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Export Templates

Introduction

When you download a project from Flywheel, by default the data is downloaded to the destination in the Flywheel hierarchy. With export templates you can customize how Flywheel organizes and labels your data on export.

Instruction Steps

This article explains how to create an export template to format your downloaded data.

Step 1: Create the export template

  1. The export template is a YAML file, so to begin, open a plain text editor (for example, Sublime, TextEdit, or Notepad)
  2. Copy and paste the default export template:

    ---
    file: 
      acquisition: "{group.label}/{project.label}/{subject.label}/{session.label}/{acquisition.label}"
    

    This template exports data in the same structure found within Flywheel. For example:

    {group.label}/ 
        {project.label}/
    {subject.label}/
        {session.label}/
      {acquisition.label}/
          file.png
      {acquisition.label}/
          file.png
      {acquisition.label}/
          file.dcm.zip
    
  3. You can add or remove the metadata fields to change the structure and the folder names.

    In this example, we will add some additional folders that are labeled with the following metadata *file type

    • file modality
    • file classification measurement We also no longer need the group or project structure, so we'll remove those.
  4. Based on the above changes, the new export template would like:

    file:
      acquisition: "{subject.label}/{session.label}/{file.type}/{file.modality}/{file.classification.measurement}"
    

Note

Use / to create subfolders

Based on the template above, downloaded data is exported in the following format:

{subject.label}     →                                       001/     
    {session.label} →                                           ses-1/
         {file.type}     →                                                     dicom/
              {file.modality} →                                                     MR/
                    {file.classification.measurement} →                   T1/
                                                                                                                 1211-file.dcm       
              {file.modality} →                                                     MR/
                   {file.classification.measurement} →                     T1/                                                                    
                                                                                                                  2342-file.dcm
             {file.modality} →                                                     MR/
                  {file.classification.measurement} →                     T1/
                                                                                                                 7575.dcm.zip
001/
   ses-1/
      dicom/
          MR/
            T1/
              1211-file.dcm
       dicom/
          MR/
            T1/
              2342-file.dcm
       dicom/
          MR/
            T1/
              7575.dcm.zip

Tip

To find metadata fields for your data, use Advanced Search

Step 2: Sync a Project to your Computer

Now that you have a template, use it in the CLI command to sync a project to your computer (the sync command also allows for syncing to an S3 bucket)

  1. If you have not already, upgrade your Flywheel CLI to version 15.1 or later.

    Tip

    check the version using the command: fw version

  2. Open the Terminal or Windows Command Prompt app, and enter the following command:

    fw sync fw://group/project ~/Documents/localFolder
    

    For example:

    fw sync fw://Lab612/Psychology ~/Documents/StudyData --export-template-file ~/Documents/export.yaml
    

    Tip

    Use the --dry-run flag to create an audit log attached to the project that shows a preview of how data would be downloaded. This allows you to review the labels and structure before actually downloading all of the data. See our article on fw sync for more information.

  3. The project data is downloaded in the format specified and the sync log is attached to the project in Flywheel.

Additional Considerations

  • If Flywheel field name is incorrect or there is no value, the export template uses "unknown" instead.
  • Export templates can also be used when syncing to an S3 bucket