SEPIA header¶

To obtain a frequency shifted map or magnetic susceptibility map with correct units, it is important to inform the corresponding algorithm(s) with information including the main magnetic field strength (B0) of the scanner, the main magnetic field direction with respect to the field of view (FOV) and the echo times (TEs) used in the acquisition. Unfortunately, such information may not be (directly) available in the NIfTI header after the DICOM conversion. As a result, if you are using NIfTI files with SEPIA, you have to also supply a special header file alongside with your multi-echo GRE data.

SEPIA requires a specific MAT-file (.mat) that stores some header information of the input data. The following example shows the variables (case-sensitive) that must be stored in the header file:

B0 = 3;                 % magnetic field strength, in Tesla
B0_dir = [0;0;1];       % main magnetic field direction, [x,y,z]
CF = 3*42.58*1e6;       % imaging frequency, in Hz (B0*gyromagnetic_ratio*1e6)
TE = [te1,te2,te3,te4]; % echo time for each GRE image, in second
delta_TE = te2-te1;     % echo spacing, in second
matrixSize = [64,64,64] % image matrix size
voxelSize = [1,1,1]     % spatial resolution of the data, in mm

You can create this file manually in Matlab. Alternatively, you can use the Utility standalone application to generate the file. Please visit the corresponding wiki page for more information about how to generate the header file.