From 8598d0591dd4ca3b7327eb4c58ef063e969e97f6 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Wed, 4 Sep 2024 13:41:04 -0400
Subject: [PATCH] Change linc mode default file format to CIFTI (#1248)

---
 docs/workflows.rst          | 2 +-
 xcp_d/cli/parser.py         | 2 +-
 xcp_d/tests/test_cli.py     | 2 ++
 xcp_d/tests/test_cli_run.py | 3 ++-
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/docs/workflows.rst b/docs/workflows.rst
index bd62ba1bf..7a0727042 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -61,7 +61,7 @@ Defaults
 By default, the ``linc`` mode will apply the following parameters,
 which may be overridden by the user:
 
--  ``--file-format nifti``: NIFTI files are used as input.
+-  ``--file-format cifti``: CIFTI files are used as input.
 -  ``--despike``: Despiking is enabled by default.
 -  ``--fd-thresh 0``: Censoring is disabled by default.
 -  ``--input-type fmriprep``: fMRIPrep outputs are expected as input.
diff --git a/xcp_d/cli/parser.py b/xcp_d/cli/parser.py
index 9df4c7d99..43d6cff88 100644
--- a/xcp_d/cli/parser.py
+++ b/xcp_d/cli/parser.py
@@ -1003,7 +1003,7 @@ def _validate_parameters(opts, build_log, parser):
         opts.combine_runs = False if opts.combine_runs == "auto" else opts.combine_runs
         opts.despike = True if (opts.despike == "auto") else opts.despike
         opts.fd_thresh = 0 if (opts.fd_thresh == "auto") else opts.fd_thresh
-        opts.file_format = "nifti" if (opts.file_format == "auto") else opts.file_format
+        opts.file_format = "cifti" if (opts.file_format == "auto") else opts.file_format
         opts.input_type = "fmriprep" if opts.input_type == "auto" else opts.input_type
         opts.linc_qc = True if (opts.linc_qc == "auto") else opts.linc_qc
         opts.output_correlations = True
diff --git a/xcp_d/tests/test_cli.py b/xcp_d/tests/test_cli.py
index 1e964fcd2..f486f4017 100644
--- a/xcp_d/tests/test_cli.py
+++ b/xcp_d/tests/test_cli.py
@@ -315,6 +315,7 @@ def test_fmriprep_without_freesurfer(data_dir, output_dir, working_dir):
         "participant",
         "--mode=linc",
         f"-w={work_dir}",
+        "--file-format=nifti",
         "--nthreads=2",
         "--omp-nthreads=2",
         "--head_radius=40",
@@ -383,6 +384,7 @@ def test_fmriprep_without_freesurfer_with_main(data_dir, output_dir, working_dir
         "participant",
         "--mode=linc",
         f"-w={work_dir}",
+        "--file-format=nifti",
         "--nthreads=2",
         "--omp-nthreads=2",
         "--head_radius=40",
diff --git a/xcp_d/tests/test_cli_run.py b/xcp_d/tests/test_cli_run.py
index 15314725d..8d7c663dd 100644
--- a/xcp_d/tests/test_cli_run.py
+++ b/xcp_d/tests/test_cli_run.py
@@ -288,6 +288,7 @@ def test_validate_parameters_linc_mode(base_opts, base_parser, capsys):
 
     assert opts.abcc_qc is False
     assert opts.linc_qc is True
+    assert opts.file_format == "cifti"
 
     # --create-matrices is not supported
     opts.dcan_correlation_lengths = [300]
@@ -649,7 +650,7 @@ def test_build_parser_05(tmp_path_factory, mode, process_surfaces, expectation):
 @pytest.mark.parametrize(
     "mode,file_format,expectation",
     [
-        ("linc", "auto", "nifti"),
+        ("linc", "auto", "cifti"),
         ("abcd", "auto", "cifti"),
         ("hbcd", "auto", "cifti"),
         ("linc", "nifti", "nifti"),