Changing the env variable modification for FreeSurfer

bip/pipelines/struct_FS/FS_proc.py

@@ -31,7 +31,7 @@ def run(ctx,
         if os.path.exists(FreeSurfer_dir):
             shutil.rmtree(FreeSurfer_dir)
 
-        subjects_dir=os.getcwd()
+        env = dict(os.environ, SUBJECTS_DIR=os.getcwd())
 
         os.environ["SUBJECTS_DIR"] = subjects_dir + "/" + ctx.subject
         T1_path = subjects_dir + "/" + T1_unbiased
@@ -42,7 +42,7 @@ def run(ctx,
         if os.path.exists(T2_FLAIR_unbiased):
             cmd += " -FLAIR " + T2_path + " -FLAIRpial"
 
-        output = run_command(log, cmd)
+        output = run_command(log, cmd, env)
 
         log.info(output)
 

bip/utils/log_utils.py

@@ -22,10 +22,10 @@ from subprocess import check_output
 from fsl import wrappers
 
 
-def run_command(logger, command):
+def run_command(logger, command, env):
     try:
         logger.info('COMMAND TO RUN: \t' + command.strip())
-        job_output = check_output(command, shell=True).decode('UTF-8')
+        job_output = check_output(command, shell=True, env=env).decode('UTF-8')
         logger.info('COMMAND OUTPUT: \t' + job_output.strip())
     except Exception as e:
         logger.error('Exception raised during: \t' + command.strip())