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Change default --min-time from 100 to 240 (PennLINC#1115)
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tsalo authored Mar 28, 2024
1 parent ccbaff4 commit 919ccc1
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Showing 3 changed files with 16 additions and 10 deletions.
20 changes: 11 additions & 9 deletions xcp_d/cli/parser.py
Original file line number Diff line number Diff line change
Expand Up @@ -406,16 +406,18 @@ def _bids_filter(value, parser):
"--min-time",
"--min_time",
required=False,
default=100,
default=240,
type=float,
help=(
"Post-scrubbing threshold to apply to individual runs in the dataset. "
"This threshold determines the minimum amount of time, in seconds, "
"needed to post-process a given run, once high-motion outlier volumes are removed. "
"This will have no impact if scrubbing is disabled "
"(i.e., if the FD threshold is zero or negative). "
"This parameter can be disabled by providing a zero or a negative value."
),
help="""\
Post-scrubbing threshold to apply to individual runs in the dataset.
This threshold determines the minimum amount of time, in seconds,
needed to post-process a given run, once high-motion outlier volumes are removed.
This will have no impact if scrubbing is disabled
(i.e., if the FD threshold is zero or negative).
This parameter can be disabled by providing a zero or a negative value.
The default is 240 (4 minutes).
""",
)

g_temporal_filter = parser.add_argument_group(
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2 changes: 1 addition & 1 deletion xcp_d/config.py
Original file line number Diff line number Diff line change
Expand Up @@ -544,7 +544,7 @@ class workflow(_Config):
"""Radius of the head in mm."""
fd_thresh = 0.3
"""Framewise displacement threshold for censoring."""
min_time = 100
min_time = 240
"""Post-scrubbing threshold to apply to individual runs in the dataset."""
bandpass_filter = True
"""Apply a band-pass filter to the data."""
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4 changes: 4 additions & 0 deletions xcp_d/tests/test_cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ def test_ds001419_nifti(data_dir, output_dir, working_dir):
"--skip-parcellation",
"--skip-dcan-qc",
"--random-seed=8675309",
"--min-time=100",
]
_run_and_generate(
test_name=test_name,
Expand Down Expand Up @@ -97,6 +98,7 @@ def test_ds001419_cifti(data_dir, output_dir, working_dir):
"--dummy-scans=auto",
"--fd-thresh=0.3",
"--upper-bpf=0.0",
"--min-time=100",
"--exact-time",
"80",
"200",
Expand Down Expand Up @@ -137,6 +139,7 @@ def test_ukbiobank(data_dir, output_dir, working_dir):
"--skip-dcan-qc",
"--min-coverage=0.1",
"--random-seed=8675309",
"--min-time=100",
]
_run_and_generate(
test_name=test_name,
Expand Down Expand Up @@ -248,6 +251,7 @@ def test_pnc_cifti_t2wonly(data_dir, output_dir, working_dir):
"--atlases",
"4S156Parcels",
"Glasser",
"--min-time=100",
]
_run_and_generate(
test_name=test_name,
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