Step 3: MEG Bids Importer

Follow the instructions in the readme for the usage here.

Make sure, you have set up Plus-Sync

Here's an extended version of the instructions:

1. Initialize You can create a new configuration file (meg_bids_importer.toml) by issueing:

   meg_bids_importer init
   

   You will be prompted to provide the ANC project slug and the name of the plus_sync remote. For example, if your study acronym is ns_lipreading, you are part of the Auditory Neuroscience Lab, and you followed the instructions in Step 2, you would enter the following:

   anc_project_slug = "bids-datasets/auditory/ns_lipreading"
   plus_sync_remote = "sinuhe"
   

   After the initializing a new configuration file at meg_bids_importer.toml is done, open it to add missing pieces.

2. A GitLab Project Access Token needs to be created and then stored in a separate file, referenced at anc_token_file in the meg_bids_importer.toml.

   anc_token_file = ".gitlab_token"
   

   Enter the name of the token file .gitlab_token to the .toml file and create it. Get the gitlab token. Therefore on your project on the ANC go to >>settings>>access_tokens.

   Currently, you do not have permission to get this gitlab token at the ANC. This workflow will be updated.

3. Add a task

   ❯  meg_bids_importer task --help
   

       Usage: meg_bids_importer task [OPTIONS] COMMAND [ARGS]...    
       Manage Tasks.                                                                           
   
       ╭─ Options ─────────────────────────────────────────────────────────────────────────────╮
       │ --help          Show this message and exit.                                           │
       ╰───────────────────────────────────────────────────────────────────────────────────────╯
       ╭─ Commands ────────────────────────────────────────────────────────────────────────────╮
       │ add                         Add a new task to the configuration.                      │
       │ add-callback-event-config   Add a callback event configuration to a task.             │
       │ add-simple-event-config     Add a simple event configuration to a task.               │
       ╰───────────────────────────────────────────────────────────────────────────────────────╯
   

   With task, new tasks can be added to the configuration file, and the function to create the event files from the data can be added.

   For the resting state issue:

   ❯  meg_bids_importer task add resting
   

   For the other tasks, you need to write a python function with the raw filename as an input, that returns three elements:

   • Events, that can be extracted with the obob_mne functionread_events_from_analogue (np.ndarray)
   • Event Metadata, that will be saved as the events.tsv (pd.DataFrame)
   • Description of the columns in the event metadata as keys (dict).

   In this case, if the task is called vis and the function is saved in utils/bids_importer.py, I can add the task and the function with this command:

   ❯  meg_bids_importer task  add-callback-event-config vis utils.bids_importer.extract_vis_events
   

   meg_bids_importer.toml this will then look like this:

   [[tasks]]
   name = "rest"
   regex = "rest|resting|restingstate"
   
   [[tasks]]
   name = "vis"
   regex = "visual"
   
   [tasks.events]
   callback_function = "utils.bids_importer.extract_vis_events"
   

4. Upload your data!

   First list the subjects in sinuhe:

   meg_bids_importer list-subjects sinuhe
   

   Select a subject and upload it with:

   meg_bids_importer upload 19891224hbau