source: plugins/map_plugins/t2.m @ 78

Last change on this file since 78 was 78, checked in by tjniskan, 10 years ago
  • Moved fMRI related plugins to their own subdirectories
  • Created a subdirectory for map calculation plugins and added a few

basic plugins for those. At the moment these plugins do not support
masking etc. and I didn't test them at all so be cautious...

  • Made a minor memory optimation to an2_readfid.m
  • Fixed a few issues in files related updating via SVN
  • Disabled some annoying warnings that Matlab R2008a and higher

generate from uitree and uitreenode functions inan2_juigetfiles.m

  • Coded something minor to an2_maptool.m. This is still stub and does

not work at all. Please don't try to use it.

  • Fixed a bug that caused Aedes to fail without generating an error

when reading VNMR FID-files that don't have PROCPAR in the same folder.

  • Fixed a javaFrame -warning (with R2008a and higher) in aedes.m

M an2_revision.m
M an2_data_read.m
M an2_maptool.m
M aedes.m
D plugins/calculate_t2_map.m
D plugins/calculate_t1r_map.m
D plugins/basic_fmri_analysis.m
D plugins/resting_state_fc.m
A plugins/fmri_plugins
A plugins/fmri_plugins/basic_fmri_analysis.m
A plugins/fmri_plugins/resting_state_fc.m
A plugins/map_plugins
A plugins/map_plugins/t2.m
A plugins/map_plugins/t1_3_parameter_fit.m
A plugins/map_plugins/t1_saturation_recovery.m
A plugins/map_plugins/t1_rho.m
A plugins/map_plugins/t2_rho.m
A plugins/map_plugins/t1_inversion_recovery.m
M an2_readfid.m
M an2_check_updates.m
M an2_juigetfiles.m
M an2_update.m

File size: 1.9 KB
Line 
1function t2(DATA,ROI,AddInfo)
2% This Aedes plugin calculates T2 map
3
4% This function is a part of Aedes - A graphical tool for analyzing
5% medical images
6%
7% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
8%
9% Department of Physics, Department of Neurobiology
10% University of Kuopio, FINLAND
11%
12% This program may be used under the terms of the GNU General Public
13% License version 2.0 as published by the Free Software Foundation
14% and appearing in the file LICENSE.TXT included in the packaging of
15% this program.
16%
17% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
18% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
19
20fit_vals = [];
21if AddInfo.isDataMixed
22  nSlices = length(DATA);
23  fit_vals = [];
24else
25  nSlices = size(DATA{1}.FTDATA,3);
26 
27  % Try to get fit values from PROCPAR
28  if isfield(DATA{1},'PROCPAR') && ~isempty(DATA{1}.PROCPAR) && ...
29        isfield(DATA{1}.PROCPAR,'ne')
30   
31    if DATA{1}.PROCPAR.ne==8
32        fit_vals=cumsum(ones(1,6)*DATA{1}.PROCPAR.te).*1000;
33        nSlices = 6;
34        DATA{1}.FTDATA = DATA{1}.FTDATA(:,:,1:6);
35    else
36        fit_vals=DATA{1}.PROCPAR.te.*1000;
37    end
38  end
39end
40
41
42resp = an2_inputdlg('Type TE values','Input dialog',...
43  {mat2str(fit_vals)});
44if isempty(resp)
45  return
46else
47  resp=resp{1};
48  fit_vals = str2num(resp);
49end
50
51% Prompt for file name
52[fname,fpath,findex]=uiputfile({'*.t2;*.T2;*.s2;*.S2',...
53                    'T2-Files (*.t2, *.s2)';...
54                    '*.*','All Files (*.*)'},...
55                               'Save T2-file',[DATA{1}.HDR.fpath, ...
56                    't2_map']);
57if isequal(fname,0) || isequal(fpath,0)
58  return
59end
60
61% Calculate the map
62[fp,fn,fe]=fileparts([fpath,fname]);
63try
64  an2_fitmaps(DATA,'t2',fit_vals,'FileName',[fp,filesep,fn]);
65catch
66  errordlg({'Could not calculate T2 maps. The following error was returned',...
67           '',lasterr},'modal')
68end
69
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