= 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.
}}}

=== 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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