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How_to_use.md

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How to Use the FmpOptBS Toolbox:

  1. Install SPM12:

  2. Copy the Toolbox:

    • Copy the FmpOptBS toolbox folder into the ~/SPM/toolbox directory.

  3. Add the Toolbox to the MATLAB Path:

    • Add the toolbox directory and all its subfolders to the MATLAB path using the addpath function or MATLAB's path manager.

  4. Run SPM for fMRI Analysis:

    • Launch SPM12 to begin your fMRI analysis.

  5. Start BS Optimization:

    • Open the SPM batch interface. Under the "SPM" tab, go to "Tools" and select the "BS Optimization" option.

  6. Prepare Your Data:

    • Add your field map or field gradients, brain mask, and regions of interest (ROIs) using the "Specify" button within the interface.

  7. Execute the Process:

    • Press the "Play" button in the batch interface to start the optimization process.

  8. Optional: Analyze BS Matrix and ROIs:

    • If you need to analyze the BS.matrix and your selected ROIs, add a pause in the epi_opt_param_TB script at line 209.

Modifying Parameters:

You can adjust the fixed protocol parameters in the following scripts:

  • SetDefaultEPIparam.m:

    • Contains fixed parameters for the EPI protocol. Modify these as needed for your experiment.

  • SetDefaultScannerParam.m:

    • Defines the default scanner settings. Adjust these to match your scanner's configuration.

  • SetDefaultSimulationParam.m:

    • Contains default parameters for the simulation environment. You can customize these to fit your specific simulation requirements.