= 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.
      Estimated mask is also saved to disk with file name as
      <output_filename>.mask.nii.gz .
}}}
=== Download Links ===
==== Required runtime packages ====
 * [[http://www.mathworks.com/products/compiler/mcr/%20|Matlab MCR 2012a]] for your platform.
 * Only for Windows: [[http://www.microsoft.com/en-us/download/details.aspx?id=14632|Visual C++ runtime package]]

==== Prepare Fieldmap Tool ====
 * [[http://neuroimage.usc.edu/resources/prepare_fieldmap_win64.zip|Windows 64 bit]]
 * Linux 64 bit
 * Mac 64 bit

'''Authors:''' [[Members|Chitresh Bhushan]]

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