map_ap_to_deriv.py

usage: map_ap_to_deriv.py [-subj_dir SUBJ_DIR] [-deriv_dir DERIV_DIR]

[-ow_mode_top OW_MODE_TOP] [-ow_mode_subj OW_MODE_SUBJ] [-verb VERB] [-ver] [-help] [-hview]

Overview

This program is used to map afni_proc.py (AP) results directory
outputs to names and file structure of FMRI BIDS derivatives.

The number of outputs may increase over time.

Options

options:
  -subj_dir SUBJ_DIR    (req) location of the input AP results directory
                        (often ".", as this program is often run from within
                        the AP results directory).
  -deriv_dir DERIV_DIR  location of the output derivatives directory, which
                        can include path as well as output directory name.
                        (def: "bids_deriv", in "-subj_dir ..").
  -ow_mode_top OW_MODE_TOP
                        set overwrite mode for top-level dir; choices are:
                        backup -> move existing dir to dir_<time>; then make
                        new dir overwrite -> purge old dir and make new dir in
                        its vacant place shy -> make new dir only if one does
                        not exist simple_ok -> make new dir, ok if pre-exist
                        (mkdir -p ..) (def: simple_ok)
  -ow_mode_subj OW_MODE_SUBJ
                        set overwrite mode for subject-level dir; choices are:
                        backup -> move existing dir to dir_<time>; then make
                        new dir overwrite -> purge old dir and make new dir in
                        its vacant place shy -> make new dir only if one does
                        not exist simple_ok -> make new dir, ok if pre-exist
                        (mkdir -p ..) (def: backup)
  -verb VERB            verbosity level (def: 0)
  -ver                  display version
  -help                 display help in terminal
  -hview                display help in a text editor

Examples

  1) Run the program from within an AP results dir, to make the output
     derivatives directory in the current spot:

     map_ap_to_deriv.py -subj_dir .

  2) Run the program from within an AP results dir, to make the output
     derivatives directory in a different group directory output:

     map_ap_to_deriv.py                               \
         -subj_dir   .                                \
         -deriv_dir  /path/to/derivatives/task_NAME

written by: PA Taylor (SSCC, NIMH, NIH, USA)