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Change some parameters in documentation
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ocommowi committed May 6, 2021
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Expand Up @@ -22,14 +22,14 @@ Multi-compartment T2 estimation

We provide from Anima 3.0 new tools for multi-compartment T2 and myelin water fraction estimation. We also provide implementations of previous methods from the literature on multi-peak T2 estimation. While this second approach is appealing, we find it more stable to use multi-compartment T2 estimation rather than multi-peak and rather provide those for comparison purposes.

* **animaGammaMixtureT2RelaxometryEstimation** implements variable projection estimation of the parameters and weights of three T2 Gamma distributions using two different modes (toggled by the ``-C`` option) [3,4]: only middle T2 compartment mean estimation or all class mean parameters estimation. In both cases, all weights are deduced from the estimated parameters using variable projection
* **animaGammaMixtureT2RelaxometryEstimation** implements variable projection estimation of the parameters and weights of three T2 Gamma distributions using two different modes (toggled by the ``-U`` option) [3,4]: only middle T2 compartment mean estimation or all class mean parameters estimation. In both cases, all weights are deduced from the estimated parameters using variable projection
* **animaGMMT2RelaxometryEstimation** implements, for robustness to clinical acquisitions, a fixed parameter estimation of a Gaussian T2 mixture [7]. In this implementation, only the weights of the three T2 compartments are estimated, their PDFs being fixed according to prior knowledge on the tissues.
* **animaMultiT2RelaxometryEstimation** provides an implementation of several methods of the literature for multi-peak T2 estimation [2,5,6]. It provides several types of regularization: Tikhonov or non local regularization. Again these methods make the deduction of myelin water fraction more difficult and quite sensitive to the regularization.

MRI simulation
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Several MR simulation tools are included in ANIMA, which simulate sequences from relaxation time maps. All of them are described in detail `here <https://team.inria.fr/visages/files/2017/08/mr_simulation_guide.pdf>`_.
Several MR simulation tools are included in ANIMA, which simulate sequences from relaxation time maps. All of them are described in detail `here <https://team.inria.fr/empenn/files/2017/08/mr_simulation_guide.pdf>`_.

References
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