AFNI program: meica.py
Output of -help
Usage: meica.py [options]
Options:
-h, --help show this help message and exit
-e TES ex: -e 14.5,38.5,62.5 Echo times (in ms)
-d DSINPUTS ex: -d RESTe1.nii.gz,RESTe2.nii.gz,RESTe3.nii.gz
-a ANAT ex: -a mprage.nii.gz Anatomical dataset (optional)
-b BASETIME ex: -b 10s OR -b 10v Time to steady-state
equilibration in seconds(s) or volumes(v). Default 0.
--MNI Warp to MNI space using high-resolution template
Additional processing options:
--qwarp Nonlinear anatomical normalization to MNI (or --space
template) using 3dQWarp, after affine
--fres=FRES Specify functional voxel dim. in mm (iso.) for
resampling during preprocessing. Default none. ex:
--fres=2.5
--space=SPACE Path to specific standard space template for affine
anatomical normalization
--no_skullstrip Anatomical is already intensity-normalized and skull-
stripped (if -a provided)
--no_despike Do not de-spike functional data. Default is to de-
spike, recommended.
--no_axialize Do not re-write dataset in axial-first order. Default
is to axialize, recommended.
--mask_mode=MASK_MODE
Mask functional with help from anatomical or standard
space images: use 'anat' or 'template'
--coreg_mode=COREG_MODE
Coregistration with Local Pearson and T2* weights
(default), or use align_epi_anat.py (edge method): use
'lp-t2s' or 'aea'
--smooth=FWHM Data FWHM smoothing (3dBlurInMask). Default off. ex:
--smooth 3mm
--align_base=ALIGN_BASE
Explicitly specify base dataset for volume
registration
--TR=TR The TR. Default read from input dataset header
--tpattern=TPATTERN
Slice timing (i.e. alt+z, see 3dTshift -help). Default
from header. (N.B. This is important!)
--align_args=ALIGN_ARGS
Additional arguments to anatomical-functional co-
registration routine
--ted_args=TED_ARGS
Additional arguments to TE-dependence analysis routine
Run optipns:
--prefix=PREFIX Prefix for final ME-ICA output datasets.
--cpus=CPUS Maximum number of CPUs (OpenMP threads) to use.
Default 2.
--label=LABEL Label to tag ME-ICA analysis folder.
--test_proc Align and preprocess 1 dataset then exit, for testing
--script_only Generate script only, then exit
--pp_only Preprocess only, then exit.
--keep_int Keep preprocessing intermediates. Default delete.
--skip_check Skip dependency checks during initialization.
--OVERWRITE If meica.xyz directory exists, overwrite.
This page auto-generated on
Wed Apr 24 22:26:13 EDT 2024