mp2rage - Create MP2RAGE image

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The complex image data acquired by an inversion recovery MR scan is often represented in the form of its modulus, as the real and imaginary images can suffer from the effect of magnetic field inhomogeneities which generate phase shifts between them. However, if additional information can be obtained to correct this phase shift, then the real image can be calculated. One method to achieve this involves acquiring complex images with two inversion times, fro mwhich the phase can be corrected and a real inversion recovery image obtained. This method has the additional benefit of performing a first order correction of B1 inhomogeneities, as the same inhomogeneities are present in both inversion times images and so cancel out. One algorithm to do this has been published as "MP2RAGE".

mp2rage is a command line program to peform this analysis. Options may be entered on the same command line; if the minium set of options are not present then the program will prompt for the relavant missing values. The phase maps should be scaled to radians, either as floating point pixels or by using appropriate scaling and offset values in the Analyze header. 

mp2rage [-ii] [-zz] [-d] [input_modulus_filename_TI1] [input_phasemap_filename_TI1] [input_modulus_filename_TI2] [input_phasemap_filename_TI2] [output_MP2RAGE_filename]
-ii
The input files may be arranged with each TI in a seperate image file, or the TIs may be interleaved in the same image file. The default is to assume that the different TIs are in seperate files, hence requiring filenames for both TIs. However, if this option is specified, then it is assumed that the input modulus and phase image files contain both TIs interleaved in the same image file.
-zz
Depending on the MR scanner configuration, the phase map may have been masked already, with the background intensity values set to zero. If conversion to radians is to be obtained by using the scaling factor and offset values in the Analyze header then the background may be converted to -π. By specifying this option, zero intensities in the input phase map are preserved regardless of the offset value in the Analyze header. However, the same will occur for true zero phase values inside the object.
-d
Displays additional diagnostic output.
input_modulus_filename_TI1
The filename of the Analyze file containing the input modulus images acquired at the first inversion time. Filenames may contain either the .img or .hdr extension, or neither. If the input_modulus_filename_TI1 is not specified on the command line then the program will prompt for a filename.
input_phasemap_filename_TI1
The filename of the Analyze file containing the input phase map acquired at the first inversion time.
input_modulus_filename_TI2
The filename of the Analyze file containing the input modulus images acquired at the second inversion time. Filenames may contain either the .img or .hdr extension, or neither.
input_phasemap_filename_TI2
The filename of the Analyze file containing the input phase map acquired at the second inversion time.
output_MP2RAGE_filename
Analyze file which will contain the calculated MP2RAGE image. If this is not specificed, then the output filename will default to the first input modulus filename appended with "mp2rage".

References