Generating the Basis File
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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.