7.1.397. auto_warp.pyΒΆ

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#++ auto_warp.py version: 0.02

auto_warp.py - Non-linear regisration

Basic Usage:

auto_warp.py -base TT_N27+tlrc -input anat.nii
-skull_strip_input yes

REQUIRED OPTIONS:

-base : name of reference or template volume
-input : name of dataset to be registered

MAJOR OPTIONS:

-help : this help message

OTHER OPTIONS:

-qblur bB bS : specify 3dQwarp blurs for base and source volumes
-qworkhard i0 i1: set the two values for 3dQwarp’s -workhard option
-qw_opts ‘OPTS’: Pass all of OPTS as extra options directly to 3dQwarp

A full list of options for auto_warp.py:

-base use: Template volume.
-input use: dataset to be aligned to the template
-keep_rm_files
use: Don’t delete any of the temporary files created here
-prep_only
use: Do preprocessing steps only without alignment
-help use: The main help describing this program with options
-limited_help
use: The main help without all available options
-option_help
use: Help for all available options
-version
use: Show version number and exit
-ver
use: Show version number and exit
-verb
use: Be verbose in messages and options
-save_script
use: save executed script in given file
-skip_affine

use: Skip the affine registration process

allowed: yes, no default: no

-skull_strip_base
 use: Do not skullstrip base/template dataset allowed: yes, no default: no
-skull_strip_input
 use: Do not skullstrip input dataset allowed: yes, no default: no
-ex_mode
use: Command execution mode.
quiet: execute commands quietly echo: echo commands executed dry_run: only echo commands

allowed: quiet, echo, dry_run, script default: script

-overwrite
use: Overwrite existing files
-suffix
default: _al
-child_anat
use: Names of child anatomical datasets
-qblur use: 3dQwarp base and source blurs (FWHM)
-qw_opts
use: 3dQwarp miscellaneous options.
Parameters will get passed directly to 3dQwarp.
-qworkhard

use: 3dQwarp -workhard values

default: [0, 1]

-warp_dxyz

use: Resolution used for computing warp (cubic only)

default: [0.0]

-affine_dxyz

use: Resolution used for computing initial transform (cubic only)

default: [0.0]

-affine_input_xmat
 
use: Affine transform to put input in standard space.
Special values are:

‘AUTO’ to use @auto_tlrc ‘ID’ to do nothing ‘FILE.1D’ for a pre-computed matrix FILE.1D will

get applied to the input before Qwarping

default: AUTO

-smooth_anat
use: Smooth anatomy before registration
-smooth_base
use: Smooth template before registration
-unifize_input

use: To unifize or not unifize the input

allowed: yes, no default: y e s

-output_dir

use: Set directory for output datasets

default: awpy

-followers
use: Specify follower datasets
-affine_followers_xmat
 use: Specify follower datasets’ affine transforms

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