diff --git a/Dockerfile b/Dockerfile index bb6a0e1..7aacd73 100644 --- a/Dockerfile +++ b/Dockerfile @@ -102,7 +102,7 @@ RUN micromamba create -y -f /tmp/env.yml && \ # Check if this is still necessary when updating the base image. ENV PATH="/opt/conda/envs/fmripost_aroma/bin:$PATH" \ UV_USE_IO_URING=0 -RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \ +RUN npm install -g svgo@^3.2.0 bids-validator@1.14.10 && \ rm -r ~/.npm # diff --git a/src/fmripost_aroma/cli/parser.py b/src/fmripost_aroma/cli/parser.py index 1603698..854b938 100644 --- a/src/fmripost_aroma/cli/parser.py +++ b/src/fmripost_aroma/cli/parser.py @@ -540,6 +540,7 @@ def parse_args(args=None, namespace=None): bids_dir = config.execution.bids_dir output_dir = config.execution.output_dir + derivatives = config.execution.derivatives work_dir = config.execution.work_dir version = config.environment.version @@ -571,8 +572,8 @@ def parse_args(args=None, namespace=None): 'Please modify the output path.' ) - # Validate inputs - if not opts.skip_bids_validation: + # Validate raw inputs if running in raw+derivatives mode + if derivatives and not opts.skip_bids_validation: from fmripost_aroma.utils.bids import validate_input_dir build_log.info( diff --git a/src/fmripost_aroma/workflows/base.py b/src/fmripost_aroma/workflows/base.py index ac82bc2..94871ee 100644 --- a/src/fmripost_aroma/workflows/base.py +++ b/src/fmripost_aroma/workflows/base.py @@ -210,6 +210,10 @@ def init_single_subject_wf(subject_id: str): f"Please check your BIDS filters: {config.execution.bids_filters}." ) + config.loggers.workflow.info( + f'Collected subject data:\n{yaml.dump(subject_data, default_flow_style=False, indent=4)}', + ) + bids_info = pe.Node( BIDSInfo( bids_dir=config.execution.bids_dir,