From ac7dd5e4be3633fa78eeefc66be701587597cdb5 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 19 Mar 2024 10:51:40 -0400
Subject: [PATCH] [DCAN] Enable DCAN QC by default (#1086)

---
 docs/outputs.rst        |  6 +++---
 docs/workflows.rst      |  2 +-
 xcp_d/cli/run.py        | 14 +++++++++++---
 xcp_d/tests/test_cli.py |  7 ++-----
 xcp_d/workflows/base.py |  6 +++---
 5 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/docs/outputs.rst b/docs/outputs.rst
index 287c6618b..c7984bc40 100644
--- a/docs/outputs.rst
+++ b/docs/outputs.rst
@@ -204,7 +204,7 @@ Denoised or residual BOLD data
 .. important::
 
    The interpolated denoised BOLD files (``desc-interpolated``) should NOT be used for analyses.
-   These files are only generated if ``--dcan-qc`` is used,
+   These files are only generated if ``--skip-dcan-qc`` is not used,
    and primarily exist for compatibility with DCAN-specific analysis tools.
 
 The sidecar json files contains parameters of the data and processing steps.
@@ -326,8 +326,8 @@ This file includes the high-motion volumes that are removed in most other deriva
    as volumes are removed by censoring, rather than regression.
 
 
-DCAN style scrubbing file (if ``--dcan-qc`` is used)
-====================================================
+DCAN style scrubbing file (if ``--skip-dcan-qc`` is not used)
+=============================================================
 
 This file is in hdf5 format (readable by h5py), and contains binary scrubbing masks from 0.0
 to 1mm FD in 0.01 steps.
diff --git a/docs/workflows.rst b/docs/workflows.rst
index a96a0c7dc..de7cf5277 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -449,7 +449,7 @@ to satisfy DCAN-specific tools.
 
 The residuals from the second step are referred to as the ``denoised, interpolated BOLD``.
 The ``denoised, interpolated BOLD`` will only be written out to the output
-directory if the ``--dcan-qc`` flag is used,
+directory if the ``--skip-dcan-qc`` flag is not used,
 as users **should not** use interpolated data directly.
 
 
diff --git a/xcp_d/cli/run.py b/xcp_d/cli/run.py
index fc8fab8be..c817f39c9 100644
--- a/xcp_d/cli/run.py
+++ b/xcp_d/cli/run.py
@@ -542,13 +542,21 @@ def get_parser():
 **IMPORTANT**: This parameter can only be run if the --cifti flag is also enabled.
 """,
     )
-    g_experimental.add_argument(
+    g_dcan_qc = g_experimental.add_mutually_exclusive_group(required=False)
+    g_dcan_qc.add_argument(
         "--dcan-qc",
         "--dcan_qc",
         action="store_true",
         dest="dcan_qc",
-        default=False,
-        help="Run DCAN QC.",
+        default=True,
+        help="Run DCAN QC. This option is deprecated as of 0.6.4 and will be removed in 0.7.0.",
+    )
+    g_dcan_qc.add_argument(
+        "--skip-dcan-qc",
+        "--skip_dcan_qc",
+        action="store_false",
+        dest="dcan_qc",
+        help="Do not run DCAN QC.",
     )
 
     return parser
diff --git a/xcp_d/tests/test_cli.py b/xcp_d/tests/test_cli.py
index b00c61a40..be386dfe2 100644
--- a/xcp_d/tests/test_cli.py
+++ b/xcp_d/tests/test_cli.py
@@ -52,6 +52,7 @@ def test_ds001419_nifti(data_dir, output_dir, working_dir):
         "--motion-filter-type=lp",
         "--band-stop-min=6",
         "--skip-parcellation",
+        "--skip-dcan-qc",
         "--random-seed=8675309",
     ]
     opts = run.get_parser().parse_args(parameters)
@@ -109,7 +110,6 @@ def test_ds001419_cifti(data_dir, output_dir, working_dir):
         "--band-stop-max=18",
         "--cifti",
         "--combineruns",
-        "--dcan-qc",
         "--dummy-scans=auto",
         "--fd-thresh=0.3",
         "--upper-bpf=0.0",
@@ -169,6 +169,7 @@ def test_ukbiobank(data_dir, output_dir, working_dir):
         "--smoothing=6",
         "--motion-filter-type=lp",
         "--band-stop-min=6",
+        "--skip-dcan-qc",
         "--min-coverage=0.1",
         "--random-seed=8675309",
     ]
@@ -242,7 +243,6 @@ def test_pnc_cifti(data_dir, output_dir, working_dir):
         "--warp-surfaces-native2std",
         "--cifti",
         "--combineruns",
-        "--dcan-qc",
         "--dummy-scans=auto",
         "--fd-thresh=0.3",
         "--upper-bpf=0.0",
@@ -316,7 +316,6 @@ def test_pnc_cifti_t2wonly(data_dir, output_dir, working_dir):
         "--warp-surfaces-native2std",
         "--cifti",
         "--combineruns",
-        "--dcan-qc",
         "--dummy-scans=auto",
         "--fd-thresh=0.3",
         "--lower-bpf=0.0",
@@ -391,7 +390,6 @@ def test_fmriprep_without_freesurfer(data_dir, output_dir, working_dir):
         "--nuisance-regressors 27P "
         "--disable-bandpass-filter "
         "--min-time 20 "
-        "--dcan-qc "
         "--dummy-scans 1 "
         f"--custom_confounds={custom_confounds_dir}"
     )
@@ -437,7 +435,6 @@ def test_nibabies(data_dir, output_dir, working_dir):
         "--head_radius=auto",
         "--smoothing=0",
         "--fd-thresh=0",
-        "--dcan-qc",
     ]
     _run_and_generate(
         test_name=test_name,
diff --git a/xcp_d/workflows/base.py b/xcp_d/workflows/base.py
index 3a6e64d66..91f59f49b 100644
--- a/xcp_d/workflows/base.py
+++ b/xcp_d/workflows/base.py
@@ -81,7 +81,7 @@ def init_xcpd_wf(
     omp_nthreads,
     layout=None,
     process_surfaces=False,
-    dcan_qc=False,
+    dcan_qc=True,
     input_type="fmriprep",
     min_coverage=0.5,
     min_time=100,
@@ -137,7 +137,7 @@ def init_xcpd_wf(
                 omp_nthreads=1,
                 layout=None,
                 process_surfaces=False,
-                dcan_qc=False,
+                dcan_qc=True,
                 input_type="fmriprep",
                 min_time=100,
                 atlases=["Glasser"],
@@ -324,7 +324,7 @@ def init_subject_wf(
                 random_seed=None,
                 fd_thresh=0.3,
                 despike=True,
-                dcan_qc=False,
+                dcan_qc=True,
                 min_coverage=0.5,
                 min_time=100,
                 exact_time=[],