From 2c67b383343b446b1dd8e9186355f4335381db8e Mon Sep 17 00:00:00 2001
From: "Daniel M. Drucker" <ddrucker@mclean.harvard.edu>
Date: Mon, 28 Oct 2024 14:21:26 -0400
Subject: [PATCH] bids-filter-file arg

---
 iris/iris-fmriprep.py | 1 +
 micc_fmriprep.py      | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/iris/iris-fmriprep.py b/iris/iris-fmriprep.py
index 5ac1290..113c642 100755
--- a/iris/iris-fmriprep.py
+++ b/iris/iris-fmriprep.py
@@ -90,6 +90,7 @@ def submit_fmriprep(config, studydir, subject):
             s += ["--" + arg]
     for arg in (
         "anat-derivatives",
+        "bids-filter-file",
         "fmriprep-version",
         "ignore",
         "ncpus",
diff --git a/micc_fmriprep.py b/micc_fmriprep.py
index 956dc3d..d8e259e 100755
--- a/micc_fmriprep.py
+++ b/micc_fmriprep.py
@@ -92,6 +92,9 @@ def make_runscript(args, workdir):
     if args.anat_derivatives:
         s += [f"--anat-derivatives {args.anat_derivatives}"]
 
+    if args.bids_filter_file:
+        s += [f"--bids-filter-file {args.bids_filter_file}"]
+
     if args.fs_subjects_dir:
         s += [f"--fs-subjects-dir {args.fs_subjects_dir}"]
 
@@ -188,6 +191,12 @@ def is_dir(dirname):
         metavar="PATH",
     )
 
+    parser.add_argument(
+        "--bids-filter-file",
+        help="A JSON file describing custom BIDS input filters using PyBIDS.",
+        metavar="FILE",
+    )
+
     parser.add_argument(
         "--fs-subjects-dir",
         help="Path to existing FreeSurfer subjects directory to reuse.",