem_gb=0.1)
# Take intersection of both masks
combine_masks = pe.Node(fsl.BinaryMaths(operation="mul"), name="combine_masks")
normalize = pe.Node(niu.Function(function=_normalize), name="normalize")
# Compute masked brain
apply_mask = pe.Node(ApplyMask(), name="apply_mask")
# fmt:off
workflow.connect([
(inputnode, n4_correct, [("in_file", "input_image"),
("pre_mask", "mask_image")]),
(inputnode, fixhdr_unifize, [("in_file", "hdr_file")]),
(inputnode, fixhdr_skullstrip2, [("in_file", "hdr_file")]),
(n4_correct, skullstrip_first_pass, [("output_image", "in_file")]),
(skullstrip_first_pass, bet_dilate, [("mask_file", "in_file")]),
(bet_dilate, bet_mask, [("out_file", "mask_file")]),
(skullstrip_first_pass, bet_mask, [("out_file", "in_file")]),
(bet_mask, unifize, [("out_file", "in_file")]),
(unifize, fixhdr_unifize, [("out_file", "in_file")]),
(fixhdr_unifize, skullstrip_second_pass, [("out_file", "in_file")]),
(skullstrip_first_pass, combine_masks, [("mask_file", "in_file")]),
(skullstrip_second_pass, fixhdr_skullstrip2, [("out_file", "in_file")]),
(fixhdr_skullstrip2, combine_masks, [("out_file", "operand_file")]),
(combine_masks, apply_mask, [("out_file", "in_mask")]),
(combine_masks, outputnode, [("out_file", "mask_file")]),
(n4_correct, normalize, [("output_image", "in_file")]),
(normalize, apply_mask, [("out", "in_file")]),
(normalize, outputnode, [("out", "bias_corrected_file")]),
(apply_mask, outputnode, [("out_file", "skull_stripped_file")]),
]
)
# fmt:on
return workflow
def init_func_preproc_wf(
workdir=None, name="func_preproc_wf", fmap_type=None, memcalc=MemoryCalculator()
):
"""
simplified from fmriprep/workflows/bold/base.py
"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(
fields=["bold_file", "fmaps", "metadata", *in_attrs_from_anat_preproc_wf]
),
name="inputnode",
)
outputnode = pe.Node(
niu.IdentityInterface(
fields=[
*func_preproc_wf_out_attrs,
"aroma_confounds",
"aroma_metadata",
"movpar_file",
"rmsd_file",
"skip_vols",
]
),
name="outputnode",
)
def get_repetition_time(dic):
return dic.get("RepetitionTime")
metadatanode = pe.Node(niu.IdentityInterface(fields=["repetition_time"]), name="metadatanode")
workflow.connect(
[(inputnode, metadatanode, [(("metadata", get_repetition_time), "repetition_time")],)]
)
# Generate a brain-masked conversion of the t1w
t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")
workflow.connect(
[(inputnode, t1w_brain, [("t1w_preproc", "in_file"), ("t1w_mask", "in_mask")])]
)
# Generate a tentative boldref
bold_reference_wf = init_bold_reference_wf(omp_nthreads=config.nipype.omp_nthreads)
bold_reference_wf.get_node("inputnode").inputs.dummy_scans = config.workflow.dummy_scans
workflow.connect(inputnode, "bold_file", bold_reference_wf, "inputnode.bold_file")
workflow.connect(bold_reference_wf, "outputnode.skip_vols", outputnode, "skip_vols")
# SDC (SUSCEPTIBILITY DISTORTION CORRECTION) or bypass ##########################
bold_sdc_wf = init_sdc_estimate_wf(fmap_type=fmap_type)
workflow.connect(
[
(
inputnode,
bold_sdc_wf,
[("fmaps", "inputnode.fmaps"), ("metadata", "inputnode.metadata")],
),
(
bold_reference_wf,
bold_sdc_wf,
[
("outputnode.ref_image", "inputnode.epi_file"),
("outputnode.ref_image_brain", "inputnode.epi_brain"),
("outputnode.bold_mask", "inputnode.epi_mask"),
],
),
]
)
# Top-level BOLD splitter
bold_split = pe.Node(FSLSplit(dimension="t"), name="bold_split", mem_gb=memcalc.series_gb * 3)
workflow.connect(inputnode, "bold_file", bold_split, "in_file")
# HMC on the BOLD
bold_hmc_wf = init_bold_hmc_wf(
name="bold_hmc_wf", mem_gb=memcalc.series_gb, omp_nthreads=config.nipype.omp_nthreads,
)
workflow.connect(
[
(
bold_reference_wf,
bold_hmc_wf,
[
("outputnode.raw_ref_image", "inputnode.raw_ref_image"),
("outputnode.bold_file", "inputnode.bold_file"),
],
),
(
bold_hmc_wf,
outputnode,
[("outputnode.movpar_file", "movpar_file"), ("outputnode.rmsd_file", "rmsd_file")],
),
]
)
# calculate BOLD registration to T1w
bold_reg_wf = init_bold_reg_wf(
freesurfer=config.workflow.run_reconall,
use_bbr=config.workflow.use_bbr,
bold2t1w_dof=config.workflow.bold2t1w_dof,
bold2t1w_init=config.workflow.bold2t1w_init,
mem_gb=memcalc.series_std_gb,
omp_nthreads=config.nipype.omp_nthreads,
use_compression=False,
)
workflow.connect(
[
(inputnode, bold_reg_wf, [("t1w_dseg", "inputnode.t1w_dseg")]),
(t1w_brain, bold_reg_wf, [("out_file", "inputnode.t1w_brain")]),
(bold_sdc_wf, bold_reg_wf, [("outputnode.epi_brain", "inputnode.ref_bold_brain")],),
]
)
# apply BOLD registration to T1w
bold_t1_trans_wf = init_bold_t1_trans_wf(
name="bold_t1_trans_wf",
freesurfer=config.workflow.run_reconall,
use_fieldwarp=fmap_type is not None,
multiecho=False,
mem_gb=memcalc.series_std_gb,
omp_nthreads=config.nipype.omp_nthreads,
use_compression=False,
)
workflow.connect(
[
(
inputnode,
bold_t1_trans_wf,
[("bold_file", "inputnode.name_source"), ("t1w_mask", "inputnode.t1w_mask")],
),
(
bold_sdc_wf,
bold_t1_trans_wf,
[
("outputnode.epi_brain", "inputnode.ref_bold_brain"),
("outputnode.epi_mask", "inputnode.ref_bold_mask"),
("outputnode.out_warp", "inputnode.fieldwarp"),
],
),
(t1w_brain, bold_t1_trans_wf, [("out_file", "inputnode.t1w_brain")]),
(bold_split, bold_t1_trans_wf, [("out_files", "inputnode.bold_split")]),
(bold_hmc_wf, bold_t1_trans_wf, [("outputnode.xforms", "inputnode.hmc_xforms")],),
(
bold_reg_wf,
bold_t1_trans_wf,
[("outputnode.itk_bold_to_t1", "inputnode.itk_bold_to_t1")],
),
]
)
# Apply transforms in 1 shot
# Only use uncompressed output if AROMA is to be run
bold_bold_trans_wf = init_bold_preproc_trans_wf(
mem_gb=memcalc.series_std_gb,
omp_nthreads=config.nipype.omp_nthreads,
use_compression=not config.execution.low_mem,
use_fieldwarp=True,
name="bold_bold_trans_wf",
)
# bold_bold_trans_wf.inputs.inputnode.name_source = ref_file
workflow.connect(
[
(inputnode, bold_bold_trans_wf, [("bold_file", "inputnode.name_source")]),
(bold_split, bold_bold_trans_wf, [("out_files", "inputnode.bold_file")]),
(bold_hmc_wf, bold_bold_trans_wf, [("outputnode.xforms", "inputnode.hmc_xforms")],),
(
bold_sdc_wf,
bold_bold_trans_wf,
[
("outputnode.out_warp", "inputnode.fieldwarp"),
("outputnode.epi_mask", "inputnode.bold_mask"),
],
),
]
)
# Apply transforms in 1 shot
# Only use uncompressed output if AROMA is to be run
bold_std_trans_wf = init_bold_std_trans_wf(
freesurfer=config.workflow.run_reconall,
mem_gb=memcalc.series_std_gb,
omp_nthreads=config.nipype.omp_nthreads,
spaces=config.workflow.spaces,
name="bold_std_trans_wf",
use_compression=not config.execution.low_mem,
use_fieldwarp=fmap_type is not None,
)
workflow.connect(
[
(
inputnode,
bold_std_trans_wf,
[
("template", "inputnode.templates"),
("anat2std_xfm", "inputnode.anat2std_xfm"),
("bold_file", "inputnode.name_source"),
],
),
(bold_split, bold_std_trans_wf, [("out_files", "inputnode.bold_split")]),
(bold_hmc_wf, bold_std_trans_wf, [("outputnode.xforms", "inputnode.hmc_xforms")],),
