population_template

Synopsis

population_template [ options ] input_dir template
  • input_dir: The input directory containing all images used to build the template
  • template: The output template image

Description

Generates an unbiased group-average template from a series of images. First a template is optimised with linear registration (rigid or affine, affine is default), then non-linear registration is used to optimise the template further.

Options

Options for the population_template script

  • -mask_dir Optionally input a set of masks inside a single directory, one per input image (with the same file name prefix). Using masks will speed up registration significantly
  • -warp_dir Output a directory containing warps from each input to the template. If the folder does not exist it will be created
  • -transformed_dir Output a directory containing the input images transformed to the template. If the folder does not exist it will be created
  • -linear_transformations_dir Output a directory containing the linear transformations used to generate the template. If the folder does not exist it will be created
  • -template_mask Output a template mask. Only works in -mask_dir has been input. The template mask is computed as the intersection of all subject masks in template space.
  • -rigid perform rigid registration instead of affine. This should be used for intra-subject registration in longitudinal analysis
  • -linear_no_pause Do not pause the script if a linear registration seems implausible
  • -linear_scale Specifiy the multi-resolution pyramid used to build the rigid or affine template, in the form of a list of scale factors (default: 0.3,0.4,0.6,0.8,1.0,1.0). This implicitly defines the number of template levels
  • -linear_lmax Specifiy the lmax used for rigid or affine registration for each scale factor, in the form of a list of integers (default: 2,2,2,4,4,4). The list must be the same length as the linear_scale factor list
  • -linear_niter Specifiy the number of registration iterations used within each level before updating the template, in the form of a list of integers (default:500 for each scale). The must be a single number or a list of same length as the linear_scale factor list
  • -linear_estimator Choose estimator for intensity difference metric. Valid choices are: l1 (least absolute: |x|), l2 (ordinary least squares), lp (least powers: |x|^1.2), Default: l2
  • -nl_scale Specifiy the multi-resolution pyramid used to build the non-linear template, in the form of a list of scale factors (default: 0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0). This implicitly defines the number of template levels
  • -nl_lmax Specifiy the lmax used for non-linear registration for each scale factor, in the form of a list of integers (default: 2,2,2,2,2,2,2,2,4,4,4,4,4,4,4,4). The list must be the same length as the nl_scale factor list
  • -nl_niter Specifiy the number of registration iterations used within each level before updating the template, in the form of a list of integers (default: 5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5). The list must be the same length as the nl_scale factor list
  • -nl_update_smooth Regularise the gradient update field with Gaussian smoothing (standard deviation in voxel units, Default 2.0 x voxel_size)
  • -nl_disp_smooth Regularise the displacement field with Gaussian smoothing (standard deviation in voxel units, Default 1.0 x voxel_size)
  • -nl_grad_step The gradient step size for non-linear registration (Default: 0.5)
  • -noreorientation Turn off FOD reorientation in mrregister. Reorientation is on by default if the number of volumes in the 4th dimension corresponds to the number of coefficients in an antipodally symmetric spherical harmonic series (i.e. 6, 15, 28, 45, 66 etc
  • -initial_alignment Method of alignment to form the initial template. Options are “mass” (default), “geometric” and “none”.

Standard options

  • -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
  • -force Force overwrite of output files if pre-existing
  • -help Display help information for the script
  • -nocleanup Do not delete temporary files during script, or temporary directory at script completion
  • -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
  • -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
  • -quiet Suppress all console output during script execution
  • -verbose Display additional information for every command invoked

Author: David Raffelt (david.raffelt@florey.edu.au) & Max Pietsch (maximilian.pietsch@kcl.ac.uk) & Thijs Dhollander thijs.dhollander@gmail.com)

Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/

MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For more details, see www.mrtrix.org