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update documentation note #51

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Jun 20, 2024
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update documentation note #51

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5 changes: 4 additions & 1 deletion docs/src/GettingStarted.md
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Example data acquired on a phantom can be downloaded [here](https://doi.org/10.5281/zenodo.10731729).
There are available [examples scripts and expected results](https://github.com/NordicMRspine/UserExample_MRINavigator) to get started.

!!! note
MRINavigator.jl is developed for and tested on data acquired with a specific set of parameters on Siemens scanners. The requirements are specified in the following paragraphs. The navigator-based correction may fail when used outside this domain.

## Data requirements
The navigator based correction can only be applied on the raw data of a gradient echo acquisitions in [MRD format](https://ismrmrd.readthedocs.io/en/latest/index.html). The gradient echo acquisition can be multi-echo or single-echo. One requirement on the acquisiton is to have maximum one concatenation, meaning that the sequence repetition time (TR) shold be long enough to acquire one line in every slice. This is necessary to correctly identify and remove the reference data from the Siemens scans. The gradient echo acquisition must include a navigator readout through the center of k-space at __the end__ of each TR. During the acquisition, it is advisable to collect the signal from a respiratory belt as a reference. This can be used to unwrap the navigator's phase estimates if phase wrapping is present.
The navigator based correction can only be applied on the raw data of a gradient echo acquisitions in [MRD format](https://ismrmrd.readthedocs.io/en/latest/index.html). The gradient echo acquisition can be multi-echo or single-echo. The slices should be positioned axially (can be angulated) and one average per repetition should be used. The concatenation value should be set to one, meaning that the sequence repetition time (TR) shold be long enough to acquire one line in every slice. This is necessary to correctly identify and remove the reference data from the Siemens scans. The gradient echo acquisition must include a navigator readout through the center of k-space at __the end__ of each TR. During the acquisition, it is advisable to collect the signal from a respiratory belt as a reference. This can be used to unwrap the navigator's phase estimates if phase wrapping is present.

Other than the main acquisition, which is usually undersampled, a lower resolution, fully sampled scan is also necessary to compute the [coils sensitivity maps](https://doi.org/10.1002/mrm.1241) and reconstruct the images. This low-resolution scan is also called a reference scan and should include only one echo. It is possible to extract a single echo from a multi echo acquisition using the `selectEcho!` function.

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