A short script to collect echo-wise processed files from an fMRIPrep working directory.

collect_fmriprep.py

"""
Collect native-space preprocessed data from fMRIPrep working directory and
copy into fMRIPrep derivatives directory, in BIDS format.

This script has only been tested on fMRIPrep v20.2.1.
It may not work with other versions.

Written by Julio Peraza (@JulioAPeraza)
"""
import argparse
import os.path as op
from glob import glob
from shutil import copyfile


def collect_fmriprep(deriv_dir, work_dir, subs):
    """
    Collect native-space preprocessed data from fMRIPrep working directory and
    copy into fMRIPrep derivatives directory, in BIDS format.

    Warning
    --------
    This script has only been tested on fMRIPrep v20.2.1. It may not work with other versions.

    Parameters
    ----------
    deriv_dir : str
        Path to fMRIPrep output directory.
    work_dir : str
        Path to fMRIPrep working directory.
    subs : list
        A list of subject IDs. Cannot include the `sub-` prefix.
    """
    for sub in subs:
        print(f"Wrangling subject {sub}", flush=True)
        sub_in_dir = op.join(work_dir, f"single_subject_{sub}_wf")
        task_dirs = glob(op.join(sub_in_dir, "func_preproc*_task_*_wf"))
        for task_dir in task_dirs:
            bb_wf_dir = op.join(task_dir, "bold_bold_trans_wf")
            bf_dirs = sorted(glob(op.join(bb_wf_dir, "_bold_file_*")))
            for bf_dir in bf_dirs:
                # Collect partially preprocessed data
                bf_dir_list = bf_dir.split("..")
                idx = bf_dir_list.index("sub-{0}".format(sub))
                sub_deriv_dir = op.join(
                    deriv_dir,
                    op.dirname("/".join(bf_dir_list[idx:])),
                )
                bf_filename = bf_dir_list[-1]

                in_file = op.join(
                    bf_dir,
                    "merge",
                    "vol0000_xform-00000_merged.nii.gz",
                )

                # Conform output name
                orig_fn_list = bf_filename.split("_")
                fn_list = orig_fn_list[:]
                fn_list.insert(-1, "space-scanner")
                fn_list.insert(-1, "desc-partialPreproc")
                out_file = op.join(sub_deriv_dir, "_".join(fn_list))
                print(f"Writing {out_file}")
                copyfile(in_file, out_file)


def _get_parser():
    parser = argparse.ArgumentParser(
        description="Collecting partially preprocesed data from fmriprep",
    )
    parser.add_argument(
        "-i",
        "--deriv_dir",
        dest="deriv_dir",
        required=True,
        help="Path to the fMRIPrep output directory, to which the files will be written.",
    )
    parser.add_argument(
        "-o",
        "--work_dir",
        dest="work_dir",
        required=True,
        help="Path to the fMRIPrep working directory, from which the files will be extracted.",
    )
    parser.add_argument(
        "-s",
        "--subs",
        dest="subs",
        required=True,
        nargs="+",
        help="List with subject IDs. These cannot include the `sub-` prefix.",
    )
    return parser


def _main(argv=None):
    option = _get_parser().parse_args(argv)
    kwargs = vars(option)
    collect_fmriprep(**kwargs)


if __name__ == "__main__":
    _main()