From 1cbbdaf09ea6a1e90392ad00c4e18853e3118414 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Mon, 15 Feb 2021 09:51:33 -0500 Subject: [PATCH] :bug: Move pipeline import earlier in configuration process --- dev/docker_data/run.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/dev/docker_data/run.py b/dev/docker_data/run.py index a09d130326..c26e06d7ef 100755 --- a/dev/docker_data/run.py +++ b/dev/docker_data/run.py @@ -477,9 +477,9 @@ def load_cpac_data_config(data_config_file, participant_label, c.update(overrides) if args.anat_only: - # TODO - # c.update({'functional_preproc': 'run': Off})? - c.update({"runFunctional": [0]}) + c.update({'FROM': 'anat-only'}) + + c = Configuration(c) # get the aws_input_credentials, if any are specified if args.aws_input_creds: @@ -524,8 +524,6 @@ def load_cpac_data_config(data_config_file, participant_label, c['pipeline_setup']['system_config']['max_cores_per_participant'], int(c['pipeline_setup']['system_config']['num_ants_threads']) ) - c = Configuration(c) - c['disable_log'] = args.disable_file_logging if args.save_working_dir is not False: