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[DOC] Addition to the multi-echo fMRI section to include more backgro…
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* Addition to the multi-echo fMRI section to include more background

* Changed links in the Why multi-echo portion
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monicayao authored and jbteves committed Jun 1, 2019
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Multi-echo fMRI
===============
In multi-echo (ME) fMRI, data are acquired for multiple echo times, resulting in
multiple time series for each voxel.
In most echo-planar image (EPI) fMRI sequences,
only one brain image is acquired at each repetition time, at the rate of radio frequency (RF).
In contrast, in multi-echo (ME) fMRI, data are acquired for multiple echo times,
resulting in multiple volumes with varying levels of contrast acquired per RF.

The physics of multi-echo fMRI
------------------------------
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For optimally combined: Rather than analyzing single-echo time series separately,
we can combine them into a "optimally combined time series".
For more information on this combination, see :ref:`approach`.
For more information on this combination, see `processing pipeline details`_.
Optimally combined data exhibits higher SNR and improves statistical power of analyses in regions
traditionally affected by drop-out.

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as well as additional information only available when looking at signal decay across multiple TEs.
We can use this information to denoise the optimally combined time series.

.. _Pruim et al., 2015: https://www.sciencedirect.com/science/article/pii/S1053811915001822
.. _processing pipeline details: https://tedana.readthedocs.io/en/latest/approach.html#optimal-combination
.. _Pruim et al. (2015): https://www.sciencedirect.com/science/article/pii/S1053811915001822

Acquisition Parameter Recommendations
-------------------------------------
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The one difference with multi-echo is a slight time cost.
For multi-echo fMRI, the shortest echo time (TE) is essentially free since it is collected in the
gap between the radio frequency (RF) pulse and the single-echo acquisition.
gap between the RF pulse and the single-echo acquisition.
The second echo tends to roughly match the single-echo TE.
Additional echoes require more time.
For example, on a 3T MRI, if the T2* weighted TE is 30ms for single echo fMRI,
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