-
Notifications
You must be signed in to change notification settings - Fork 0
/
ctf_mri2brainstorm.m
109 lines (85 loc) · 3.85 KB
/
ctf_mri2brainstorm.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
function [Comment, Cube, PCS, Segment, Voxsize] = ctf_mri2brainstorm(mri)
% ctf_mri2brainstorm - create subjectimage variables from ctf .mri file
%
% [Comment, Cube, PCS, Segment, Voxsize] = ctf_mri2brainstorm(mri)
%
% The purpose of this function is to convert a CTF .mri volume into
% brainstorm subjectimage variables. The returned variables can be saved
% into *_subjectimage.mat using the matlab save command.
%
% The mri struct input for this function is returned by ctf_read_mri.
%
% <>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> %
% < > %
% < DISCLAIMER: > %
% < > %
% < THIS PROGRAM IS INTENDED FOR RESEARCH PURPOSES ONLY. > %
% < THIS PROGRAM IS IN NO WAY INTENDED FOR CLINICAL OR > %
% < OFFICIAL USE. > %
% < > %
% <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<> %
%
% $Revision: 1.1 $ $Date: 2009-01-30 03:49:27 $
% Copyright (C) 2004 Darren L. Weber
%
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 2
% of the License, or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
% History: 05/2004, Darren.Weber_at_radiology.ucsf.edu
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ver = '[$Revision: 1.1 $]';
fprintf('\nCTF_MRI2BRAINSTORM [v%s]\n',ver(12:16)); tic;
Comment = 'CTF';
% CTF .mri files are always 256x256x256 voxels, 1mm^3
Voxsize = [1 1 1];
% Initialize the Segment variable; As of 05/2004, the codes for this field
% are not clear to me. They are defined in David Shattuck's
% BrainSuite MRI processing software.
Segment = [];
% the ctf mri.img orientation is
% +X right
% +Y posterior
% +Z inferior
% the brainstorm Cube orientation is
% +X right
% +Y anterior
% +Z superior
temp = mri.img;
temp = flipdim(temp,2);
Cube = flipdim(temp,3);
% -----
% Patient Coordinate System
PCS.Comment = 'CTF';
PCS.R = zeros(3,3); % not clear how to get this
PCS.t = zeros(3,1); % not clear how to get this
PCS.PCSFiducial = zeros(3,4); % not clear how to get this
PCS.CubeFiducial = zeros(3,4);
PCS.CubeFiducial(1,1) = mri.hdr.HeadModel_Info.Nasion_Sag;
PCS.CubeFiducial(2,1) = 256 - mri.hdr.HeadModel_Info.Nasion_Cor;
PCS.CubeFiducial(3,1) = 256 - mri.hdr.HeadModel_Info.Nasion_Axi;
PCS.CubeFiducial(1,2) = mri.hdr.HeadModel_Info.LeftEar_Sag;
PCS.CubeFiducial(2,2) = 256 - mri.hdr.HeadModel_Info.LeftEar_Cor;
PCS.CubeFiducial(3,2) = 256 - mri.hdr.HeadModel_Info.LeftEar_Axi;
PCS.CubeFiducial(1,3) = mri.hdr.HeadModel_Info.RightEar_Sag;
PCS.CubeFiducial(2,3) = 256 - mri.hdr.HeadModel_Info.RightEar_Cor;
PCS.CubeFiducial(3,3) = 256 - mri.hdr.HeadModel_Info.RightEar_Axi;
% set the origin at half way between the left and right ears
PCS.CubeFiducial(1,4) = PCS.CubeFiducial(1,3) - PCS.CubeFiducial(1,2);
PCS.CubeFiducial(2,4) = PCS.CubeFiducial(2,3) - PCS.CubeFiducial(2,2);
PCS.CubeFiducial(3,4) = PCS.CubeFiducial(3,2) + (PCS.CubeFiducial(3,3) - PCS.CubeFiducial(3,2));
PCS.FiducialName = {'NAS' 'LPA' 'RPA' 'Origin'};
PCS.PERM = [1 2 3]; % not sure what this is
PCS.FLP = [1 1 0]; % not sure what this is
t=toc; fprintf('...done (%5.2f sec).\n\n',t);
return