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- #!/usr/bin/bash
- # ==============================================================================
- # SCRIPT INFORMATION:
- # ==============================================================================
- # SCRIPT: RUN BIDS VALIDATOR COMMAND LINE TOOL THROUGH SINGULARITY
- # PROJECT: HIGHSPEED
- # WRITTEN BY LENNART WITTKUHN, 2018 - 2020
- # CONTACT: WITTKUHN AT MPIB HYPHEN BERLIN DOT MPG DOT DE
- # MAX PLANCK RESEARCH GROUP NEUROCODE
- # MAX PLANCK INSTITUTE FOR HUMAN DEVELOPMENT
- # MAX PLANCK UCL CENTRE FOR COMPUTATIONAL PSYCHIATRY AND AGEING RESEARCH
- # LENTZEALLEE 94, 14195 BERLIN, GERMANY
- # ==============================================================================
- # DEFINE ALL PATHS:
- # ==============================================================================
- PATH_BASE="${HOME}"
- PROJECT="highspeed"
- PATH_CONTAINER="${PATH_BASE}/tools/bids_validator/validator_1.3.12.sif"
- PATH_INPUT="${PATH_BASE}/${PROJECT}/bids"
- PATH_OUTPUT="${PATH_BASE}/${PROJECT}/derivatives/bids_validator"
- # ==============================================================================
- # CREATE RELEVANT DIRECTORIES:
- # ==============================================================================
- # create output directory:
- if [ ! -d ${PATH_OUTPUT} ]; then
- mkdir -p ${PATH_OUTPUT}
- echo "created ${PATH_OUTPUT}"
- fi
- # ==============================================================================
- # RUN BIDS-VALIDATOR:
- # ==============================================================================
- # run bids-validator and save the output in a text file:
- singularity run -B ${PATH_INPUT}:/input:ro ${PATH_CONTAINER} /input/ | tee -a ${PATH_OUTPUT}/bids_validation.txt
- # run the bids-validator and save the output in a .json file:
- singularity run -B ${PATH_INPUT}:/input:ro ${PATH_CONTAINER} /input/ --json | tee -a ${PATH_OUTPUT}/bids_validation.json
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