% Set the default values for the FieldMap toolbox
%
% FORMAT pm_defaults_Trio_al_64
%_______________________________________________________________________
%
% This file is intended for use with the Siemens fieldmap sequence
% on the Trio scanner at the AMRIG/FIL and the al_128 EPI sequences with
% PE blips=-1:
% 
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging

% Chloe Hutton and Jesper Andersson
% $Id: pm_defaults_Trio_al_64.m 7211 2017-11-13 10:38:15Z guillaume $

global pm_def

% Defaults for creating field map. (See pm_make_fieldmap.m and 
%                                   FieldMap.man for more info.)
%=======================================================================
pm_def.INPUT_DATA_FORMAT = 'PM';      % 'RI' = load two real and 
                                      % imaginary image pairs
                                      % 'PM' = load one or two
                                      % phase and magnitude image
                                      % pairs.
pm_def.SHORT_ECHO_TIME = 10.0;        % Short echo time in ms for Trio
pm_def.LONG_ECHO_TIME = 12.46;        % Long echo time in ms for Trio
pm_def.MASKBRAIN = 1;                 % Do brain masking (1 or 0,
                      % 0 for EPI fieldmaps)

% Defaults for unwrapping options. (See pm_make_fieldmap.m and 
%                                   FieldMap.man for more info.)
%=======================================================================
pm_def.UNWRAPPING_METHOD = 'Mark3D';  % Unwrapping options are:
                                      % 'Huttonish', 'Mark3D' or 'Mark2D'
pm_def.FWHM = 10;                     % FWHM of Gaussian filter used to 
                                      % implement weighted smoothing of
                                      % unwrapped maps.
pm_def.PAD = 0;                       % Size of padding kernel if required.
pm_def.WS = 1;                        % Weighted or normal smoothing.

% Flags for brain extraction
%=======================================================================
pm_def.MFLAGS.TEMPLATE = fullfile(spm('Dir'),'toolbox','FieldMap','T1.nii');
pm_def.MFLAGS.FWHM = 5;     % In mm
pm_def.MFLAGS.NERODE = 2;   % In voxels
pm_def.MFLAGS.NDILATE = 4;  % In voxels
pm_def.MFLAGS.THRESH = 0.5;
pm_def.MFLAGS.REG = 0.02;   % A larger value helps segmentation to converge
pm_def.MFLAGS.GRAPHICS = 0; % A larger value helps segmentation to converge

% Defaults for converting field map to voxel displacement map.
%=======================================================================
pm_def.EPI_BASED_FIELDMAPS = 0;         % EPI=1, other=0.
pm_def.K_SPACE_TRAVERSAL_BLIP_DIR = -1; % +ve k-space = 1, -ve = -1.
pm_def.TOTAL_EPI_READOUT_TIME = 18;   % Trio al_mepi_3d 3mm-res EPI: (1+0.125)*64/2*0.5 (Acceleration factor 2 along phase direction)

% Defaults for Unwarping.
%=======================================================================
pm_def.DO_JACOBIAN_MODULATION = 0;    % Do jacobian modulation to adjust 
                                      % for compression or stretching
                                      % No = 0, Yes = 1
                      
                      