(
bold_reg_wf,
bold_std_trans_wf,
[("outputnode.itk_bold_to_t1", "inputnode.itk_bold_to_t1")],
),
(
bold_bold_trans_wf,
bold_std_trans_wf,
[("outputnode.bold_mask", "inputnode.bold_mask")],
),
(bold_sdc_wf, bold_std_trans_wf, [("outputnode.out_warp", "inputnode.fieldwarp")],),
(
bold_std_trans_wf,
outputnode,
[
("outputnode.bold_std", "bold_std"),
("outputnode.bold_std_ref", "bold_std_ref"),
("outputnode.bold_mask_std", "bold_mask_std"),
],
),
]
)
ica_aroma_wf = init_ica_aroma_wf(
mem_gb=memcalc.series_std_gb,
metadata={"RepetitionTime": np.nan},
omp_nthreads=config.nipype.omp_nthreads,
use_fieldwarp=True,
err_on_aroma_warn=config.workflow.aroma_err_on_warn,
aroma_melodic_dim=config.workflow.aroma_melodic_dim,
name="ica_aroma_wf",
)
ica_aroma_wf.get_node("ica_aroma").inputs.denoise_type = "no"
ica_aroma_wf.remove_nodes([ica_aroma_wf.get_node("add_nonsteady")])
workflow.connect(
[
(inputnode, ica_aroma_wf, [("bold_file", "inputnode.name_source")]),
(
metadatanode,
ica_aroma_wf,
[("repetition_time", "melodic.tr_sec",), ("repetition_time", "ica_aroma.TR")],
),
(bold_hmc_wf, ica_aroma_wf, [("outputnode.movpar_file", "inputnode.movpar_file")]),
(bold_reference_wf, ica_aroma_wf, [("outputnode.skip_vols", "inputnode.skip_vols")]),
(
bold_std_trans_wf,
ica_aroma_wf,
[
("outputnode.bold_std", "inputnode.bold_std"),
("outputnode.bold_mask_std", "inputnode.bold_mask_std"),
("outputnode.spatial_reference", "inputnode.spatial_reference"),
],
),
(
ica_aroma_wf,
outputnode,
[
("outputnode.aroma_noise_ics", "aroma_noise_ics"),
("outputnode.melodic_mix", "melodic_mix"),
("outputnode.nonaggr_denoised_file", "nonaggr_denoised_file"),
("outputnode.aroma_confounds", "aroma_confounds"),
("outputnode.aroma_metadata", "aroma_metadata"),
],
),
]
)
bold_confounds_wf = init_bold_confs_wf(
mem_gb=memcalc.series_std_gb,
metadata={},
regressors_all_comps=config.workflow.regressors_all_comps,
regressors_fd_th=config.workflow.regressors_fd_th,
regressors_dvars_th=config.workflow.regressors_dvars_th,
name="bold_confounds_wf",
)
bold_confounds_wf.get_node("inputnode").inputs.t1_transform_flags = [False]
workflow.connect(
[
(
inputnode,
bold_confounds_wf,
[("t1w_tpms", "inputnode.t1w_tpms"), ("t1w_mask", "inputnode.t1w_mask")],
),
(
bold_hmc_wf,
bold_confounds_wf,
[
("outputnode.movpar_file", "inputnode.movpar_file"),
("outputnode.rmsd_file", "inputnode.rmsd_file"),
],
),
(
bold_reg_wf,
bold_confounds_wf,
[("outputnode.itk_t1_to_bold", "inputnode.t1_bold_xform")],
),
(
bold_reference_wf,
bold_confounds_wf,
[("outputnode.skip_vols", "inputnode.skip_vols")],
),
(bold_confounds_wf, outputnode, [("outputnode.confounds_file", "confounds")]),
(
bold_confounds_wf,
outputnode,
[("outputnode.confounds_metadata", "confounds_metadata")],
),
(
metadatanode,
bold_confounds_wf,
[
("repetition_time", "acompcor.repetition_time"),
("repetition_time", "tcompcor.repetition_time"),
],
),
(
bold_bold_trans_wf,
bold_confounds_wf,
[
("outputnode.bold", "inputnode.bold"),
("outputnode.bold_mask", "inputnode.bold_mask"),
],
),
]
)
carpetplot_wf = init_carpetplot_wf(
mem_gb=memcalc.series_std_gb,
metadata={"RepetitionTime": np.nan},
cifti_output=config.workflow.cifti_output,
name="carpetplot_wf",
)
carpetplot_select_std = pe.Node(
KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"),
name="carpetplot_select_std",
run_without_submitting=True,
)
workflow.connect(
[
(
inputnode,
carpetplot_select_std,
[("std2anat_xfm", "std2anat_xfm"), ("template", "keys")],
),
(carpetplot_select_std, carpetplot_wf, [("std2anat_xfm", "inputnode.std2anat_xfm")],),
(
bold_bold_trans_wf,
carpetplot_wf,
[
("outputnode.bold", "inputnode.bold"),
("outputnode.bold_mask", "inputnode.bold_mask"),
],
),
(
bold_reg_wf,
carpetplot_wf,
[("outputnode.itk_t1_to_bold", "inputnode.t1_bold_xform")],
),
(
bold_confounds_wf,
carpetplot_wf,
[("outputnode.confounds_file", "inputnode.confounds_file")],
),
(metadatanode, carpetplot_wf, [("repetition_time", "conf_plot.tr")]),
]
)
# Custom
make_reportnode(workflow)
assert workdir is not None
make_reportnode_datasink(workflow, workdir)
return workflow
def init_bold_reference_wf(
omp_nthreads,
bold_file=None,
sbref_files=None,
brainmask_thresh=0.85,
pre_mask=False,
multiecho=False,
name="bold_reference_wf",
gen_report=False,
):
"""
Build a workflow that generates reference BOLD images for a series.
The raw reference image is the target of :abbr:`HMC (head motion correction)`, and a
contrast-enhanced reference is the subject of distortion correction, as well as
boundary-based registration to T1w and template spaces.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from niworkflows.func.util import init_bold_reference_wf
wf = init_bold_reference_wf(omp_nthreads=1)
Parameters
----------
omp_nthreads : :obj:`int`
Maximum number of threads an individual process may use
bold_file : :obj:`str`
BOLD series NIfTI file
sbref_files : :obj:`list` or :obj:`bool`
Single band (as opposed to multi band) reference NIfTI file.
If ``True`` is passed, the workflow is built to accommodate SBRefs,
but the input is left undefined (i.e., it is left open for connection)
brainmask_thresh: :obj:`float`
Lower threshold for the probabilistic brainmask to obtain
the final binary mask (default: 0.85).
pre_mask : :obj:`bool`
Indicates whether the ``pre_mask`` input will be set (and thus, step 1
should be skipped).
multiecho : :obj:`bool`
If multiecho data was supplied, data from the first echo
will be selected
name : :obj:`str`
Name of workflow (default: ``bold_reference_wf``)
gen_report : :obj:`bool`
Whether a mask report node should be appended in the end
Inputs
------
bold_file : str
BOLD series NIfTI file
bold_mask : bool
A tentative brain mask to initialize the workflow (requires ``pre_mask``
parameter set ``True``).
dummy_scans : int or None
Number of non-steady-state volumes specified by user at beginning of ``bold_file``
sbref_file : str
single band (as opposed to multi band) reference NIfTI file
Outputs
-------
bold_file : str
Validated BOLD series NIfTI file
raw_ref_image : str
Reference image to which BOLD series is motion corrected
skip_vols : int
Number of non-steady-state volumes selected at beginning of ``bold_file``
algo_dummy_scans : int
Number of non-steady-state volumes agorithmically detected at
beginning of ``bold_file``
ref_image : str
Contrast-enhanced reference image
ref_image_brain : str
Skull-stripped reference image
bold_mask : str
Skull-stripping mask of reference image
validation_report : str
HTML reportlet indicating whether ``bold_file`` had a valid affine
Subworkflows
* :py:func:`~niworkflows.func.util.init_enhance_and_skullstrip_wf`
"""
workflow = Workflow(name=name)
workflow.__desc__ = f"""\
First, a reference volume and its skull-stripped version were generated
{'from the shortest echo of the BOLD run' * multiecho} using a custom
methodology of *fMRIPrep*.
