make mni2009c normalization optional

Author: smeisler

ingress2qsirecon/cli/main.py

@@ -25,6 +25,7 @@ def _ingress2qsirecon(**kwargs):
     input_pipeline = kwargs["input_pipeline"]
     participant_label = kwargs["participant_label"]
     work_dir = Path(kwargs["work_dir"])
+    skip_mni2009c_norm = kwargs["skip_mni2009c_norm"]
     check_gradients = kwargs["check_gradients"]
     dry_run = kwargs["dry_run"]
     symlink = kwargs["symlink"]
@@ -55,7 +56,7 @@ def _ingress2qsirecon(**kwargs):
     layouts = create_layout(input_dir, output_dir, input_pipeline, participant_label)
 
     # Create and run overall workflow, which will be broken down to single subject workflows
-    ingress2qsirecon_wf = create_ingress2qsirecon_wf(layouts, base_dir=work_dir)
+    ingress2qsirecon_wf = create_ingress2qsirecon_wf(layouts, base_dir=work_dir, skip_mni2009c_norm=skip_mni2009c_norm)
     ingress2qsirecon_wf.run()
 
 

ingress2qsirecon/cli/parser.py

@@ -76,6 +76,13 @@ def _drop_sub(value):
         help="The working directory for the processing. "
         "If not specified, the current working directory will be used.",
     )
+    optional.add_argument(
+        "--skip-mni2009c-norm",
+        "--skip_mni2009c_norm",
+        action="store_true",
+        default=False,
+        help="Skip MNI normalization step. MNI normalization is not required for all pipelines in QSIRecon.",
+    )
     optional.add_argument(
         "--check_gradients",
         "--check-gradients",

ingress2qsirecon/utils/workflows.py

@@ -26,7 +26,7 @@ def parse_layout(subject_layout):
     return tuple(subject_layout.values())
 
 
-def create_single_subject_wf(subject_layout):
+def create_single_subject_wf(subject_layout, skip_mni2009c_norm=False):
     """
     Create a nipype workflow to ingest a single subject.
 
@@ -252,7 +252,7 @@ def create_single_subject_wf(subject_layout):
 
     # Now get transform to MNI2009cAsym
     MNI_template = subject_layout["MNI_template"]
-    if MNI_template != "MNI152NLin2009cAsym":
+    if MNI_template != "MNI152NLin2009cAsym" and skip_mni2009c_norm == False:
         # Get MNI brain and mask
         MNI2009cAsym_brain_path = str(
             tflow.get('MNI152NLin2009cAsym', desc="brain", suffix="T1w", resolution=1, extension=".nii.gz")
@@ -333,7 +333,7 @@ def save_xfm_outputs(
     return wf
 
 
-def create_ingress2qsirecon_wf(layouts, name="ingress2qsirecon_wf", base_dir=os.getcwd()):
+def create_ingress2qsirecon_wf(layouts, name="ingress2qsirecon_wf", base_dir=os.getcwd(), skip_mni2009c_norm=False):
     """
     Creates the overall ingress2qsirecon workflow.
 
@@ -361,7 +361,7 @@ def create_ingress2qsirecon_wf(layouts, name="ingress2qsirecon_wf", base_dir=os.
     print(f"Subject(s) to run: {subjects_to_run}")
 
     for subject_layout in layouts:
-        single_subject_wf = create_single_subject_wf(subject_layout)
+        single_subject_wf = create_single_subject_wf(subject_layout, skip_mni2009c_norm=skip_mni2009c_norm)
         wf.add_nodes([single_subject_wf])
 
     return wf