launchcontainers 0.4.3

A Python based soft to launch neuroimaging containers on clusters

launchcontainers

Launchcontainers is a Python-based tool for automatically launching parallel computing tasks on HPC or local clusters. It was designed to:

1. Prepare folder structures and input files automatically for Neuroimaging pipelines
2. Backup the input configs for data provenance
3. Deploy jobs in local HPC, SGE, or SLURM in parallel

Currently, launchcontainers works along with anatROIs, RTP-preproc, and RTP2-pipeline.

To use the newest version, please pip install launchcontainers==0.4.3

NEW FEATURES

• Update to 0.4.3. Add feature QC rtp2pipelines, it was integrated in the code launchcontainers/launchcontainers /quality_control/, you can use it by doing python qc_rtp2pipeline_output.py analysis_dir, it will read if all the tracts is finished for you
• Update to 0.4.2. Refactor the launchcontainer command-line interaction to make it more user-friendly
  • For prepare mode, the user will do: lc --log-dir path/to/log/dir prepare -lcc path/to/lc_yaml -ssl path/to/subseslist -cc path/to/cc
    • The prepare mode will create symlink and prepare analysis folder structure. it will output analysis_dir in the commandline for run mode
  • For run mode, the user will do: lc --log-dir path/to/log/dir run -w path/to/analysis_dir --run_lc
    • The run mode will do a independent check on analysis dir to see if the configs there is correct
    • Then it will summarize the config settings and folder structure (using the cli tree command) to the user and ask for user input
    • Once user type y or yes, the program will launch
  • Several helper functions also implemented in the cli lc :
    • lc --copy_configs -o path/to/working/dir you can type this to copy all the example configs to the working directory
    • lc --create_bids -csc path/to/csc/yaml -ssl path/to/subseslist you can use this to create a fake BIDS folder for testing
  • for more info, pip install lc and type lc -h
• The update 0.3.5 will be capable work with heudiconv, Presurfer and NORDIC_raw, there will be a new derivatives folder called Processed_nifti, it will stored the processed .nii.gz by NORDIC_raw and Presurfer
• 0.3.5: The add_intended_for function from heudiconv will be used here to edit the fmap _epi.json
• Add requests into pyproject.toml, remove version limit to common package such as nibabel and numpy
• Changed rtp/rtp2-preproc multishell option to separateed_shell_files
• Edited lc_config.yaml comment about dask_worker options
• Fixed error message by dask progress (0.3.18)
• launchcontainers --copy_configs "~/path/to/working_directory" will copy the corresponding config files to your specified directory!
• We updated the lc_config.yaml for RTP2-pipelines, please have a look!

check the How to use for more information

Check also:

• Home
• Installation
• Manual
  • Edit configs
  • Launch prepare mode
  • Launch run mode
• Reporting, Contribution, and citation
• Supplement: How to use HeuDiConv