"""
inputnode = pe.Node(
niu.IdentityInterface(
fields=["bold_file", "bold_mask", "dummy_scans", "sbref_file"]
),
name="inputnode",
)
outputnode = pe.Node(
niu.IdentityInterface(
fields=[
"bold_file",
"raw_ref_image",
"skip_vols",
"algo_dummy_scans",
"ref_image",
"ref_image_brain",
"bold_mask",
"validation_report",
"mask_report",
]
),
name="outputnode",
)
# Simplify manually setting input image
if bold_file is not None:
inputnode.inputs.bold_file = bold_file
val_bold = pe.MapNode(
ValidateImage(),
name="val_bold",
mem_gb=DEFAULT_MEMORY_MIN_GB,
iterfield=["in_file"],
)
get_dummy = pe.Node(NonsteadyStatesDetector(), name="get_dummy")
gen_avg = pe.Node(RobustAverage(), name="gen_avg", mem_gb=1)
calc_dummy_scans = pe.Node(
niu.Function(function=_pass_dummy_scans, output_names=["skip_vols_num"]),
name="calc_dummy_scans",
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB,
)
bold_1st = pe.Node(
niu.Select(index=[0]), name="bold_1st", run_without_submitting=True
)
validate_1st = pe.Node(
niu.Select(index=[0]), name="validate_1st", run_without_submitting=True
)
# fmt: off
workflow.connect([
(inputnode, val_bold, [(("bold_file", listify), "in_file")]),
(inputnode, get_dummy, [(("bold_file", pop_file), "in_file")]),
(inputnode, calc_dummy_scans, [("dummy_scans", "dummy_scans")]),
(val_bold, bold_1st, [(("out_file", listify), "inlist")]),
(get_dummy, calc_dummy_scans, [("n_dummy", "algo_dummy_scans")]),
(calc_dummy_scans, outputnode, [("skip_vols_num", "skip_vols")]),
(gen_avg, outputnode, [("out_file", "raw_ref_image")]),
(val_bold, validate_1st, [(("out_report", listify), "inlist")]),
(bold_1st, outputnode, [("out", "bold_file")]),
(validate_1st, outputnode, [("out", "validation_report")]),
(get_dummy, outputnode, [("n_dummy", "algo_dummy_scans")]),
])
# fmt: on
if not pre_mask:
from nirodents.workflows.brainextraction import init_rodent_brain_extraction_wf
brain_extraction_wf = init_rodent_brain_extraction_wf(
ants_affine_init=False,
debug=config.execution.debug is True
)
# fmt: off
workflow.connect([
(gen_avg, brain_extraction_wf, [
("out_file", "inputnode.in_files"),
]),
(brain_extraction_wf, outputnode, [
("outputnode.out_corrected", "ref_image"),
("outputnode.out_mask", "bold_mask"),
("outputnode.out_brain", "ref_image_brain"),
]),
])
# fmt: on
else:
from niworkflows.interfaces.nibabel import ApplyMask
mask_brain = pe.Node(ApplyMask(), name="mask_brain")
# fmt: off
workflow.connect([
(inputnode, mask_brain, [("bold_mask", "in_mask")]),
(inputnode, outputnode, [("bold_mask", "bold_mask")]),
(gen_avg, outputnode, [("out_file", "ref_image")]),
(gen_avg, mask_brain, [("out_file", "in_file")]),
(mask_brain, outputnode, [("out_file", "ref_image_brain")]),
])
# fmt: on
if not sbref_files:
# fmt: off
workflow.connect([
(val_bold, gen_avg, [(("out_file", pop_file), "in_file")]), # pop first echo of ME-EPI
(get_dummy, gen_avg, [("t_mask", "t_mask")]),
])
# fmt: on
return workflow
from niworkflows.interfaces.nibabel import MergeSeries
nsbrefs = 0
if sbref_files is not True:
# If not boolean, then it is a list-of or pathlike.
inputnode.inputs.sbref_file = sbref_files
nsbrefs = 1 if isinstance(sbref_files, str) else len(sbref_files)
val_sbref = pe.MapNode(
ValidateImage(),
name="val_sbref",
mem_gb=DEFAULT_MEMORY_MIN_GB,
iterfield=["in_file"],
)
merge_sbrefs = pe.Node(MergeSeries(), name="merge_sbrefs")
# fmt: off
workflow.connect([
(inputnode, val_sbref, [(("sbref_file", listify), "in_file")]),
(val_sbref, merge_sbrefs, [("out_file", "in_files")]),
(merge_sbrefs, gen_avg, [("out_file", "in_file")]),
])
# fmt: on
# Edit the boilerplate as the SBRef will be the reference
workflow.__desc__ = f"""\
First, a reference volume and its skull-stripped version were generated
by aligning and averaging{' the first echo of' * multiecho}
{nsbrefs or ''} single-band references (SBRefs).
"""
if gen_report:
mask_reportlet = pe.Node(SimpleShowMaskRPT(), name="mask_reportlet")
# fmt: off
workflow.connect([
(outputnode, mask_reportlet, [
("ref_image", "background_file"),
("bold_mask", "mask_file"),
]),
])
# fmt: on
return workflow
def init_func_preproc_wf(bold_file):
"""
This workflow controls the functional preprocessing stages of *fMRIPrep*.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from fprodents.workflows.tests import mock_config
from fprodents import config
from fprodents.workflows.bold.base import init_func_preproc_wf
with mock_config():
bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
/ 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
wf = init_func_preproc_wf(str(bold_file))
Inputs
------
bold_file
BOLD series NIfTI file
t1w_preproc
Bias-corrected structural template image
t1w_mask
Mask of the skull-stripped template image
anat_dseg
Segmentation of preprocessed structural image, including
gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)
t1w_asec
Segmentation of structural image, done with FreeSurfer.
t1w_aparc
Parcellation of structural image, done with FreeSurfer.
anat_tpms
List of tissue probability maps in T1w space
template
List of templates to target
anat2std_xfm
List of transform files, collated with templates
std2anat_xfm
List of inverse transform files, collated with templates
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
t1w2fsnative_xfm
LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space
fsnative2t1w_xfm
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
Outputs
-------
bold_t1
BOLD series, resampled to T1w space
bold_mask_t1
BOLD series mask in T1w space
bold_std
BOLD series, resampled to template space
bold_mask_std
BOLD series mask in template space
confounds
TSV of confounds
surfaces
BOLD series, resampled to FreeSurfer surfaces
aroma_noise_ics
Noise components identified by ICA-AROMA
melodic_mix
FSL MELODIC mixing matrix
See Also
--------
* :py:func:`~fprodents.workflows.bold.stc.init_bold_stc_wf`
* :py:func:`~fprodents.workflows.bold.hmc.init_bold_hmc_wf`
* :py:func:`~fprodents.workflows.bold.t2s.init_bold_t2s_wf`
* :py:func:`~fprodents.workflows.bold.registration.init_bold_t1_trans_wf`
* :py:func:`~fprodents.workflows.bold.registration.init_bold_reg_wf`
* :py:func:`~fprodents.workflows.bold.confounds.init_bold_confounds_wf`
* :py:func:`~fprodents.workflows.bold.confounds.init_ica_aroma_wf`
* :py:func:`~fprodents.workflows.bold.resampling.init_bold_std_trans_wf`
* :py:func:`~fprodents.workflows.bold.resampling.init_bold_preproc_trans_wf`
* :py:func:`~fprodents.workflows.bold.resampling.init_bold_surf_wf`
"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
from niworkflows.interfaces.nibabel import ApplyMask
from niworkflows.interfaces.utility import KeySelect, DictMerge
from nipype.interfaces.freesurfer.utils import LTAConvert
from ...patch.utils import extract_entities
mem_gb = {"filesize": 1, "resampled": 1, "largemem": 1}
bold_tlen = 10
# Have some options handy
omp_nthreads = config.nipype.omp_nthreads
spaces = config.workflow.spaces
output_dir = str(config.execution.output_dir)
# Extract BIDS entities and metadata from BOLD file(s)
entities = extract_entities(bold_file)
layout = config.execution.layout
# Take first file as reference
ref_file = pop_file(bold_file)
metadata = layout.get_metadata(ref_file)
echo_idxs = listify(entities.get("echo", []))
multiecho = len(echo_idxs) > 2
if len(echo_idxs) == 1:
config.loggers.warning(
f"Running a single echo <{ref_file}> from a seemingly multi-echo dataset."
)
bold_file = ref_file # Just in case - drop the list
if len(echo_idxs) == 2:
raise RuntimeError(
"Multi-echo processing requires at least three different echos (found two)."
)
if multiecho:
# Drop echo entity for future queries, have a boolean shorthand
entities.pop("echo", None)
# reorder echoes from shortest to largest
tes, bold_file = zip(*sorted([(layout.get_metadata(bf)["EchoTime"], bf)
for bf in bold_file]))
ref_file = bold_file[0] # Reset reference to be the shortest TE
if os.path.isfile(ref_file):
bold_tlen, mem_gb = _create_mem_gb(ref_file)
wf_name = _get_wf_name(ref_file)
config.loggers.workflow.debug(
"Creating bold processing workflow for <%s> (%.2f GB / %d TRs). "
"Memory resampled/largemem=%.2f/%.2f GB.",
ref_file,
mem_gb["filesize"],
bold_tlen,
mem_gb["resampled"],
mem_gb["largemem"],
)
# Find associated sbref, if possible
entities["suffix"] = "sbref"
entities["extension"] = ["nii", "nii.gz"] # Overwrite extensions
sbref_files = layout.get(return_type="file", **entities)
sbref_msg = f"No single-band-reference found for {os.path.basename(ref_file)}."
if sbref_files and "sbref" in config.workflow.ignore:
sbref_msg = "Single-band reference file(s) found and ignored."
elif sbref_files:
sbref_msg = "Using single-band reference file(s) {}.".format(",".join(
[os.path.basename(sbf) for sbf in sbref_files]))
config.loggers.workflow.info(sbref_msg)
# Check whether STC must/can be run
run_stc = (bool(metadata.get("SliceTiming"))
and 'slicetiming' not in config.workflow.ignore)
# Build workflow
workflow = Workflow(name=wf_name)
workflow.__postdesc__ = """\
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
transform matrices, susceptibility distortion correction when available,
and co-registrations to anatomical and output spaces).
Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
configured with Lanczos interpolation to minimize the smoothing
effects of other kernels [@lanczos].
Non-gridded (surface) resamplings were performed using `mri_vol2surf`
(FreeSurfer).
"""
inputnode = pe.Node(
niu.IdentityInterface(fields=[
"bold_file",
"ref_file",
"bold_ref_xfm",
"n_dummy_scans",
"validation_report",
"subjects_dir",
"subject_id",
"anat_preproc",
"anat_mask",
"anat_dseg",
"anat_tpms",
"anat2std_xfm",
"std2anat_xfm",
"template",
"anat2fsnative_xfm",
"fsnative2anat_xfm",
]),
name="inputnode",
)
inputnode.inputs.bold_file = bold_file
outputnode = pe.Node(
niu.IdentityInterface(fields=[
"bold_mask",
"bold_t1",
"bold_t1_ref",
"bold_mask_t1",
"bold_std",
"bold_std_ref",
"bold_mask_std",
"bold_native",
"surfaces",
"confounds",
"aroma_noise_ics",
"melodic_mix",
"nonaggr_denoised_file",
"confounds_metadata",
]),
name="outputnode",
)
# Generate a brain-masked conversion of the t1w and bold reference images
t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")
lta_convert = pe.Node(LTAConvert(out_fsl=True, out_itk=True),
name="lta_convert")
# BOLD buffer: an identity used as a pointer to either the original BOLD
# or the STC'ed one for further use.
boldbuffer = pe.Node(niu.IdentityInterface(fields=["bold_file"]),
name="boldbuffer")
summary = pe.Node(
FunctionalSummary(
slice_timing=run_stc,
registration="FSL",
registration_dof=config.workflow.bold2t1w_dof,
registration_init=config.workflow.bold2t1w_init,
pe_direction=metadata.get("PhaseEncodingDirection"),
echo_idx=echo_idxs,
tr=metadata.get("RepetitionTime"),
distortion_correction="<not implemented>",
),
name="summary",
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
run_without_submitting=True,
)
summary.inputs.dummy_scans = config.workflow.dummy_scans
func_derivatives_wf = init_func_derivatives_wf(
bids_root=layout.root,
metadata=metadata,
output_dir=output_dir,
spaces=spaces,
use_aroma=config.workflow.use_aroma,
)
# fmt:off
workflow.connect([
(outputnode, func_derivatives_wf, [
('bold_t1', 'inputnode.bold_t1'),
('bold_t1_ref', 'inputnode.bold_t1_ref'),
('bold_mask_t1', 'inputnode.bold_mask_t1'),
('bold_native', 'inputnode.bold_native'),
('confounds', 'inputnode.confounds'),
('surfaces', 'inputnode.surf_files'),
('aroma_noise_ics', 'inputnode.aroma_noise_ics'),
('melodic_mix', 'inputnode.melodic_mix'),
('nonaggr_denoised_file', 'inputnode.nonaggr_denoised_file'),
('confounds_metadata', 'inputnode.confounds_metadata'),
]),
])
# fmt:on
# Top-level BOLD splitter
bold_split = pe.Node(FSLSplit(dimension="t"),
name="bold_split",
mem_gb=mem_gb["filesize"] * 3)
# calculate BOLD registration to T1w
bold_reg_wf = init_bold_reg_wf(
bold2t1w_dof=config.workflow.bold2t1w_dof,
bold2t1w_init=config.workflow.bold2t1w_init,
mem_gb=mem_gb["resampled"],
name="bold_reg_wf",
omp_nthreads=omp_nthreads,
use_compression=False,
)
# apply BOLD registration to T1w
bold_t1_trans_wf = init_bold_t1_trans_wf(
name="bold_t1_trans_wf",
use_fieldwarp=False,
multiecho=multiecho,
mem_gb=mem_gb["resampled"],
omp_nthreads=omp_nthreads,
use_compression=False,
)
t1w_mask_bold_tfm = pe.Node(ApplyTransforms(interpolation="MultiLabel"),
name="t1w_mask_bold_tfm",
mem_gb=0.1)
# get confounds
bold_confounds_wf = init_bold_confs_wf(
mem_gb=mem_gb["largemem"],
metadata=metadata,
regressors_all_comps=config.workflow.regressors_all_comps,
regressors_fd_th=config.workflow.regressors_fd_th,
regressors_dvars_th=config.workflow.regressors_dvars_th,
name="bold_confounds_wf",
)
bold_confounds_wf.get_node("inputnode").inputs.t1_transform_flags = [False]
# Apply transforms in 1 shot
# Only use uncompressed output if AROMA is to be run
bold_bold_trans_wf = init_bold_preproc_trans_wf(
mem_gb=mem_gb["resampled"],
omp_nthreads=omp_nthreads,
use_compression=not config.execution.low_mem,
use_fieldwarp=False,
name="bold_bold_trans_wf",
)
bold_bold_trans_wf.inputs.inputnode.name_source = ref_file
# SLICE-TIME CORRECTION (or bypass) #############################################
if run_stc:
bold_stc_wf = init_bold_stc_wf(name="bold_stc_wf", metadata=metadata)
# fmt:off
workflow.connect([
(inputnode, bold_stc_wf, [("n_dummy_scans", "inputnode.skip_vols")
]),
(bold_stc_wf, boldbuffer, [("outputnode.stc_file", "bold_file")]),
])
# fmt:on
if not multiecho:
# fmt:off
workflow.connect([(inputnode, bold_stc_wf,
[('bold_file', 'inputnode.bold_file')])])
# fmt:on
else: # for meepi, iterate through stc_wf for all workflows
meepi_echos = boldbuffer.clone(name="meepi_echos")
meepi_echos.iterables = ("bold_file", bold_file)
# fmt:off
workflow.connect([(meepi_echos, bold_stc_wf,
[('bold_file', 'inputnode.bold_file')])])
# fmt:on
elif not multiecho: # STC is too short or False
# bypass STC from original BOLD to the splitter through boldbuffer
# fmt:off
workflow.connect([(inputnode, boldbuffer, [('bold_file', 'bold_file')])
])
# fmt:on
else:
# for meepi, iterate over all meepi echos to boldbuffer
boldbuffer.iterables = ("bold_file", bold_file)
# MULTI-ECHO EPI DATA #############################################
if multiecho:
from niworkflows.func.util import init_skullstrip_bold_wf
skullstrip_bold_wf = init_skullstrip_bold_wf(name="skullstrip_bold_wf")
inputnode.inputs.bold_file = ref_file # Replace reference w first echo
join_echos = pe.JoinNode(
niu.IdentityInterface(fields=["bold_files"]),
joinsource=("meepi_echos" if run_stc is True else "boldbuffer"),
joinfield=["bold_files"],
name="join_echos",
)
# create optimal combination, adaptive T2* map
bold_t2s_wf = init_bold_t2s_wf(
echo_times=tes,
mem_gb=mem_gb["resampled"],
omp_nthreads=omp_nthreads,
name="bold_t2smap_wf",
)
# fmt:off
workflow.connect([
(skullstrip_bold_wf, join_echos,
[('outputnode.skull_stripped_file', 'bold_files')]),
(join_echos, bold_t2s_wf, [('bold_files', 'inputnode.bold_file')]),
])
# fmt:on
# MAIN WORKFLOW STRUCTURE #######################################################
# fmt:off
workflow.connect([
(inputnode, bold_reg_wf, [('anat_preproc', 'inputnode.t1w_brain'),
('ref_file', 'inputnode.ref_bold_brain')]),
(inputnode, t1w_brain, [('anat_preproc', 'in_file'),
('anat_mask', 'in_mask')]),
# convert bold reference LTA transform to other formats
(inputnode, lta_convert, [('bold_ref_xfm', 'in_lta')]),
# BOLD buffer has slice-time corrected if it was run, original otherwise
(boldbuffer, bold_split, [('bold_file', 'in_file')]),
(inputnode, summary, [('n_dummy_scans', 'algo_dummy_scans')]),
# EPI-T1 registration workflow
(inputnode, bold_t1_trans_wf, [('bold_file', 'inputnode.name_source'),
('anat_mask', 'inputnode.t1w_mask'),
('ref_file', 'inputnode.ref_bold_brain')
]),
(t1w_brain, bold_t1_trans_wf, [('out_file', 'inputnode.t1w_brain')]),
(lta_convert, bold_t1_trans_wf, [('out_itk', 'inputnode.hmc_xforms')]),
(bold_reg_wf, bold_t1_trans_wf, [('outputnode.bold2anat',
'inputnode.bold2anat')]),
(bold_t1_trans_wf, outputnode, [('outputnode.bold_t1', 'bold_t1'),
('outputnode.bold_t1_ref',
'bold_t1_ref')]),
# transform T1 mask to BOLD
(inputnode, t1w_mask_bold_tfm, [('anat_mask', 'input_image'),
