Generating the Basis File
=========================

Why a Basis File?
-----------------

The basis file is a simulated library of metabolite spectra that LCModel uses to fit your experimental data. It defines the expected spectral signatures of individual metabolites and is crucial for accurate quantification.

.. image:: ../graphic/basis.png
   :alt: Example of a basis file showing simulated metabolite spectra
   :align: center

Simulation Using MRSCloud
-------------------------

1. **Accessing MRSCloud**
   Visit `MRSCloud <https://braingps.mricloud.org/>`_ and sign in with your credentials.

2. **Configuration for Simulation**
    * **Module:** Select "MRSCloud"
    * **Phantom Case:** Choose the phantom case that matches your experimental setup
    * **Metabolites:** Select the corresponding metabolites (e.g., the seven metabolites present in your phantom)
    * **Simulation Settings:**
        * **Localization:** PRESS
        * **Vendor:** Siemens
        * **Editing:** unEdited
        * **TE:** 30 ms

.. image:: ../graphic/mrscloud1.png
   :alt: MRSCloud configuration interface
   :align: center

.. image:: ../graphic/mrscloud2.png
   :alt: MRSCloud configuration interface
   :align: center

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.. image:: ../graphic/mrscloud3.png
   :alt: MRSCloud configuration interface
   :align: center

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.. image:: ../graphic/mrscloud5.png
   :alt: MRSCloud configuration interface
   :align: center

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.. image:: ../graphic/mrscloud5.png
   :alt: MRSCloud configuration interface
   :align: center

3. **Download and Extract**
   Submit the simulation. Once processed, download the ZIP file containing the simulated basis set. Unzip the file and select the file with the `.BASIS` extension. This file will be used later in LCModel.