From 6b19dd03bb84c6f7542746cde2c682c8b0aa6207 Mon Sep 17 00:00:00 2001
From: Fidel Alfaro Almagro <falmagro@fmrib.ox.ac.uk>
Date: Fri, 10 Feb 2023 09:21:54 +0000
Subject: [PATCH] Changing the env variable modification for FreeSurfer
---
bip/pipelines/struct_FS/FS_proc.py | 4 ++--
bip/utils/log_utils.py | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/bip/pipelines/struct_FS/FS_proc.py b/bip/pipelines/struct_FS/FS_proc.py
index 1a72558..4022122 100755
--- a/bip/pipelines/struct_FS/FS_proc.py
+++ b/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)
diff --git a/bip/utils/log_utils.py b/bip/utils/log_utils.py
index abcc870..d40dd90 100755
--- a/bip/utils/log_utils.py
+++ b/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())
--
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