('ref_file', 'reference_image')]),
(bold_reg_wf, t1w_mask_bold_tfm, [('outputnode.anat2bold',
'transforms')]),
(t1w_mask_bold_tfm, outputnode, [('output_image', 'bold_mask')]),
# Connect bold_confounds_wf
(inputnode, bold_confounds_wf, [('anat_tpms', 'inputnode.anat_tpms'),
('anat_mask', 'inputnode.t1w_mask')]),
(lta_convert, bold_confounds_wf, [('out_fsl', 'inputnode.movpar_file')
]),
(bold_reg_wf, bold_confounds_wf, [('outputnode.anat2bold',
'inputnode.anat2bold')]),
(inputnode, bold_confounds_wf, [('n_dummy_scans',
'inputnode.skip_vols')]),
(t1w_mask_bold_tfm, bold_confounds_wf, [('output_image',
'inputnode.bold_mask')]),
(bold_confounds_wf, outputnode, [('outputnode.confounds_file',
'confounds')]),
(bold_confounds_wf, outputnode, [('outputnode.confounds_metadata',
'confounds_metadata')]),
# Connect bold_bold_trans_wf
(inputnode, bold_bold_trans_wf, [('ref_file', 'inputnode.bold_ref')]),
(t1w_mask_bold_tfm, bold_bold_trans_wf, [('output_image',
'inputnode.bold_mask')]),
(bold_split, bold_bold_trans_wf, [('out_files', 'inputnode.bold_file')
]),
(lta_convert, bold_bold_trans_wf, [('out_itk', 'inputnode.hmc_xforms')
]),
# Summary
(outputnode, summary, [('confounds', 'confounds_file')]),
])
# fmt:on
# for standard EPI data, pass along correct file
if not multiecho:
# fmt:off
workflow.connect([
(inputnode, func_derivatives_wf, [('bold_file',
'inputnode.source_file')]),
(bold_bold_trans_wf, bold_confounds_wf, [('outputnode.bold',
'inputnode.bold')]),
(bold_split, bold_t1_trans_wf, [('out_files',
'inputnode.bold_split')]),
])
# fmt:on
else: # for meepi, create and use optimal combination
# fmt:off
workflow.connect([
# update name source for optimal combination
(inputnode, func_derivatives_wf,
[(('bold_file', combine_meepi_source), 'inputnode.source_file')]),
(bold_bold_trans_wf, skullstrip_bold_wf, [('outputnode.bold',
'inputnode.in_file')]),
(bold_t2s_wf, bold_confounds_wf, [('outputnode.bold',
'inputnode.bold')]),
(bold_t2s_wf, bold_t1_trans_wf, [('outputnode.bold',
'inputnode.bold_split')]),
])
# fmt:on
# Map final BOLD mask into T1w space (if required)
nonstd_spaces = set(spaces.get_nonstandard())
if nonstd_spaces.intersection(("T1w", "anat")):
from niworkflows.interfaces.fixes import (
FixHeaderApplyTransforms as ApplyTransforms, )
boldmask_to_t1w = pe.Node(
ApplyTransforms(interpolation="MultiLabel"),
name="boldmask_to_t1w",
mem_gb=0.1,
)
# fmt:off
workflow.connect([
(bold_reg_wf, boldmask_to_t1w, [('outputnode.bold2anat',
'transforms')]),
(bold_t1_trans_wf, boldmask_to_t1w, [('outputnode.bold_mask_t1',
'reference_image')]),
(t1w_mask_bold_tfm, boldmask_to_t1w, [('output_image',
'input_image')]),
(boldmask_to_t1w, outputnode, [('output_image', 'bold_mask_t1')]),
])
# fmt:on
if nonstd_spaces.intersection(("func", "run", "bold", "boldref", "sbref")):
# fmt:off
workflow.connect([
(bold_bold_trans_wf, outputnode, [('outputnode.bold',
'bold_native')]),
(bold_bold_trans_wf, func_derivatives_wf,
[('outputnode.bold_ref', 'inputnode.bold_native_ref'),
('outputnode.bold_mask', 'inputnode.bold_mask_native')]),
])
# fmt:on
if spaces.get_spaces(nonstandard=False, dim=(3, )):
# Apply transforms in 1 shot
# Only use uncompressed output if AROMA is to be run
bold_std_trans_wf = init_bold_std_trans_wf(
mem_gb=mem_gb["resampled"],
omp_nthreads=omp_nthreads,
spaces=spaces,
name="bold_std_trans_wf",
use_compression=not config.execution.low_mem,
use_fieldwarp=False,
)
# fmt:off
workflow.connect([
(inputnode, bold_std_trans_wf,
[('template', 'inputnode.templates'),
('anat2std_xfm', 'inputnode.anat2std_xfm'),
('bold_file', 'inputnode.name_source')]),
(t1w_mask_bold_tfm, bold_std_trans_wf, [('output_image',
'inputnode.bold_mask')]),
(lta_convert, bold_std_trans_wf, [('out_itk',
'inputnode.hmc_xforms')]),
(bold_reg_wf, bold_std_trans_wf, [('outputnode.bold2anat',
'inputnode.bold2anat')]),
(bold_std_trans_wf, outputnode,
[('outputnode.bold_std', 'bold_std'),
('outputnode.bold_std_ref', 'bold_std_ref'),
('outputnode.bold_mask_std', 'bold_mask_std')]),
])
# fmt:on
if not multiecho:
# fmt:off
workflow.connect([
(bold_split, bold_std_trans_wf, [("out_files",
"inputnode.bold_split")]),
])
# fmt:on
else:
split_opt_comb = bold_split.clone(name="split_opt_comb")
# fmt:off
workflow.connect([(bold_t2s_wf, split_opt_comb,
[('outputnode.bold', 'in_file')]),
(split_opt_comb, bold_std_trans_wf,
[('out_files', 'inputnode.bold_split')])])
# fmt:on
# func_derivatives_wf internally parametrizes over snapshotted spaces.
# fmt:off
workflow.connect([
(bold_std_trans_wf, func_derivatives_wf, [
('outputnode.template', 'inputnode.template'),
('outputnode.spatial_reference',
'inputnode.spatial_reference'),
('outputnode.bold_std_ref', 'inputnode.bold_std_ref'),
('outputnode.bold_std', 'inputnode.bold_std'),
('outputnode.bold_mask_std', 'inputnode.bold_mask_std'),
]),
])
# fmt:on
if config.workflow.use_aroma: # ICA-AROMA workflow
from .confounds import init_ica_aroma_wf
ica_aroma_wf = init_ica_aroma_wf(
mem_gb=mem_gb["resampled"],
metadata=metadata,
omp_nthreads=omp_nthreads,
use_fieldwarp=False,
err_on_aroma_warn=config.workflow.aroma_err_on_warn,
aroma_melodic_dim=config.workflow.aroma_melodic_dim,
name="ica_aroma_wf",
)
join = pe.Node(
niu.Function(output_names=["out_file"], function=_to_join),
name="aroma_confounds",
)
mrg_conf_metadata = pe.Node(
niu.Merge(2),
name="merge_confound_metadata",
run_without_submitting=True,
)
mrg_conf_metadata2 = pe.Node(
DictMerge(),
name="merge_confound_metadata2",
run_without_submitting=True,
)
# fmt:off
workflow.disconnect([
(bold_confounds_wf, outputnode, [
('outputnode.confounds_file', 'confounds'),
]),
(bold_confounds_wf, outputnode, [
('outputnode.confounds_metadata', 'confounds_metadata'),
]),
])
workflow.connect([
(inputnode, ica_aroma_wf,
[('bold_file', 'inputnode.name_source'),
('n_dummy_scans', 'inputnode.skip_vols')]),
(lta_convert, ica_aroma_wf, [('out_fsl',
'inputnode.movpar_file')]),
(bold_confounds_wf, join, [('outputnode.confounds_file',
'in_file')]),
(bold_confounds_wf, mrg_conf_metadata,
[('outputnode.confounds_metadata', 'in1')]),
(ica_aroma_wf, join, [('outputnode.aroma_confounds',
'join_file')]),
(ica_aroma_wf, mrg_conf_metadata,
[('outputnode.aroma_metadata', 'in2')]),
(mrg_conf_metadata, mrg_conf_metadata2, [('out', 'in_dicts')]),
(ica_aroma_wf, outputnode,
[('outputnode.aroma_noise_ics', 'aroma_noise_ics'),
('outputnode.melodic_mix', 'melodic_mix'),
('outputnode.nonaggr_denoised_file', 'nonaggr_denoised_file')
]),
(join, outputnode, [('out_file', 'confounds')]),
(mrg_conf_metadata2, outputnode, [('out_dict',
'confounds_metadata')]),
(bold_std_trans_wf, ica_aroma_wf,
[('outputnode.bold_std', 'inputnode.bold_std'),
('outputnode.bold_mask_std', 'inputnode.bold_mask_std'),
('outputnode.spatial_reference',
'inputnode.spatial_reference')]),
])
# fmt:on
if spaces.get_spaces(nonstandard=False, dim=(3, )):
carpetplot_wf = init_carpetplot_wf(
mem_gb=mem_gb["resampled"],
metadata=metadata,
name="carpetplot_wf",
)
