tedana_wrapper.py

usage: /home/afniHQ/afni.build/pub.dist/bin/linux_ubuntu_24_64/tedana_wrapper.py

[-h] -input DSETS [DSETS …] -TE ms [ms …] -mask MASK [-help] [-results_dir DIR] [-prefix PREFIX] [-save_all] [-prep_only] [-tedana_prog TEDANA_PROG] [-tedana_is_exec] [-ted_label LABEL] [-tedana_opts ‘OPTS’]

Overview

Internal wrapper to run tedana.py.
Usually only run from within afni_proc.py.

Caveats

Nearly all of the tedana.py options will be the defaults unless the user
specifies them with the -tedana_prog argument. See the help from tedana.py
for valid options.

Example

tedana_wrapper.py -TE 11 22.72 34.44 \
-mask masked_bandit+tlrc \
-input echo_01+tlrc echo_02+tlrc echo_03+tlrc \
-tedana_opts "--initcost=tanh --conv=2.5e-5 --kdaw=10"

Options

Required arguments:
  -input DSETS [DSETS ...]
                        4D dataset for each echo.
  -TE ms [ms ...]       Echo time (ms) for each echo.
  -mask MASK            Mask in same space/grid as the input datasets.

tedana arguments:
  -prep_only            Do not run tedana.py, stop at 3dZcat.
  -tedana_prog TEDANA_PROG
                        Path and name of the version of tedana.py that will be
                        run.Default is meica.libs/tedana.py in the afni
                        binaries directory.
  -tedana_is_exec       Run 'tedana.py' rather than 'python tedana.py'.
  -ted_label LABEL      Suffix for output folder. Adds suffix like TED.LABEL
                        (NOT A PATH)
  -tedana_opts 'OPTS'   Additional options to pass to tedana.py. (In quotes)
                        Example: '--initcost=tanh --conv=2.5e-5'

Optional arguments:
  -h, --help            show this help message and exit
  -help                 Show this help.
  -results_dir DIR      Folder to be created for all outputs. Default
                        [./Bunnymen].
  -prefix PREFIX        Prefix for dataset names. Default [Bunnymen].
  -save_all             Save intermediate datasets. Default is to save only
                        the 3dZcat stacked dataset (and tedana stuff)

Justin Rajendra circa 02/2018
I hope this will be useful for someone...
Keep on keeping on!