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docs: update docs for mtsat R1 and delta max
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jeremie-fouquet authored and spinicist committed May 24, 2024
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Expand Up @@ -249,7 +249,7 @@ If you use a custom contrasts file then the outputs will have the names specifie
qi mtsat
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Implementation of Gunther Helm's MT-Sat method. Calculates R1, apparent PD and the semi-quantitative MT-Saturation parameter "delta". This is the fractional reduction in the longitudinal magnetization during one TR, expressed as a percentage. Arguably could be included in the :doc:`Relaxometry` module instead. Outputs R1 instead of T1 as this is more common in the MTSat / MPM literature. If using multi-echo input data the input should be passed through `qi mpm_r2s` first and the output ``S0`` files used as input to `qi mtsat`. By default, does not use the original small flip angle approximation to compute R1 and PD because of the results presented in Edwards et al., 2021. To still use the small flip angle approximation (e.g., for backward compatibility), use the --smallangle (-s) flag.
Implementation of Gunther Helm's MT-Sat method. Calculates R1, apparent PD and the semi-quantitative MT-Saturation parameter "delta". This is the fractional reduction in the longitudinal magnetization during one TR, expressed as a percentage. Arguably could be included in the :doc:`Relaxometry` module instead. Outputs R1 instead of T1 as this is more common in the MTSat / MPM literature. If using multi-echo input data the input should be passed through `qi mpm_r2s` first and the output ``S0`` files used as input to `qi mtsat`. By default, does not use the original small flip angle approximation to compute R1 and PD because of the results presented in Edwards et al., 2021. To still use the small flip angle approximation (e.g., for backward compatibility), use the --smallangle (-s) flag. By default, R1 values above 10 1/s and delta values above 10% are clamped, but you can change these numbers. All delta, R1, and PD values lower than 0 are set to 0.

**Example Command Line**

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