Home > vbmeg > functions > common > morphology > vb_face_extract.m

vb_face_extract

PURPOSE ^

Extract face surface from MRI image

SYNOPSIS ^

function [F, V] = vb_face_extract(imagefile, Radius, step, pmax, Bval, hstep)

DESCRIPTION ^

 Extract face surface from MRI image
  [F, V] = vb_face_extract(imagefile, Radius, step)
  [F, V] = vb_face_extract(imagefile, Radius, step, pmax, Bval, hstep)

 ---- Output
  V  : Face vertex coordinate: (x,y,z)  [Nvertex x 3]
  F  : Triangle patch index [Npatch x 3]
 ---- Input
  imagefile  : MRI Analyze/NIFTI image file name

 ----- Optional input
 Radius = [ -2 2 6 -6]; [mm]
        : Radius of Morfology operation
  R > 0 : dilation
  R < 0 : erosion

 step  : subsampling step size [mm]
 pmax  : Prob. to detrmine Threshold value for face extraction (0.998)
 Bval  : Threshold value for background separation
         This value is automatically determined in the default mode
 hstep : step size to round the value of image intensity
 --------------------------------------------------
 MRI構造画像から顔表面画像の抽出
  V  : 顔表面頂点        face vertex
  F  : その三角面パッチ  patch index

 Masa-aki Sato 2010-10-18
  Image intensity is rounded by deviding 'hstep'
  before making mask to avoid noisy fluctuation
 2011-06-20 taku-y
  [minor] Progress message was added. 

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [F, V] = vb_face_extract(imagefile, Radius, step, pmax, Bval, hstep)
0002 % Extract face surface from MRI image
0003 %  [F, V] = vb_face_extract(imagefile, Radius, step)
0004 %  [F, V] = vb_face_extract(imagefile, Radius, step, pmax, Bval, hstep)
0005 %
0006 % ---- Output
0007 %  V  : Face vertex coordinate: (x,y,z)  [Nvertex x 3]
0008 %  F  : Triangle patch index [Npatch x 3]
0009 % ---- Input
0010 %  imagefile  : MRI Analyze/NIFTI image file name
0011 %
0012 % ----- Optional input
0013 % Radius = [ -2 2 6 -6]; [mm]
0014 %        : Radius of Morfology operation
0015 %  R > 0 : dilation
0016 %  R < 0 : erosion
0017 %
0018 % step  : subsampling step size [mm]
0019 % pmax  : Prob. to detrmine Threshold value for face extraction (0.998)
0020 % Bval  : Threshold value for background separation
0021 %         This value is automatically determined in the default mode
0022 % hstep : step size to round the value of image intensity
0023 % --------------------------------------------------
0024 % MRI構造画像から顔表面画像の抽出
0025 %  V  : 顔表面頂点        face vertex
0026 %  F  : その三角面パッチ  patch index
0027 %
0028 % Masa-aki Sato 2010-10-18
0029 %  Image intensity is rounded by deviding 'hstep'
0030 %  before making mask to avoid noisy fluctuation
0031 % 2011-06-20 taku-y
0032 %  [minor] Progress message was added.
0033 %
0034 % Copyright (C) 2011, ATR All Rights Reserved.
0035 % License : New BSD License(see VBMEG_LICENSE.txt)
0036 
0037 if nargin < 2, Radius = [ -2 2 ]; end;
0038 if nargin < 3, step = 2; end;
0039 if nargin < 4, pmax = 0.998; end;
0040 if nargin < 5, Bval = []; end;
0041 if nargin < 6, hstep = 1; end;
0042 
0043 h = waitbar(0,'Wait for face extraction');
0044 vb_disp_nonl('  0 % processed');
0045 
0046 %
0047 % Load 3D MRI image to analyze_right_hand coordinate
0048 %
0049 % Vdim  : Voxel dimension of Analyze image
0050 % Vsize : Voxel size of Analyze image
0051 % --- Analyze righthand voxel coordinate
0052 % X: Left(1)   -> Right (Vdim(1))
0053 % Y: Back(1)   -> Front (Vdim(2))
0054 % Z: Bottom(1) -> Top   (Vdim(3))
0055 [B, Vdim, Vsize] = vb_load_analyze_to_right(imagefile);
0056 
0057 waitbar(0.1);
0058 for ii=1:15; vb_disp_nonl(sprintf('\b')); end
0059 vb_disp_nonl(' 10 % processed');
0060 
0061 % Calculate background noise threshold value
0062 % by estimating backgound distribution
0063 if isempty(Bval)
0064     [Bval, hstep] = vb_back_threshold(B, pmax);
0065 end
0066 
0067 waitbar(0.2);
0068 for ii=1:15; vb_disp_nonl(sprintf('\b')); end
0069 vb_disp_nonl(' 20 % processed');
0070 
0071 B    = round(B/hstep);
0072 Bval = round(Bval/hstep);
0073 
0074 % 閾値より大きい値を持つボクセルを頭部として抽出
0075 % Make mask image from MRI data
0076 Bmask = vb_image_to_mask(B, Bval, step);
0077 
0078 if vb_matlab_version > 6, Bmask = int8(Bmask); end;
0079 
0080 % Expand Z-axis to avoid top head reaches to image boundary
0081 Zex = ceil(10/step); % 10 mm
0082 [Nx,Ny,Nz]=size(Bmask);
0083 
0084 % vb_disp_nonl(sprintf('\nExpand image'));
0085 
0086 if vb_matlab_version > 6,
0087     B = zeros(Nx,Ny,Nz + Zex, 'int8');
0088     B(1:Nx,1:Ny,1:Nz) = Bmask;
0089 else
0090     B = zeros(Nx,Ny,Nz + Zex);
0091     B(1:Nx,1:Ny,1:Nz) = Bmask;
0092 end
0093 
0094 waitbar(0.4);
0095 for ii=1:15; vb_disp_nonl(sprintf('\b')); end
0096 vb_disp_nonl(' 40 % processed');
0097 
0098 % Apply morphology operations
0099 % Dilation/erosion are done consecutively according to Radius
0100 B = vb_morphology_operation(B, Radius, step);
0101 
0102 waitbar(0.8);
0103 for ii=1:15; vb_disp_nonl(sprintf('\b')); end
0104 vb_disp_nonl(' 80 % processed');
0105 
0106 % face extraction
0107 %  V  : 顔表面頂点        face vertex
0108 %  F  : その三角面パッチ  patch index
0109 
0110 [F, V]  = vb_surf_extract(B, step);
0111 
0112 waitbar(0.95);
0113 for ii=1:15; vb_disp_nonl(sprintf('\b')); end
0114 vb_disp_nonl(' 95 % processed');
0115 
0116 % Change Analyze Left-hand voxcel coordinate to Right-hand SPM (m) coord.
0117 %   Transformation from Analyze to SPM is not changed
0118 %   despite of mask image expansion along Z-axis
0119 %   since SPM is defined in original image
0120 V = vb_analyze_right_to_spm_right(V,Vdim,Vsize);
0121 
0122 close(h);
0123 drawnow;

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