7.1.457. meica.pyΒΆ

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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!)
–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.

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