Brainvoyager batch fmr preprocessing scripting example.

bv_fmr_preprocessing.js

// Brainvoyager batch script for functional MRI data (.fmr) preprocessing.
//
// For more information, check the scripting guide:
// http://support.brainvoyager.com/automation-aamp-development/46-writing-scripts/133-scripting-reference-guide.html

var bvqx = BrainVoyagerQX;
bvqx.PrintToLog("---");

//----------------------------------------------------------------

// Enter the following values:
var RunPrefix = "RUN_";
var NumberOfRuns = 4;

// Enter fmr file paths
var InFmrList = ["/path/to/your/subject/RUN_1/S01_RUN_01.fmr",
                 "/path/to/your/subject/RUN_2/S01_RUN_02.fmr",
                 "/path/to/your/subject/RUN_3/S01_RUN_03.fmr",
                 "/path/to/your/subject/RUN_4/S01_RUN_04.fmr"]

//Enter the reference fmr volume path.
var TargetVolumeFile = "/path/to/your/subject/RUN_4/S01_RUN_04.fmr"

//----------------------------------------------------------------
for(count = 1; count <= NumberOfRuns; count++){

    var InFmrPath = InFmrList[count-1];

    // Open the run
    var docFMR = bvqx.OpenDocument(InFmrPath);

    // Slice scan time correction
   docFMR.CorrectSliceTimingUsingTimeTable(2); // 0: trilinear, 1: cubic spline, 2: windowed sinc
   ResultFileName = docFMR.FileNameOfPreprocessdFMR;
   docFMR.Close();
   docFMR = bvqx.OpenDocument(ResultFileName);

    // Motion Corection
    docFMR.CorrectMotionTargetVolumeInOtherRunEx(TargetVolumeFile,
                                                 1, 	   // target volume number
                                                 2, 	   // 0 and 1:trilin./trilin., 2:trilin/sinc, 3:sinc/sinc
                                                 false,  // use full data set(default: false)
                                                 150,    // maximum number of iterations(default: 100)
                                                 false,  // generate movie
                                                 true    // motion estimation parameters in a text file
                                                 );
    ResultFileName = docFMR.FileNameOfPreprocessdFMR;
    docFMR.Close();
    docFMR = bvqx.OpenDocument(ResultFileName);

    // High-pass filtering (note: BV first applies linear trend removal [LTR])
    docFMR.TemporalHighPassFilterGLMFourier(6);
    ResultFileName = docFMR.FileNameOfPreprocessdFMR;
    docFMR.Close();
    docFMR = bvqx.OpenDocument(ResultFileName);

    // Temporal smoothing
    docFMR.TemporalGaussianSmoothing(2, "TR");
    ResultFileName = docFMR.FileNameOfPreprocessdFMR;
    docFMR.Close();
    docFMR = bvqx.OpenDocument(ResultFileName);

    bvqx.PrintToLog(InFmrPath + " is done.");
};

bvqx.PrintToLog("Finished.");