pattern

Use in combination with regex or variable values to use some or all of the file name for the container label in Flywheel.

You can use this value to set the label for Flywheel Group and Projects. 

- pattern: "sub_{subject}"

and

- pattern: "Anxiety Study"
- pattern: "{subject}"
- pattern: "anx_{session}" 
# Sets the project label to Anxiety Study
# no matter what the folder name is in your dataset

select

Used to start an expression where you set parameters or logical operators to determine what data is imported.

- pattern: "{acquisition}"
- select:   
  - pattern: Exams    
    packfile_type: dicom  
  - pattern: .*    
    ignore: true

scan

Scanners are import methods that are optimized for certain filetypes. The scanners can automatically determine metadata and where to place the data in the Flywheel hierarchy.

Scan options are: dicom, parrec, and filename

See below

scan: dicom

Uses the DICOM file standard to place images in containers and add metadata

- select:
  - pattern: "DTI 2mm 30dir 2x b100"    
    scan: dicom

scan: parrec

Uses the PAR REC file standard to places images in containers and add metadata

- select:
  - pattern: "Study 002"
    scan: parrec

scan:filename

Allows you to designate part of a filename as an attribute in Flywheel

- pattern: "{project}"    
 - pattern: "{subject}"           
 - select:
   scan: filename                          
 - pattern: "{session}-(?P<acquisition>\\w+)\\..+"

packfile_type

Groups related images in to an acquisition. This is useful when you have a folder of images. Possible packfile_type values are: dicom and zip.

Use packfile_name to define a name for the file. If the packfile type is .zip the generated packfile name is the following: {container.label or container.id}.zip. If the packfile type is not 'zip', the format is the following: {container.label or container.id}.{packfile_type}.zip

- pattern: "{acquisition}"
 - select:     
   - pattern: Exams             
     packfile_type: dicom  

packfile_name

Names the packfile

- pattern:
   packfile_name: some_exams.zip

ignore

Does not import files that match the regex pattern. Values can be true/false

- pattern: "{acquisition}"
select:     
  - pattern: Exams                    
    packfile_type: dicom   
  - pattern: .* 
    ignore: true

{group}

Variable that uses the designated part of the filename or folder as the Flywheel group label. If used alone, the entire filename or folder name is used for the Flywheel group label

- pattern: "{group}"

{project}

Variable that uses the designated part of the filename or folder name as the Flywheel project label. If used alone, the entire filename or folder name is used for the Flywheel project label

- pattern: "{project}"

{subject}

Variable that uses the designated part of the filename or folder name as the Flywheel project label. If used alone, the entire filename or folder name is used for the Flywheel project label

- pattern: "amyg_s{subject}_amyg_{session}_pcolA"

{session}

Variable that uses the designated part of the filename or folder name as the Flywheel session label. If used alone, the entire filename or folder name is used for the Flywheel session label

- pattern: "{session}&{acquisition}"

{acquisition}

Variable that uses the designated part of the filename or folder name as the Flywheel acquisition label. If used alone, the entire filename or folder name is used for the Flywheel acquisition label

- pattern: "{acquisition}"

Regular expressions (regex)

You can use regex for pattern matching file or folder names you want to import. You can learn more about regex operators and test out your regex at regex101

- select:  
  - pattern: .*    
    scan: dicom

Flywheel metadata

Sets metadata for the Project, Subject, Session, or Acquisition containers.

- pattern: "(?P<session.info.ClinicalTrialSiteId>[^-]+)-{session}"