From 5605dd90af908154084ab7d4a2b176bbc4c835f1 Mon Sep 17 00:00:00 2001 From: Gab-D-G Date: Fri, 22 Sep 2023 16:52:12 -0400 Subject: [PATCH] Test analysis stage with --nativespace_analysis on --- scripts/error_check_rabies.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/scripts/error_check_rabies.py b/scripts/error_check_rabies.py index 33715d9..20ac22a 100755 --- a/scripts/error_check_rabies.py +++ b/scripts/error_check_rabies.py @@ -42,12 +42,21 @@ shell=True, ) -#command = f"rabies --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --data_diagnosis" -#process = subprocess.run( -# command, -# check=True, -# shell=True, -# ) +# rerunning confound correction without censoring, which removes all scans +os.remove(f'{tmppath}/outputs/rabies_confound_correction.pkl') +command = f"rabies --verbose 1 confound_correction {tmppath}/outputs {tmppath}/outputs --nativespace_analysis" +process = subprocess.run( + command, + check=True, + shell=True, + ) + +command = f"rabies --verbose 1 analysis {tmppath}/outputs {tmppath}/outputs --data_diagnosis" +process = subprocess.run( + command, + check=True, + shell=True, + ) shutil.rmtree(f'{tmppath}/inputs/') generate_token_data(tmppath, number_scans=3)