# Xform to 'Fischer344' is always computed.
carpetplot_select_std = pe.Node(
KeySelect(fields=["std2anat_xfm"], key="Fischer344"),
name="carpetplot_select_std",
run_without_submitting=True,
)
# fmt:off
workflow.connect([
(inputnode, carpetplot_select_std, [('std2anat_xfm',
'std2anat_xfm'),
('template', 'keys')]),
(carpetplot_select_std, carpetplot_wf,
[('std2anat_xfm', 'inputnode.std2anat_xfm')]),
(bold_bold_trans_wf if not multiecho else bold_t2s_wf,
carpetplot_wf, [('outputnode.bold', 'inputnode.bold')]),
(t1w_mask_bold_tfm, carpetplot_wf, [('output_image',
'inputnode.bold_mask')]),
(bold_reg_wf, carpetplot_wf, [('outputnode.anat2bold',
'inputnode.anat2bold')]),
(bold_confounds_wf, carpetplot_wf, [('outputnode.confounds_file',
'inputnode.confounds_file')]),
])
# fmt:on
# REPORTING ############################################################
ds_report_summary = pe.Node(
DerivativesDataSink(desc="summary",
datatype="figures",
dismiss_entities=("echo", )),
name="ds_report_summary",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
ds_report_validation = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
desc="validation",
datatype="figures",
dismiss_entities=("echo", ),
),
name="ds_report_validation",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
# fmt:off
workflow.connect([
(summary, ds_report_summary, [('out_report', 'in_file')]),
(inputnode, ds_report_validation, [('validation_report', 'in_file')]),
])
# fmt:on
# Fill-in datasinks of reportlets seen so far
for node in workflow.list_node_names():
if node.split(".")[-1].startswith("ds_report"):
workflow.get_node(node).inputs.base_directory = output_dir
workflow.get_node(node).inputs.source_file = ref_file
return workflow
def init_infant_brain_extraction_wf(
age_months=None,
ants_affine_init=False,
bspline_fitting_distance=200,
sloppy=False,
skull_strip_template="UNCInfant",
template_specs=None,
interim_checkpoints=True,
mem_gb=3.0,
mri_scheme="T1w",
name="infant_brain_extraction_wf",
atropos_model=None,
omp_nthreads=None,
output_dir=None,
use_float=True,
use_t2w=False,
):
"""
Build an atlas-based brain extraction pipeline for infant T1w/T2w MRI data.
Pros/Cons of available templates
--------------------------------
* MNIInfant
+ More cohorts available for finer-grain control
+ T1w/T2w images available
- Template masks are poor
* UNCInfant
+ Accurate masks
- No T2w image available
Parameters
----------
ants_affine_init : :obj:`bool`, optional
Set-up a pre-initialization step with ``antsAI`` to account for mis-oriented images.
"""
# handle template specifics
template_specs = template_specs or {}
if skull_strip_template == 'MNIInfant':
template_specs['resolution'] = 2 if sloppy else 1
if not template_specs.get('cohort'):
if age_months is None:
raise KeyError(
f"Age or cohort for {skull_strip_template} must be provided!")
template_specs['cohort'] = cohort_by_months(skull_strip_template,
age_months)
inputnode = pe.Node(
niu.IdentityInterface(fields=["t1w", "t2w", "in_mask"]),
name="inputnode")
outputnode = pe.Node(niu.IdentityInterface(
fields=["t1w_corrected", "t1w_corrected_brain", "t1w_mask"]),
name="outputnode")
if not use_t2w:
raise RuntimeError("A T2w image is currently required.")
tpl_target_path = get_template(
skull_strip_template,
suffix='T1w', # no T2w template
desc=None,
**template_specs,
)
if not tpl_target_path:
raise RuntimeError(
f"An instance of template <tpl-{skull_strip_template}> with MR scheme "
f"'{'T1w' or mri_scheme}' could not be found.")
tpl_brainmask_path = get_template(skull_strip_template,
label="brain",
suffix="probseg",
**template_specs) or get_template(
skull_strip_template,
desc="brain",
suffix="mask",
**template_specs)
tpl_regmask_path = get_template(skull_strip_template,
label="BrainCerebellumExtraction",
suffix="mask",
**template_specs)
# validate images
val_tmpl = pe.Node(ValidateImage(), name='val_tmpl')
val_t1w = val_tmpl.clone("val_t1w")
val_t2w = val_tmpl.clone("val_t2w")
val_tmpl.inputs.in_file = _pop(tpl_target_path)
gauss_tmpl = pe.Node(niu.Function(function=_gauss_filter),
name="gauss_tmpl")
# Spatial normalization step
lap_tmpl = pe.Node(ImageMath(operation="Laplacian", op2="0.4 1"),
name="lap_tmpl")
lap_t1w = lap_tmpl.clone("lap_t1w")
lap_t2w = lap_tmpl.clone("lap_t2w")
# Merge image nodes
mrg_tmpl = pe.Node(niu.Merge(2), name="mrg_tmpl")
mrg_t2w = mrg_tmpl.clone("mrg_t2w")
mrg_t1w = mrg_tmpl.clone("mrg_t1w")
norm_lap_tmpl = pe.Node(niu.Function(function=_trunc),
name="norm_lap_tmpl")
norm_lap_tmpl.inputs.dtype = "float32"
norm_lap_tmpl.inputs.out_max = 1.0
norm_lap_tmpl.inputs.percentile = (0.01, 99.99)
norm_lap_tmpl.inputs.clip_max = None
norm_lap_t1w = norm_lap_tmpl.clone('norm_lap_t1w')
norm_lap_t2w = norm_lap_t1w.clone('norm_lap_t2w')
# Set up initial spatial normalization
ants_params = "testing" if sloppy else "precise"
norm = pe.Node(
Registration(from_file=pkgr_fn(
"niworkflows.data", f"antsBrainExtraction_{ants_params}.json")),
name="norm",
n_procs=omp_nthreads,
mem_gb=mem_gb,
)
norm.inputs.float = use_float
if tpl_regmask_path:
norm.inputs.fixed_image_masks = tpl_regmask_path
# Set up T2w -> T1w within-subject registration
norm_subj = pe.Node(
Registration(
from_file=pkgr_fn("nibabies.data", "within_subject_t1t2.json")),
name="norm_subj",
n_procs=omp_nthreads,
mem_gb=mem_gb,
)
norm_subj.inputs.float = use_float
# main workflow
wf = pe.Workflow(name)
# Create a buffer interface as a cache for the actual inputs to registration
buffernode = pe.Node(
niu.IdentityInterface(fields=["hires_target", "smooth_target"]),
name="buffernode")
# truncate target intensity for N4 correction
clip_tmpl = pe.Node(niu.Function(function=_trunc), name="clip_tmpl")
clip_t2w = clip_tmpl.clone('clip_t2w')
clip_t1w = clip_tmpl.clone('clip_t1w')
# INU correction of the t1w
init_t2w_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
save_bias=False,
copy_header=True,
n_iterations=[50] * (4 - sloppy),
convergence_threshold=1e-7,
shrink_factor=4,
bspline_fitting_distance=bspline_fitting_distance,
),
n_procs=omp_nthreads,
name="init_t2w_n4",
)
init_t1w_n4 = init_t2w_n4.clone("init_t1w_n4")
clip_t2w_inu = pe.Node(niu.Function(function=_trunc), name="clip_t2w_inu")
clip_t1w_inu = clip_t2w_inu.clone("clip_t1w_inu")
map_mask_t2w = pe.Node(ApplyTransforms(interpolation="Gaussian",
float=True),
name="map_mask_t2w",
mem_gb=1)
map_mask_t1w = map_mask_t2w.clone("map_mask_t1w")
# map template brainmask to t2w space
map_mask_t2w.inputs.input_image = str(tpl_brainmask_path)
thr_t2w_mask = pe.Node(Binarize(thresh_low=0.80), name="thr_t2w_mask")
thr_t1w_mask = thr_t2w_mask.clone('thr_t1w_mask')
bspline_grid = pe.Node(niu.Function(function=_bspline_distance),
name="bspline_grid")
# Refine INU correction
final_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
bspline_fitting_distance=bspline_fitting_distance,
save_bias=True,
copy_header=True,
n_iterations=[50] * 5,
convergence_threshold=1e-7,
rescale_intensities=True,
shrink_factor=4,
),
n_procs=omp_nthreads,
name="final_n4",
)
final_mask = pe.Node(ApplyMask(), name="final_mask")
if atropos_model is None:
atropos_model = tuple(ATROPOS_MODELS[mri_scheme].values())
atropos_wf = init_atropos_wf(
use_random_seed=False,
omp_nthreads=omp_nthreads,
mem_gb=mem_gb,
in_segmentation_model=atropos_model,
)
# if tpl_regmask_path:
# atropos_wf.get_node('inputnode').inputs.in_mask_dilated = tpl_regmask_path
sel_wm = pe.Node(niu.Select(index=atropos_model[-1] - 1),
