BIDS Script

Script to get data from the server into BIDS.

What it should do

• create the folder structure according to BIDS with folders for
  • functional MRI
  • structural MRI
  • fieldmaps
  • (DWI)
• merge functional files
• copy files in their respective folders
• for fieldmap data
  • get both echotimes and add them to the right json file

What it does (so far)

General:

• creates folders for all subjects
• creates participants.tsv with the following columns:
  • participant_id: Subject ID as specified in BIDS
  • server_id: Subject ID that was assigned when getting the data from the server

Anatomical data:

• creates anat folder for each participant
• copies T1 weighted image to this folder
• renames this image according to BIDS criteria

How to run it

This script can be run from the command line, with the following structure:

python3 bids_script.py path/to/sourcedata path/to/bids_folder --task taskname --anat anatomical_naming_scheme --func functional_naming_scheme --fmap fieldmap_naming_scheme --normal

From the help text of the script:

usage: Creates folders and copies files from imaging data set
    according to BIDS.

positional arguments:
  data         Absolute path to where the data are stored. The script expects
               all subfolders to be sub- jects with respective folders for the
               given modalities (string)
  bids_folder  Absolute path to the folder where the BIDS data should be
               stored (string)

optional arguments:
  -h, --help   show this help message and exit
  --task TASK  Name of the fMRI task
  --anat ANAT  Folder name of T1 image (without 00X__)
  --func FUNC  Folder name of functional images
  --fmap FMAP  Folder name of fieldmap images
  --normal     Should the prenormalized T1 image be used? Defaults to False if
               not specified