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Yntiglei edited this page Jan 16, 2024 · 15 revisions

This section describes the main steps we go through from raw dicoms to final tractography results using launchcontainers. You can follow this manual for your analysis.

Sequences used:

  • structural MRI: MP2RAGE
  • diffusion MRI: NORDIC

Main steps:

1. Make project folder following BIDS specification, and put dicom data under basedir/dicom/

  • The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging and behavioral data. Below is a typical structure of a BIDS-valid project folder:

    basedir/
   ├──BIDS/
       ├── dataset_description.json
       ├── participants.tsv
       ├── README
       └── sub-01/
           └── anat/     
              ├── sub-01_T1w.nii.gz
              ├── sub-01_T1w.json
              ├── sub-01_T2w.nii.gz
              └── sub-01_T2w.json
           ├── func/
           ├── dwi/
           ├── fmap/
           └── beh/
       ├── sub-02/
       ├── ...
       └── derivatives/
           └── container_name/     
               └── analysis-xxx
                    ├── sub-01/
                    ├── sub-02/
                    ├── ...
                   
   ├──dicom/
   ├──derivatives/
   ├──code/ 
   ├── ...

2. Convert dicoms to nifti. Store the nifti under basedir/BIDS/

  • (optional) Use HeuDiConv to convert dicom files to nifti files.
  • Under nifti folder, preprocess raw nifti to final nifti.

3. Move the example config files to a local working directory

> cp path_to_launchcontainers/example_configs/example_lc_config.yaml PROJECT_NAME/code/lc_config.yaml

> cp path_to_launchcontainers/example_configs/example_subSesList.txt PROJECT_NAME/code/subSesList.txt

> # take anatrois as an example 
> cp path_to_launchcontainers/example_configs/example_anatrois_config.json PROJECT_NAME/code/anatrois_config.json
  • launchcontainers takes path as input and reads the config files by itself. Thus, having a short and easy-to-input path will facilitate your analysis
  • Usually, we copy config files from launchcontainers/example_configs/ to basedir/code
  • IMPORTANT: This file will be dynamic, every time we use it, it will be copied to the corresponding container/analysis folder, so that we have a copy of what was run in this specific analysis. You can edit this file as much as you need and delete it at the end.

4. Edit the configs

5. Run launchcontainers in prepare mode. (Descriptions in workflow)

  • (optional) Check the documentation and help for launchcontainer, it will give you some explanation on the flags:
launchcontainers -h

or

launchcontainers --help
  • Run prepare mode to create symlinks and auto-check if all the required files are in place.
launchcontainers --lcc $path_to_config.yml -ssl $path_to_subseslist.txt -cc $path_to_config_file(s)
  • ATTENTION If your container has more than one container_config, put them here one after the other separated with one white space .

6. Check that all the symlinks are successfully created and all the configs are copied

  • Use 'tree' command with color coding to check that there are no broken links

7. Run launchcontainers in run mode (Descriptions in workflow)

launchcontainers --lcc $path_to_config.yml -ssl $path_to_subseslist.txt -cc $path_to_config_file(s) --run_lc

More:

  • there are 3 levels of verbosity you can control when running Launchcontainers in the command line. The levels are controlled by command line input, and one parameters in the config.yml file:
    • CRITICAL level: print_command_only == True in the config.yml
    • CRITICAL and INFO level: in the command line input add -v --verbose flag or set print_command_only == False in the config.yml
    • DEBUG level: in the command line input add --DEBUG flag
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