:orphan:

.. _ahelp_abids_tool.py:

*************
abids_tool.py
*************

.. contents:: :local:


| 

    usage: /home/afniHQ/afni.build/pub.dist/bin/linux_ubuntu_16_64/abids_tool.py
           -input DSET [DSET ...] [-help]
           (-TR_match | -add_TR | -add_slice_times | -copy PREFIX [PREFIX ...])
    

Overview
========

.. code-block:: none

    
        This program does various things with BIDS formatted datasets created
        with dcm2niix_afni or dcm2niix.  The main point as of now is to pull
        information from the matching json file and 3drefit the input dataset.
        If you just want info from the matching json file, use abids_json_info.py.
    

Caveats
=======

.. code-block:: none

    
        This assumes that the nifti dataset was converted from dicoms using
        dcm2niix_afni or dcm2niix with the -b (BIDS) option. So a json file and
        matching dataset in NIFTI format should be present. (NO AFNI FORMAT...)
    
        The json file should end in .json (lower case) as outputted from dcm2niix.
        The program will try to find a json file that matches the prefix of the
        input dataset.
        Like this:
             my_bids_fmri.nii.gz <-> my_bids_fmri.json
    
        For most options, 3drefit will be run on the -input dataset(s).
        So the dataset(s) will be overwritten!!
        Make sure you want to do this!!
        All of the caveates for 3drefit apply here...!!
        (https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/3drefit_sphx.html)
    
        For example, when using -add_TR, if the dataset has slice time offsets,
        these will be scaled by the factor newTR/oldTR. So you may want to
        use -add_TR BEFORE -add_slice_times. However, afni_dcm2niix usually
        adds the correct TR to the dataset header automatically. So you
        should not need -add_TR...
    
        Also, this has only been tested with 3d+time fMRI data acquired in the
        axial (z or k) direction. If you have problems with data acquired in the
        sagittal or coronal direction, post to the message board.
    

Example
=======

.. code-block:: none

    
        abids_tool.py -add_slice_times -input my_bids_fmri.nii.gz
    
    

Options
=======

.. code-block:: none

    
    Required arguments:
      -input DSET [DSET ...]
                            At least one 3d+time dataset.
    
    Only one of these:
      -TR_match             Check if the TR in the json file matches the TR from
                            input dataset header. (1 if match)
      -add_TR               Add the TR from the BIDS json file to the input
                            dataset using 3drefit.
      -add_slice_times      Add the slice times from the BIDS json file to the
                            input dataset using 3drefit.
      -copy PREFIX [PREFIX ...]
                            Copy both the NIFTI dataset(s) AND matching .json
                            file(s) to PREFIX. Must have the same number of
                            prefixes as datasets!
    
    Optional arguments:
      -help                 Show this help and exit.
    
    Justin Rajendra circa 05/2018
    For Wolverine, hiya Bub...
    Keep on keeping on!