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Initial commit

Initial commit of r219-hotfix version of aedes.
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mjnissi committed Dec 11, 2019
1 parent c9d493d commit d18b18afe5b3a207ccf83a239aea3be599584f11
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  1. BIN about_aedes.png
  2. +11,187 −0 aedes.m
  3. +60 −0 aedes_calc_wait.m
  4. BIN aedes_cdata.mat
  5. +52 −0 aedes_cellsprintf.m
  6. +88 −0 aedes_cellwrite.m
  7. +64 −0 aedes_check_file_exist.m
  8. +112 −0 aedes_check_updates.m
  9. +149 −0 aedes_copy_roi.m
  10. +542 −0 aedes_createmosaic.m
  11. +670 −0 aedes_data_read.m
  12. +60 −0 aedes_dialoglocation.m
  13. +467 −0 aedes_editstack.m
  14. +61 −0 aedes_errordump.m
  15. +1,394 −0 aedes_export_gui.m
  16. +978 −0 aedes_fitmaps.m
  17. +369 −0 aedes_fmri_analysis.m
  18. +900 −0 aedes_fmri_gui.m
  19. +108 −0 aedes_fmri_smooth.m
  20. +122 −0 aedes_getcurrentmonitor.m
  21. +196 −0 aedes_getdataformat.m
  22. +98 −0 aedes_getfilefilter.m
  23. +52 −0 aedes_getmatlabversion.m
  24. +139 −0 aedes_gui_defaults.m
  25. +1,040 −0 aedes_headerbrowser.m
  26. +190 −0 aedes_helpabout.m
  27. +160 −0 aedes_inputdlg.m
  28. +37 −0 aedes_iseven.m
  29. +1,448 −0 aedes_juigetfiles.m
  30. +54 −0 aedes_killfigs.m
  31. BIN aedes_logo.png
  32. +479 −0 aedes_maptool.m
  33. +765 −0 aedes_read_nifti.m
  34. +1,057 −0 aedes_readbruker.m
  35. +554 −0 aedes_readctdata.m
  36. +207 −0 aedes_readfdf.m
  37. +1,865 −0 aedes_readfid.m
  38. +512 −0 aedes_readfidprefs.m
  39. +229 −0 aedes_readjcamp.m
  40. +196 −0 aedes_readphasetable.m
  41. +176 −0 aedes_readprocpar.m
  42. +215 −0 aedes_readswiftsgl.m
  43. +1,410 −0 aedes_readvnmr.m
  44. +214 −0 aedes_res2table.m
  45. +1,160 −0 aedes_resviewer.m
  46. +95 −0 aedes_revision.m
  47. +389 −0 aedes_roi_copy_gui.m
  48. +250 −0 aedes_roi_stats.m
  49. +112 −0 aedes_roifill.m
  50. +86 −0 aedes_rot3d.m
  51. +310 −0 aedes_rotateflip.m
  52. +332 −0 aedes_saveres.m
  53. +246 −0 aedes_smisread.m
  54. +169 −0 aedes_smiswrite.m
  55. +65 −0 aedes_tdist.m
  56. +55 −0 aedes_trendest.m
  57. +292 −0 aedes_update.m
  58. +44 −0 aedes_wbar.m
  59. +1,061 −0 aedes_write_nifti.m
  60. +29 −0 bruker_recon/example_recon.m
  61. BIN icons/Folder.gif
  62. BIN icons/MyComputer.gif
  63. BIN icons/arrowleft.gif
  64. BIN icons/arrowright.gif
  65. BIN icons/arrowup.gif
  66. BIN icons/driveicon.gif
  67. BIN icons/floppyicon.gif
  68. BIN icons/new.gif
  69. BIN icons/openfoldericon.gif
  70. BIN icons/x_office_spreadsheet.png
  71. +343 −0 license.txt
  72. +72 −0 misclib/addicon.m
  73. +150 −0 misclib/dcm_info.m
  74. +120 −0 misclib/fdf2nifti.m
  75. +67 −0 misclib/filter_fmri_data.m
  76. +302 −0 misclib/fmri_blob_overlay.m
  77. +79 −0 misclib/fmri_corr.m
  78. +127 −0 misclib/fmri_filter.m
  79. +57 −0 misclib/fmri_global_norm.m
  80. +158 −0 misclib/fmri_spm_volumes.m
  81. +38 −0 misclib/linebroad.m
  82. +108 −0 misclib/makelcmraw.m
  83. +169 −0 misclib/nifti3dto4d.m
  84. +101 −0 misclib/nifti4dto3d.m
  85. +81 −0 misclib/pcorr.m
  86. +42 −0 misclib/shiftind.m
  87. +103 −0 misclib/spectrsum.m
  88. +170 −0 plugins/brain_masking.m
  89. +225 −0 plugins/calc_asl_cbf.m
  90. +114 −0 plugins/calculate_snr.m
  91. +282 −0 plugins/copy_data_to_workspace.m
  92. +347 −0 plugins/fat_analysis.m
  93. +415 −0 plugins/fmri_plugins/correlation_mapping.m
  94. +20 −0 plugins/fmri_plugins/fmri_analysis.m
  95. +80 −0 plugins/fmri_plugins/motion_estimate.m
  96. +96 −0 plugins/fmri_plugins/network_analysis.m
  97. +417 −0 plugins/fmri_plugins/old_fmri_analysis.m
  98. +60 −0 plugins/fmri_plugins/resting_state_fc.m
  99. +89 −0 plugins/fmri_plugins/roi_averages.m
  100. +92 −0 plugins/histograms.m
  101. +54 −0 plugins/map_plugins/t1_3_parameter_fit.m
  102. +65 −0 plugins/map_plugins/t1_inversion_recovery.m
  103. +60 −0 plugins/map_plugins/t1_rho.m
  104. +54 −0 plugins/map_plugins/t1_saturation_recovery.m
  105. +69 −0 plugins/map_plugins/t2.m
  106. +60 −0 plugins/map_plugins/t2_rho.m
  107. +27 −0 plugins/open_in_imtool.m
  108. +49 −0 plugins/plot_profile.m
  109. +67 −0 plugins/save_overlay_as_roi.m
  110. +101 −0 plugins/save_roi_as_mask.m
  111. +146 −0 plugins/take_snapshot.m
  112. +118 −0 plugins/view_kspace.m
  113. +55 −0 plugins/write_difference_images.m
  114. +64 −0 startup.m
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  185. +6 −0 tablib/isis_new.tab
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  199. +9 −0 tablib/table_steam9T
  200. +29 −0 vnmr_recon/cine_recon.m
  201. +351 −0 vnmr_recon/epi_recon.m
  202. +19 −0 vnmr_recon/mge3d_recon.m
BIN +76.4 KB about_aedes.png
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11,187 aedes.m

