flirt.py

This support tool implements volume extraction (for 4D datasets), brain extraction, and/or registration via FSL’s FLIRT. Specifically, this tools supports paralleled computation implemented from connect_flirt. A flowchart showing the order of operations is depicted in Fig. 13.

Note

NEED TO PROVIDE A REFERENCE TO CONNECT_FLIRT.py

See also

This support tool requires JSON control files to specify input parameters for FLIRT and any additional processing such as volume extraction and brain extraction.

Flowchart for the CoNNECT custom flirt.py batch processing support tool.

flirt(IN_FILE, DATA_DIR, FLIRT_PARAMS, *args, **kwargs)

This function performed FLIRT registration between secondary and/or standard (reference) images. Brain extraction will be performed prior to registration on the input file if bet_params is specified.

flirt(IN_FILE,DATA_DIR,FLIRT_PARAMS,overwrite=False,bet_params=None,progress=False)

Parameters:

• IN_FILE (str or None or Pathlike object) – REQUIRED String or pathlike object to an input NIfTI file.

• DATA_DIR (str or None or Pathlike object) – REQUIRED String or pathlike object to the project’s data directory (project’s ‘dataDir’ credential)

• FLIRT_PARAMS (str or None or Pathlike object) – REQUIRED String or pathlike object to the input file’s FLIRT parameter file

• overwrite (bool) – OPTIONAL overwrite any existing files (default False)

• bet_params (str or None or Pathlike object) – OPTIONAL String or pathlike object to the input file’s BET parameter file (default None)

• progress (bool) – OPTIONAL operate in verbose mode (default False)

Raises:

Error – If path does not exist.

Returns:

None

Return type:

None

flirt.py also supports execution via command-line:

$ ./flirt.py <IN_FILE> <DATA_DIR> <FLIRT_PARAMS> --overwrite --bet-params <BET_PARAMS> --progress