:orphan:

.. _ahelp_map_ap_to_deriv.py:

******************
map_ap_to_deriv.py
******************

.. contents:: :local:


| 

    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
========

.. code-block:: none

    
    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
=======

.. code-block:: none

    
    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
========

.. code-block:: none

    
      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)