Update.

PennLINC · Nov 27, 2023 · 8e2dbb9 · 8e2dbb9
1 parent 1d7d0d6
commit 8e2dbb9
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 28 deletions.
diff --git a/aslprep/interfaces/cbf.py b/aslprep/interfaces/cbf.py
@@ -87,7 +87,7 @@ class _ExtractCBFInputSpec(BaseInterfaceInputSpec):
     m0scan = traits.Either(
         File(exists=True),
         None,
-        mandatory=True,
+        mandatory=False,
         desc="m0scan file associated with the ASL file. Only defined if M0Type is 'Separate'.",
     )
     m0scan_metadata = traits.Either(

diff --git a/aslprep/workflows/asl/util.py b/aslprep/workflows/asl/util.py
@@ -250,21 +250,17 @@ def init_validate_asl_wf(asl_file=None, name="validate_asl_wf"):
 
     asl_1st = pe.Node(niu.Select(index=[0]), name="asl_1st", run_without_submitting=True)
 
-    # fmt:off
     workflow.connect([
         (val_asl, asl_1st, [(("out_file", listify), "inlist")]),
         (asl_1st, outputnode, [("out", "asl_file")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     validate_1st = pe.Node(niu.Select(index=[0]), name="validate_1st", run_without_submitting=True)
 
-    # fmt:off
     workflow.connect([
         (val_asl, validate_1st, [(("out_report", listify), "inlist")]),
         (validate_1st, outputnode, [("out", "validation_report")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     return workflow
 
@@ -403,14 +399,12 @@ def init_asl_reference_wf(
         name="select_reference_volumes",
     )
 
-    # fmt:off
     workflow.connect([
         (inputnode, select_reference_volumes, [
             ("asl_file", "asl_file"),
             ("aslcontext", "aslcontext"),
         ]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     val_asl = pe.MapNode(
         ValidateImage(),
@@ -423,19 +417,16 @@ def init_asl_reference_wf(
 
     gen_ref = pe.Node(EstimateReferenceImage(), name="gen_ref", mem_gb=1)
 
-    # fmt:off
     workflow.connect([
         (val_asl, gen_ref, [("out_file", "in_file")]),
         (gen_ref, outputnode, [
             ("ref_image", "raw_ref_image"),
             ("n_volumes_to_discard", "algo_dummy_scans"),
         ]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     enhance_and_skullstrip_asl_wf = init_enhance_and_skullstrip_asl_wf(pre_mask=pre_mask)
 
-    # fmt:off
     workflow.connect([
         (inputnode, enhance_and_skullstrip_asl_wf, [("asl_mask", "inputnode.pre_mask")]),
         (gen_ref, enhance_and_skullstrip_asl_wf, [("ref_image", "inputnode.in_file")]),
@@ -444,31 +435,26 @@ def init_asl_reference_wf(
             ("outputnode.mask_file", "asl_mask"),
             ("outputnode.skull_stripped_file", "ref_image_brain"),
         ]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     calc_dummy_scans = pe.Node(
         niu.Function(function=pass_dummy_scans, output_names=["skip_vols_num"]),
         name="calc_dummy_scans",
         run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
-    # fmt:off
     workflow.connect([
         (inputnode, calc_dummy_scans, [("dummy_scans", "dummy_scans")]),
         (gen_ref, calc_dummy_scans, [("n_volumes_to_discard", "algo_dummy_scans")]),
         (calc_dummy_scans, outputnode, [("skip_vols_num", "skip_vols")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     asl_1st = pe.Node(niu.Select(index=[0]), name="asl_1st", run_without_submitting=True)
 
-    # fmt:off
     workflow.connect([
         (val_asl, asl_1st, [(("out_file", listify), "inlist")]),
         (asl_1st, outputnode, [("out", "asl_file")]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     validate_1st = pe.Node(niu.Select(index=[0]), name="validate_1st", run_without_submitting=True)
 

diff --git a/aslprep/workflows/base.py b/aslprep/workflows/base.py
@@ -512,13 +512,11 @@ def init_single_subject_wf(subject_id: str):
             run_without_submitting=True,
         )
         if any(estimator.method == fm.EstimatorType.ANAT for estimator in fmap_estimators):
-            # fmt:off
             workflow.connect([
                 (anat_fit_wf, fmap_select_std, [
                     ("outputnode.std2anat_xfm", "std2anat_xfm"),
                     ("outputnode.template", "keys")]),
-            ])
-            # fmt:on
+            ])  # fmt:skip
 
         for estimator in fmap_estimators:
             config.loggers.workflow.info(
@@ -564,7 +562,6 @@ def init_single_subject_wf(subject_id: str):
                 syn_preprocessing_wf.inputs.inputnode.in_epis = sources
                 syn_preprocessing_wf.inputs.inputnode.in_meta = source_meta
 
-                # fmt:off
                 workflow.connect([
                     (anat_fit_wf, syn_preprocessing_wf, [
                         ("outputnode.t1w_preproc", "inputnode.in_anat"),
@@ -580,8 +577,7 @@ def init_single_subject_wf(subject_id: str):
                         ("outputnode.anat_mask", f"in_{estimator.bids_id}.anat_mask"),
                         ("outputnode.sd_prior", f"in_{estimator.bids_id}.sd_prior"),
                     ]),
-                ])
-                # fmt:on
+                ])  # fmt:skip
 
     # Append the functional section to the existing anatomical excerpt
     # That way we do not need to stream down the number of asl datasets