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ENH: Framewise displacement head radius flag #104

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Merged
merged 1 commit into from
Sep 21, 2021
Merged

ENH: Framewise displacement head radius flag #104

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6 changes: 6 additions & 0 deletions nibabies/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -594,6 +594,12 @@ def _bids_filter(value):
"--segmentation-atlases-dir",
help="Directory containing precalculated segmentations to use for JointLabelFusion."
)
g_baby.add_argument(
"--fd-radius",
type=float,
default=45,
help="Head radius in mm for framewise displacement calculation",
)
return parser


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2 changes: 2 additions & 0 deletions nibabies/config.py
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Expand Up @@ -505,6 +505,8 @@ class workflow(_Config):
"""Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
dummy_scans = None
"""Set a number of initial scans to be considered nonsteady states."""
fd_radius = 45
"""Head radius in mm for framewise displacement calculation"""
fmap_bspline = None
"""Regularize fieldmaps with a field of B-Spline basis."""
fmap_demean = None
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1 change: 1 addition & 0 deletions nibabies/workflows/bold/base.py
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Expand Up @@ -421,6 +421,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
regressors_all_comps=config.workflow.regressors_all_comps,
regressors_fd_th=config.workflow.regressors_fd_th,
regressors_dvars_th=config.workflow.regressors_dvars_th,
fd_radius=config.workflow.fd_radius,
name='bold_confounds_wf')
bold_confounds_wf.get_node('inputnode').inputs.t1_transform_flags = [False]

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11 changes: 7 additions & 4 deletions nibabies/workflows/bold/confounds.py
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Expand Up @@ -27,6 +27,8 @@ def init_bold_confs_wf(
regressors_dvars_th,
regressors_fd_th,
freesurfer=False,
*,
fd_radius=45,
name="bold_confs_wf",
):
"""
Expand Down Expand Up @@ -78,8 +80,6 @@ def init_bold_confs_wf(
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
Expand All @@ -88,7 +88,10 @@ def init_bold_confs_wf(
Criterion for flagging DVARS outliers
regressors_fd_th : :obj:`float`
Criterion for flagging framewise displacement outliers

fd_radius : :obj:`float`
Radius in mm to calculate angular FDs (default: 45)
name : :obj:`str`
Name of workflow (default: ``bold_confs_wf``)
Inputs
------
bold
Expand Down Expand Up @@ -200,7 +203,7 @@ def init_bold_confs_wf(
name="dvars", mem_gb=mem_gb)

# Frame displacement
fdisp = pe.Node(nac.FramewiseDisplacement(parameter_source="SPM"),
fdisp = pe.Node(nac.FramewiseDisplacement(parameter_source="SPM", radius=fd_radius),
name="fdisp", mem_gb=mem_gb)

# Generate aCompCor probseg maps
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