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Run ANTs buildtemplateparallel.sh script and generate templates.

Project description

ANTs - buildtemplateparallel

A Flywheel gear wrapping ANTs buildtemplateparallel.sh script. This script builds a population template iteratively from NIfTI input images and uses multiple CPU cores on host to parallelize the registration of each subject to the template.

NOTE: ANTs buildtemplateparallel can take a very long to run. It is recommended to run this gear on a host with significant number of CPUs to decrease runtime.

Usage

This gear can be run at the Project, Subject or Session level. Input NIfTI files to be used in the parallelized registration are downloaded dynamically during the job run based on the configuration options.

Inputs

This gear has no input.

Configuration

  • Image Dimension: Dimensionality of the input NIfTI files (default 2). 2 or 3 for single volume registration, 4 for template generation of time-series data.

  • Max Iterations: Max-Iterations in form: JxKxL (default 30x50x30) where

    • J = max iterations at coarsest resolution (here, reduce by power of 2^2)
    • K = middle resolution iterations (here,reduce by power of 2)
    • L = fine resolution iterations (here, full resolution). This level takes much more time per iteration. Adding an extra value before JxKxL (i.e. resulting in IxJxKxL) would add another iteration level.
  • N4 Bias Field Correction: N4BiasFieldCorrection of moving image (default True) False == off, True == on. If True, will run N4 before each registration. It is more efficient to run N4BiasFieldCorrection on the input images once, then build a template from the corrected images.

  • Similarity Metric: Type of similarity metric used for registration (default: GR).

    • For intramodal image registration, use:
      • CC = cross-correlation
      • MI = mutual information
      • PR = probability mapping
      • MSQ = mean square difference (Demons-like)
      • SSD = sum of squared differences
    • For intermodal image registration, use:
      • MI = mutual information
      • PR = probability mapping"
  • Transformation Model: Type of transformation model used for registration: (EL = elastic transformation model, SY = SyN with time, arbitrary number of time points, S2 = SyN with time, optimized for 2 time points, GR = greedy SyN, EX = exponential, DD = diffeomorphic demons style exponential, mapping, RI = purely rigid, RA = Affine rigid). Default = GR.

  • Output File Prefix: A prefix that is prepended to all output files.

  • Target Template: Volume to be used as the target of all inputs (default MNI152_T1_1mm.nii.gz). When set to None, the script will create an unbiased starting point by averaging all inputs.

  • Rigid-body Registration: Do rigid-body registration of inputs before creating template (default False). Only useful when you do not have an initial template.

  • Input Glob Pattern: Glob pattern (Unix style pathname pattern expansion) that matches filename to be used as inputs. (Default ''). reference.

  • Input Regex: Regular expression that matches files to be used as inputs (default .*nii\\.gz). reference.

  • Input Tags: Tag(s) that matches files to be used as inputs. When multiple tags are specified, they must be comma separated (e.g. T1template,ANTs)

  • debug: Enable debug log message (default false)

NOTE: When Input Glob Pattern, Input Regex and Input Tags are used simultaneously, the filename matches on (Input Regex OR Input Glob Pattern) AND Input Tags.

Contributing

For more information about how to get started contributing to that gear, checkout CONTRIBUTING.md.

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