Fix rmsd and SVD issues.

PennLINC · Sep 18, 2024 · 76915f0 · 76915f0
1 parent a46343e
commit 76915f0
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/xcp_d/interfaces/censoring.py b/xcp_d/interfaces/censoring.py
@@ -709,6 +709,9 @@ def _run_interface(self, runtime):
 
                         new_confound_df[column] = confound_df[column]
 
+                    # Replace NaNs in new column with zeros
+                    new_confound_df[column].fillna(0, inplace=True)
+
                 # Collect column metadata
                 for column in new_confound_df.columns:
                     if column in confound_metadata:

diff --git a/xcp_d/utils/confounds.py b/xcp_d/utils/confounds.py
@@ -60,6 +60,7 @@ def load_motion(
     motion_confounds_df : pandas.DataFrame
         The six motion regressors.
         The three rotations are listed first, then the three translations.
+        Plus rmsd, and possibly filtered motion regressors.
 
     References
     ----------
@@ -91,10 +92,16 @@ def load_motion(
             columns=[f"{c}_filtered" for c in motion_confounds_df.columns],
         )
         motion_confounds_df = pd.concat(
-            [motion_confounds_df, filtered_motion_confounds_df, confounds_df[["rmsd"]]],
+            [motion_confounds_df, filtered_motion_confounds_df],
             axis=1,
         )
 
+    # Add RMSD column (used for QC measures later on)
+    motion_confounds_df = pd.concat(
+        [motion_confounds_df, confounds_df[["rmsd"]]],
+        axis=1,
+    )
+
     return motion_confounds_df