Relaxometry scripts

This section describes Anima scripts for relaxometry processing.

T2 relaxometry script

This script combines several processing steps to compute from a 4D T2 relaxomaetry sequence (plus possible additional images) T2 maps or multi-T2 maps following [1]. This script performs the following preprocessing:

  • brain masking either from the provided T1-weighted high resolution image provided using the -m option or by default the first volume of the input 4D image
  • computation of the mono T2 maps with B1 correction using animaT2EPGRelaxometryEstimation [2]
  • computation of multi-T2 weight maps (modeled as three Gaussians as in [1]) as well as the myelin water fraction using animaGMMT2RelaxometryEstimation [1]

Some of these steps may be discarded using the --no-\* options available in the script help. If provided, the EPG algorithms may use an external T1 image provided by the user with the -t option. Results of this script are specified using the -o and -g options.


  1. S. Chatterjee, O. Commowick, O. Afacan, B. Combes, A. Kerbrat, S.K. Warfield, C. Barillot. A 3-year follow-up study of enhancing and non enhancing multiple sclerosis lesions in MS patients with clinically isolated syndrom using a multi-compartment T2 relaxometry model, ISMRM, 2018.
  2. Kelvin J Layton, Mark Morelande, David Wright, Peter M Farrell, Bill Moran, Leigh Johnston. Modelling and estimation of multicomponent T2 distributions. IEEE transactions on medical imaging, 32(8):1423–34, 2013.