Prepare Fieldmap

prepare_fieldmap is a command line tool for converting scanner saved fieldmap to units of radians/sec. As of now it only works with fieldmap saved with Siemens sequence 'gre_field_mapping'. prepare_fieldmap can be run from command line using following syntax:

Windows:
prepare_fieldmap.exe --in=<scanner_saved_fieldmap> --out=<output_filename> [options]

Linux and Mac:
prepare_fieldmap.sh --in=<scanner_saved_fieldmap> --out=<output_filename> [options]

where, <scanner_saved_fieldmap> is the input filename of scanner saved 
  fieldmap in NIfTI format (.nii or .nii.gz), <output_filename> is the
  output filename.

Optional Arguments:
--ref-vol=<reference_volume>
      <reference_volume> is filename of reference volume which can be
      used to estimate a mask of head to extrapolate fieldmap outside
      the mask. This can be the 3D/4D magnitude image used for fieldmap
      estimation and saved by the scanner OR it can be a manually drawn
      mask. It is used to replace inaccurate fieldmap estimation by
      realistic values estimated based on smoothness of fieldmap. No
      values inside the mask is modified.

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Required runtime packages

• Matlab MCR 2012a for your platform.

• Only for Windows: Visual C++ runtime package

Prepare Fieldmap Tool

• Windows 64 bit

• Linux 64 bit
• Mac 64 bit

Authors: Chitresh Bhushan