Usage: meica.py [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!)
–daw=DAW Weight to increase ICA dimensionality, default 10. Use
-1 for low tSNR data
--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.