some fixes

aramis-lab · Apr 4, 2023 · ef3c471 · ef3c471
1 parent a4ed52b
commit ef3c471
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Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/...pipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_pipeline.py b/...pipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_pipeline.py
@@ -390,7 +390,7 @@ def build_core_nodes(self):
                 init_node,
                 fmap_calibration_and_registration,
                 [
-                    ("fmap_magnitude", "inputnode.magnitude_fmap"),
+                    ("fmap_magnitude", "inputnode.bias_magnitude_fmap"),
                     ("fmap_phasediff", "inputnode.fmap_phasediff"),
                     ("delta_echo_time", "inputnode.delta_echo_time"),
                 ],

diff --git a/...ipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_workflows.py b/...ipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_workflows.py
@@ -501,16 +501,16 @@ def calibrate_and_register_fmap(
             [("out_file", "in_file")],
         ),
         # Output connections
-        (smooth_calibrated_fmap, outputnode, ["out_file", "smooth_calibrated_fmap"]),
+        (smooth_calibrated_fmap, outputnode, [("out_file", "smooth_calibrated_fmap")]),
         (
             register_bet_magnitude_fmap_onto_b0,
             outputnode,
-            ["out_file", "bet_magnitude_fmap_registered_onto_b0"],
+            [("out_file", "bet_magnitude_fmap_registered_onto_b0")],
         ),
         (
             apply_xfm_on_calibrated_fmap,
             outputnode,
-            ["out_file", "registered_calibrated_fmap"],
+            [("out_file", "registered_calibrated_fmap")],
         ),
     ]
 

diff --git a/test/nonregression/pipelines/test_run_pipelines_dwi.py b/test/nonregression/pipelines/test_run_pipelines_dwi.py
@@ -176,7 +176,10 @@ def test_prepare_phasediff_fmap(cmdopt, tmp_path):
 
 @pytest.mark.fast
 def test_dwi_calibrate_and_register_fmap(cmdopt, tmp_path):
-    """Test step 2 of pipeline DWIPreprocessingUsingPhaseDiff."""
+    """Test step 2 of pipeline DWIPreprocessingUsingPhaseDiff.
+
+    This is a fast test which should run in about 1 minute.
+    """
     from clinica.pipelines.dwi_preprocessing_using_fmap.dwi_preprocessing_using_phasediff_fmap_workflows import (
         calibrate_and_register_fmap,
     )
@@ -193,7 +196,7 @@ def test_dwi_calibrate_and_register_fmap(cmdopt, tmp_path):
     )
     delta_echo_time = abs(echo_time2 - echo_time1)
 
-    wf = calibrate_and_register_fmap()
+    wf = calibrate_and_register_fmap(output_dir=str(tmp_path / "tmp"))
     wf.inputs.inputnode.reference_b0 = str(
         input_dir / "sub-01_ses-M000_avg_b0_brain.nii.gz"
     )