added --data_norm flag to the react script

ottaviadipasquale · May 5, 2021 · 797188c · 797188c
1 parent 83d13f5
commit 797188c
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Showing 2 changed files with 14 additions and 2 deletions.
diff --git a/react/__init__.py b/react/__init__.py
@@ -1,2 +1,2 @@
-__version__ = '0.1.1'
+__version__ = '0.1.2'
 from . import utils
diff --git a/script/react b/script/react
@@ -85,6 +85,13 @@ def get_parsed_args():
         help='If set, saves the Z-stats as `<out_react>_react_stage2_z.nii.gz`.'
     )
 
+    parser.add_argument(
+        '--data_norm',
+        action='store_true',
+        help='If set, normalizes the input data of stage 2 to unit standard '
+             'deviation.'
+    )
+
     parser.add_argument(
         '--force',
         action='store_true',
@@ -184,7 +191,12 @@ def main():
     # Stage 2
     logging.info('Initiating stage 2')
 
-    scaler_y = StandardScaler(with_mean=True, with_std=False)
+    dat_norm = False
+    if args.data_norm:
+        dat_norm = True
+        logging.info('Normalising input data of stage 2 since `--data_norm` '
+                     'was specified')
+    scaler_y = StandardScaler(with_mean=True, with_std=dat_norm)
     y = scaler_y.fit_transform(rsfmri.T)[:, mask_stage2]
 
     scaler_x = StandardScaler(with_mean=True, with_std=True)