From 919ccc13b67bdff437265345dfa22dbc41b986b2 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Thu, 28 Mar 2024 10:52:12 -0400
Subject: [PATCH] Change default `--min-time` from 100 to 240 (#1115)

---
 xcp_d/cli/parser.py     | 20 +++++++++++---------
 xcp_d/config.py         |  2 +-
 xcp_d/tests/test_cli.py |  4 ++++
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/xcp_d/cli/parser.py b/xcp_d/cli/parser.py
index b51bb6fad..9be52ad1f 100644
--- a/xcp_d/cli/parser.py
+++ b/xcp_d/cli/parser.py
@@ -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(
diff --git a/xcp_d/config.py b/xcp_d/config.py
index 2f3fe2d0f..7dbe500e3 100644
--- a/xcp_d/config.py
+++ b/xcp_d/config.py
@@ -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."""
diff --git a/xcp_d/tests/test_cli.py b/xcp_d/tests/test_cli.py
index 7ff25fae8..783999993 100644
--- a/xcp_d/tests/test_cli.py
+++ b/xcp_d/tests/test_cli.py
@@ -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,
@@ -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",
@@ -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,
@@ -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,