diff --git a/bip/pipelines/struct_FS/FS_proc.py b/bip/pipelines/struct_FS/FS_proc.py
index 4022122455152c2f2eef26f3964d0da9de891033..3782d8d194eaa699cd4852e110157eb3b4ac304b 100755
--- a/bip/pipelines/struct_FS/FS_proc.py
+++ b/bip/pipelines/struct_FS/FS_proc.py
@@ -31,9 +31,8 @@ def run(ctx,
         if os.path.exists(FreeSurfer_dir):
             shutil.rmtree(FreeSurfer_dir)
 
-        env = dict(os.environ, SUBJECTS_DIR=os.getcwd())
+        env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
 
-        os.environ["SUBJECTS_DIR"] = subjects_dir + "/" + ctx.subject
         T1_path = subjects_dir + "/" + T1_unbiased
         T2_path = subjects_dir + "/" + T2_FLAIR_unbiased