name='sel_wm',
run_without_submitting=True)
wf.connect([
# 1. massage template
(val_tmpl, clip_tmpl, [("out_file", "in_file")]),
(clip_tmpl, lap_tmpl, [("out", "op1")]),
(clip_tmpl, mrg_tmpl, [("out", "in1")]),
(lap_tmpl, norm_lap_tmpl, [("output_image", "in_file")]),
(norm_lap_tmpl, mrg_tmpl, [("out", "in2")]),
# 2. massage T2w
(inputnode, val_t2w, [('t2w', 'in_file')]),
(val_t2w, clip_t2w, [('out_file', 'in_file')]),
(clip_t2w, init_t2w_n4, [('out', 'input_image')]),
(init_t2w_n4, clip_t2w_inu, [("output_image", "in_file")]),
(clip_t2w_inu, lap_t2w, [('out', 'op1')]),
(clip_t2w_inu, mrg_t2w, [('out', 'in1')]),
(lap_t2w, norm_lap_t2w, [("output_image", "in_file")]),
(norm_lap_t2w, mrg_t2w, [("out", "in2")]),
# 3. normalize T2w to target template (UNC)
(mrg_t2w, norm, [("out", "moving_image")]),
(mrg_tmpl, norm, [("out", "fixed_image")]),
# 4. map template brainmask to T2w space
(inputnode, map_mask_t2w, [('t2w', 'reference_image')]),
(norm, map_mask_t2w, [("reverse_transforms", "transforms"),
("reverse_invert_flags",
"invert_transform_flags")]),
(map_mask_t2w, thr_t2w_mask, [("output_image", "in_file")]),
# 5. massage T1w
(inputnode, val_t1w, [("t1w", "in_file")]),
(val_t1w, clip_t1w, [("out_file", "in_file")]),
(clip_t1w, init_t1w_n4, [("out", "input_image")]),
(init_t1w_n4, clip_t1w_inu, [("output_image", "in_file")]),
(clip_t1w_inu, lap_t1w, [('out', 'op1')]),
(clip_t1w_inu, mrg_t1w, [('out', 'in1')]),
(lap_t1w, norm_lap_t1w, [("output_image", "in_file")]),
(norm_lap_t1w, mrg_t1w, [("out", "in2")]),
# 6. normalize within subject T1w to T2w
(mrg_t1w, norm_subj, [("out", "moving_image")]),
(mrg_t2w, norm_subj, [("out", "fixed_image")]),
(thr_t2w_mask, norm_subj, [("out_mask", "fixed_image_mask")]),
# 7. map mask to T1w space
(thr_t2w_mask, map_mask_t1w, [("out_mask", "input_image")]),
(inputnode, map_mask_t1w, [("t1w", "reference_image")]),
(norm_subj, map_mask_t1w, [
("reverse_transforms", "transforms"),
("reverse_invert_flags", "invert_transform_flags"),
]),
(map_mask_t1w, thr_t1w_mask, [("output_image", "in_file")]),
# 8. T1w INU
(inputnode, final_n4, [("t1w", "input_image")]),
(inputnode, bspline_grid, [("t1w", "in_file")]),
(bspline_grid, final_n4, [("out", "args")]),
(map_mask_t1w, final_n4, [("output_image", "weight_image")]),
(final_n4, final_mask, [("output_image", "in_file")]),
(thr_t1w_mask, final_mask, [("out_mask", "in_mask")]),
# 9. Outputs
(final_n4, outputnode, [("output_image", "t1w_corrected")]),
(thr_t1w_mask, outputnode, [("out_mask", "t1w_mask")]),
(final_mask, outputnode, [("out_file", "t1w_corrected_brain")]),
])
if ants_affine_init:
ants_kwargs = dict(
metric=("Mattes", 32, "Regular", 0.2),
transform=("Affine", 0.1),
search_factor=(20, 0.12),
principal_axes=False,
convergence=(10, 1e-6, 10),
search_grid=(40, (0, 40, 40)),
verbose=True,
)
if ants_affine_init == 'random':
ants_kwargs['metric'] = ("Mattes", 32, "Random", 0.2)
if ants_affine_init == 'search':
ants_kwargs['search_grid'] = (20, (20, 40, 40))
init_aff = pe.Node(
AI(**ants_kwargs),
name="init_aff",
n_procs=omp_nthreads,
)
if tpl_regmask_path:
init_aff.inputs.fixed_image_mask = _pop(tpl_regmask_path)
wf.connect([
(clip_tmpl, init_aff, [("out", "fixed_image")]),
(clip_t2w_inu, init_aff, [("out", "moving_image")]),
(init_aff, norm, [("output_transform", "initial_moving_transform")
]),
])
return wf
def init_infant_brain_extraction_wf(
ants_affine_init=False,
bspline_fitting_distance=200,
debug=False,
in_template="MNIInfant",
template_specs=None,
interim_checkpoints=True,
mem_gb=3.0,
mri_scheme="T2w",
name="infant_brain_extraction_wf",
atropos_model=None,
omp_nthreads=None,
output_dir=None,
use_float=True,
):
"""
Build an atlas-based brain extraction pipeline for infant T2w MRI data.
Parameters
----------
ants_affine_init : :obj:`bool`, optional
Set-up a pre-initialization step with ``antsAI`` to account for mis-oriented images.
"""
inputnode = pe.Node(niu.IdentityInterface(fields=["in_files", "in_mask"]),
name="inputnode")
outputnode = pe.Node(niu.IdentityInterface(
fields=["out_corrected", "out_brain", "out_mask"]),
name="outputnode")
template_specs = template_specs or {}
# Find a suitable target template in TemplateFlow
tpl_target_path = get_template(in_template,
suffix=mri_scheme,
**template_specs)
if not tpl_target_path:
raise RuntimeError(
f"An instance of template <tpl-{in_template}> with MR scheme '{mri_scheme}'"
" could not be found.")
# tpl_brainmask_path = get_template(
# in_template, desc="brain", suffix="probseg", **template_specs
# )
# if not tpl_brainmask_path:
# ignore probseg for the time being
tpl_brainmask_path = get_template(in_template,
desc="brain",
suffix="mask",
**template_specs)
tpl_regmask_path = get_template(in_template,
desc="BrainCerebellumExtraction",
suffix="mask",
**template_specs)
# validate images
val_tmpl = pe.Node(ValidateImage(), name='val_tmpl')
val_tmpl.inputs.in_file = _pop(tpl_target_path)
val_target = pe.Node(ValidateImage(), name='val_target')
# Resample both target and template to a controlled, isotropic resolution
res_tmpl = pe.Node(RegridToZooms(zooms=HIRES_ZOOMS),
name="res_tmpl") # testing
res_target = pe.Node(RegridToZooms(zooms=HIRES_ZOOMS),
name="res_target") # testing
gauss_tmpl = pe.Node(niu.Function(function=_gauss_filter),
name="gauss_tmpl")
# Spatial normalization step
lap_tmpl = pe.Node(ImageMath(operation="Laplacian", op2="0.4 1"),
name="lap_tmpl")
lap_target = pe.Node(ImageMath(operation="Laplacian", op2="0.4 1"),
name="lap_target")
# Merge image nodes
mrg_target = pe.Node(niu.Merge(2), name="mrg_target")
mrg_tmpl = pe.Node(niu.Merge(2), name="mrg_tmpl")
norm_lap_tmpl = pe.Node(niu.Function(function=_trunc),
name="norm_lap_tmpl")
norm_lap_tmpl.inputs.dtype = "float32"
norm_lap_tmpl.inputs.out_max = 1.0
norm_lap_tmpl.inputs.percentile = (0.01, 99.99)
norm_lap_tmpl.inputs.clip_max = None
norm_lap_target = pe.Node(niu.Function(function=_trunc),
name="norm_lap_target")
norm_lap_target.inputs.dtype = "float32"
norm_lap_target.inputs.out_max = 1.0
norm_lap_target.inputs.percentile = (0.01, 99.99)
norm_lap_target.inputs.clip_max = None
# Set up initial spatial normalization
ants_params = "testing" if debug else "precise"
norm = pe.Node(
Registration(from_file=pkgr_fn(
"niworkflows.data", f"antsBrainExtraction_{ants_params}.json")),
name="norm",
n_procs=omp_nthreads,
mem_gb=mem_gb,
)
norm.inputs.float = use_float
# main workflow
wf = pe.Workflow(name)
# Create a buffer interface as a cache for the actual inputs to registration
buffernode = pe.Node(
niu.IdentityInterface(fields=["hires_target", "smooth_target"]),
name="buffernode")
# truncate target intensity for N4 correction
clip_target = pe.Node(
niu.Function(function=_trunc),
name="clip_target",
)
clip_tmpl = pe.Node(
niu.Function(function=_trunc),
name="clip_tmpl",
)
#clip_tmpl.inputs.in_file = _pop(tpl_target_path)
# INU correction of the target image
init_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
save_bias=False,
copy_header=True,
n_iterations=[50] * (4 - debug),
convergence_threshold=1e-7,
shrink_factor=4,
bspline_fitting_distance=bspline_fitting_distance,
),
n_procs=omp_nthreads,
name="init_n4",
)
clip_inu = pe.Node(
niu.Function(function=_trunc),
name="clip_inu",
)
gauss_target = pe.Node(niu.Function(function=_gauss_filter),
name="gauss_target")
wf.connect([
# truncation, resampling, and initial N4
(inputnode, val_target, [(("in_files", _pop), "in_file")]),
