Running the sample script (process_data.sh
) using sct_run_batch
ΒΆ
In your working directory, you should have the batch processing script, a config file, and a data directory containing three subjects in BIDS dataset structure. You can double-check this using the ls
command:
ls
# Output should be: data/ config.yml process_data.sh README.txt
ls data
# Output should be: sub-01 sub-03 sub-05
In order to apply the process_data.sh
script to the multi-subject dataset, we can use an SCT tool called sct_run_batch. This command loops across each subject directory and launches the script individually for each subject.
Running this command will take 10-30m depending on the capabilities of your processor.
sct_run_batch -script process_data.sh -config config.yml
- Input arguments:
-script
: The path to the script you wish to run. This script should be written to accept a single argument (a path to the subject folder). That way, sct_run_batch can launch the script once for each subject, passing along each subject folder as an argument to the script.-config
: A config file containing input arguments for sct_run_batch. Inside this file, you will find:path-data
: Path to the folder containing the BIDS dataset. sct_run_batch will look for subject folders inside, so that it can loop across subjects.subject-prefix
: The prefix that each subject folder has.path-output
: Path to save the output to. This path is what determines the output directories for results, QC reports, and logs.path-segmanual
: Path to the folder containing manually-corrected segmentations.jobs
: Number of jobs for parallel processing.itk-threads
: Number of jobs for ANTs routines.
- Output files/folders:
./output/results/
: A folder containing the processed data, as well as CSV files containing computed metrics (CSA, and MTR in WM). This is equivalent to thederivatives/
folder of BIDS-compliant datasets../output/qc/
: A folder containing the Quality Control (QC) reports for the commands in the pipeline../output/log/
: A folder containing the log files for each subject. This is where you would go to troubleshoot any errors or issues that occur during the processing.
Note
We strongly recommend using a config file as shown here (rather than passing arguments directly to sct_run_batch) because it helps with reproducibility.
To learn about the full list of options that are available to tweak in your config file, run sct_run_batch -h
.