# (inputnode, res_target, [(("in_files", _pop), "in_file")]),
(val_target, res_target, [("out_file", "in_file")]),
(res_target, clip_target, [("out_file", "in_file")]),
(val_tmpl, clip_tmpl, [("out_file", "in_file")]),
(clip_tmpl, res_tmpl, [("out", "in_file")]),
(clip_target, init_n4, [("out", "input_image")]),
(init_n4, clip_inu, [("output_image", "in_file")]),
(clip_inu, gauss_target, [("out", "in_file")]),
(clip_inu, buffernode, [("out", "hires_target")]),
(gauss_target, buffernode, [("out", "smooth_target")]),
(res_tmpl, gauss_tmpl, [("out_file", "in_file")]),
# (clip_tmpl, gauss_tmpl, [("out", "in_file")]),
])
# Graft a template registration-mask if present
if tpl_regmask_path:
hires_mask = pe.Node(ApplyTransforms(
input_image=_pop(tpl_regmask_path),
transforms="identity",
interpolation="NearestNeighbor",
float=True),
name="hires_mask",
mem_gb=1)
wf.connect([
(res_tmpl, hires_mask, [("out_file", "reference_image")]),
])
map_brainmask = pe.Node(ApplyTransforms(interpolation="Gaussian",
float=True),
name="map_brainmask",
mem_gb=1)
map_brainmask.inputs.input_image = str(tpl_brainmask_path)
thr_brainmask = pe.Node(Binarize(thresh_low=0.80), name="thr_brainmask")
bspline_grid = pe.Node(niu.Function(function=_bspline_distance),
name="bspline_grid")
# Refine INU correction
final_n4 = pe.Node(
N4BiasFieldCorrection(
dimension=3,
save_bias=True,
copy_header=True,
n_iterations=[50] * 5,
convergence_threshold=1e-7,
rescale_intensities=True,
shrink_factor=4,
),
n_procs=omp_nthreads,
name="final_n4",
)
final_mask = pe.Node(ApplyMask(), name="final_mask")
if atropos_model is None:
atropos_model = tuple(ATROPOS_MODELS[mri_scheme].values())
atropos_wf = init_atropos_wf(
use_random_seed=False,
omp_nthreads=omp_nthreads,
mem_gb=mem_gb,
in_segmentation_model=atropos_model,
)
# if tpl_regmask_path:
# atropos_wf.get_node('inputnode').inputs.in_mask_dilated = tpl_regmask_path
sel_wm = pe.Node(niu.Select(index=atropos_model[-1] - 1),
name='sel_wm',
run_without_submitting=True)
wf.connect([
(inputnode, map_brainmask, [(("in_files", _pop), "reference_image")]),
(inputnode, final_n4, [(("in_files", _pop), "input_image")]),
(inputnode, bspline_grid, [(("in_files", _pop), "in_file")]),
# (bspline_grid, final_n4, [("out", "bspline_fitting_distance")]),
(bspline_grid, final_n4, [("out", "args")]),
# merge laplacian and original images
(buffernode, lap_target, [("smooth_target", "op1")]),
(buffernode, mrg_target, [("hires_target", "in1")]),
(lap_target, norm_lap_target, [("output_image", "in_file")]),
(norm_lap_target, mrg_target, [("out", "in2")]),
# Template massaging
(res_tmpl, lap_tmpl, [("out_file", "op1")]),
(res_tmpl, mrg_tmpl, [("out_file", "in1")]),
(lap_tmpl, norm_lap_tmpl, [("output_image", "in_file")]),
(norm_lap_tmpl, mrg_tmpl, [("out", "in2")]),
# spatial normalization
(mrg_target, norm, [("out", "moving_image")]),
(mrg_tmpl, norm, [("out", "fixed_image")]),
(norm, map_brainmask, [("reverse_transforms", "transforms"),
("reverse_invert_flags",
"invert_transform_flags")]),
(map_brainmask, thr_brainmask, [("output_image", "in_file")]),
# take a second pass of N4
(map_brainmask, final_n4, [("output_image", "weight_image")]),
(final_n4, final_mask, [("output_image", "in_file")]),
(thr_brainmask, final_mask, [("out_mask", "in_mask")]),
(final_n4, outputnode, [("output_image", "out_corrected")]),
(thr_brainmask, outputnode, [("out_mask", "out_mask")]),
(final_mask, outputnode, [("out_file", "out_brain")]),
])
# wf.disconnect([
# (get_brainmask, apply_mask, [('output_image', 'mask_file')]),
# (copy_xform, outputnode, [('out_mask', 'out_mask')]),
# ])
# wf.connect([
# (init_n4, atropos_wf, [
# ('output_image', 'inputnode.in_files')]), # intensity image
# (thr_brainmask, atropos_wf, [
# ('out_mask', 'inputnode.in_mask')]),
# (atropos_wf, sel_wm, [('outputnode.out_tpms', 'inlist')]),
# (sel_wm, final_n4, [('out', 'weight_image')]),
# ])
# wf.connect([
# (atropos_wf, outputnode, [
# ('outputnode.out_mask', 'out_mask'),
# ('outputnode.out_segm', 'out_segm'),
# ('outputnode.out_tpms', 'out_tpms')]),
# ])
if tpl_regmask_path:
wf.connect([
(hires_mask, norm, [("output_image", "fixed_image_masks")]),
# (hires_mask, atropos_wf, [
# ("output_image", "inputnode.in_mask_dilated")]),
])
if interim_checkpoints:
final_apply = pe.Node(ApplyTransforms(interpolation="BSpline",
float=True),
name="final_apply",
mem_gb=1)
final_report = pe.Node(SimpleBeforeAfter(
before_label=f"tpl-{in_template}",
after_label="target",
out_report="final_report.svg"),
name="final_report")
wf.connect([
(inputnode, final_apply, [(("in_files", _pop), "reference_image")
]),
(res_tmpl, final_apply, [("out_file", "input_image")]),
(norm, final_apply, [("reverse_transforms", "transforms"),
("reverse_invert_flags",
"invert_transform_flags")]),
(final_apply, final_report, [("output_image", "before")]),
(outputnode, final_report, [("out_corrected", "after"),
("out_mask", "wm_seg")]),
])
if output_dir:
from nipype.interfaces.io import DataSink
ds_final_inu = pe.Node(DataSink(base_directory=str(output_dir.parent)),
name="ds_final_inu")
ds_final_msk = pe.Node(DataSink(base_directory=str(output_dir.parent)),
name="ds_final_msk")
ds_report = pe.Node(DataSink(base_directory=str(output_dir.parent)),
name="ds_report")
wf.connect([
(outputnode, ds_final_inu,
[("out_corrected", f"{output_dir.name}.@inu_corrected")]),
(outputnode, ds_final_msk, [("out_mask",
f"{output_dir.name}.@brainmask")]),
(final_report, ds_report, [("out_report",
f"{output_dir.name}.@report")]),
])
if not ants_affine_init:
return wf
# Initialize transforms with antsAI
lowres_tmpl = pe.Node(RegridToZooms(zooms=LOWRES_ZOOMS),
name="lowres_tmpl")
lowres_target = pe.Node(RegridToZooms(zooms=LOWRES_ZOOMS),
name="lowres_target")
init_aff = pe.Node(
AI(
metric=("Mattes", 32, "Regular", 0.25),
transform=("Affine", 0.1),
search_factor=(15, 0.1),
principal_axes=False,
convergence=(10, 1e-6, 10),
search_grid=(40, (0, 40, 40)),
verbose=True,
),
name="init_aff",
n_procs=omp_nthreads,
)
wf.connect([
(gauss_tmpl, lowres_tmpl, [("out", "in_file")]),
(lowres_tmpl, init_aff, [("out_file", "fixed_image")]),
(gauss_target, lowres_target, [("out", "in_file")]),
(lowres_target, init_aff, [("out_file", "moving_image")]),
(init_aff, norm, [("output_transform", "initial_moving_transform")]),
])
if tpl_regmask_path:
lowres_mask = pe.Node(ApplyTransforms(
input_image=_pop(tpl_regmask_path),
transforms="identity",
interpolation="MultiLabel",
float=True),
name="lowres_mask",
mem_gb=1)
wf.connect([
(lowres_tmpl, lowres_mask, [("out_file", "reference_image")]),
(lowres_mask, init_aff, [("output_image", "fixed_image_mask")]),
])
if interim_checkpoints:
init_apply = pe.Node(ApplyTransforms(interpolation="BSpline",
float=True),
name="init_apply",
mem_gb=1)
init_report = pe.Node(SimpleBeforeAfter(
before_label=f"tpl-{in_template}",
after_label="target",
out_report="init_report.svg"),
name="init_report")
wf.connect([
(lowres_target, init_apply, [("out_file", "input_image")]),
(res_tmpl, init_apply, [("out_file", "reference_image")]),
(init_aff, init_apply, [("output_transform", "transforms")]),
(init_apply, init_report, [("output_image", "after")]),
(res_tmpl, init_report, [("out_file", "before")]),
])
if output_dir:
ds_init_report = pe.Node(
DataSink(base_directory=str(output_dir.parent)),
name="ds_init_report")
wf.connect(init_report, "out_report", ds_init_report,
f"{output_dir.name}.@init_report")
return wf