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@@ -0,0 +1,60 @@
function [h,txh] = aedes_calc_wait(str)
% AEDES_CALC_WAIT - Wait message box
%
% Synopsis:
% [h,txh] = aedes_calc_wait(str)
%
% Description:
% Displays wait message box with text 'str'. Output argument 'h' is
% handle to message box and 'txh' is handle to text string.
%
% Examples:
% [h,txh] = aedes_calc_wait('Demo');
% pause(1)
% set(txh,'String','Almost ready.');
% pause(1)
% delete(h)
%
% See also:
% AEDES_WBAR, AEDES

% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
%
% Special Thanks to Perttu Ranta-aho for this marvelous piece of code...
% :-)

h = msgbox(str,'Processing...','help');

% - Replace 'OK'-button with text 'Wait...' -
txh = findall(findobj(h,'type','axes'),'tag','MessageBox');
set(txh,'Fontsize',8);
btn_h = findobj(h,'style','pushbutton');
set(btn_h,'units','normal')
pos = get(btn_h,'position');
set(btn_h,...
'String','Please wait...',...
'Style','Text',...
'position',[0 pos(2) 1 pos(4)], ...
'Fontsize',12)

% - Set pointer -
set(h,'Pointer','watch','Units','normal');

% - Commit changes -
set(h,'visible','on')
drawnow

BIN +75.2 KB aedes_cdata.mat
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@@ -0,0 +1,52 @@
function C = aedes_cellsprintf(form_str,s)
% AEDES_CELLSPRINTF - CELLSTR with SPRINTF formalism
%
%
% Synopsis:
%
% Description:
%
% Examples:
%
% See also:
% CELLSTR, SPRINTF

% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.


%% - Check input arguments -
if nargin<1
error('Too few input arguments')
elseif nargin<2
error('Second input argument not defined')
end

if ndims(s)~=2, error('S must be 2-D.'); end


if isempty(s)
C = {''};
end

C = cell(size(s));
for ii=1:size(s,1)
for jj=1:size(s,2)
C{ii,jj} = sprintf(form_str,s(ii,jj));
end
end


@@ -0,0 +1,88 @@
function [done,msg] = aedes_cellwrite(incell,filename,varargin)
% AEDES_CELLWRITE - Write cell array to a text file
%
%
% Synopsis:
% [done,msg] = aedes_cellwrite(incell,filename,varargin)
%
% Description:
%
% Examples:
%
% See also:
% AEDES

% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.



% Defaults
done = false;
delim = ';';

% Check input arguments
if nargin<2
error('Too few input arguments')
elseif ~iscell(incell)
error('First input argument must be a cell array')
elseif ~ischar(filename)
error('Filename must be of class char')
end

% Parse Input arguments
for ii=1:2:length(varargin)
switch varargin{ii}
case 'delimitter'
if strcmpi(varargin{ii+1},'tab')
delim = '\t';
elseif strcmpi(varargin{ii+1},'space')
delim = ' ';
else
delim=varargin{ii+1};
end
otherwise
msg = sprintf('Unknown parameter "%s"!',varargin{ii});
return
end
end

% Open file for writing
fid = fopen(filename,'w');
if fid<0
msg = sprintf('Could not open file "%s" for writing',filename);
return
end

nRows = size(incell,1);
nCols = size(incell,2);

% Write cell to file
for ii=1:nRows
for kk=1:nCols
fprintf(fid,['%s',delim],incell{ii,kk});
end
fprintf(fid,'\r\n');
end

% Close file
fclose(fid);

% All went well...
done=true;
msg='';

% - EOF -
@@ -0,0 +1,64 @@
function ind = aedes_check_file_exist(fnames,fpath)
% AEDES_CHECK_FILE_EXIST - Check if files exist in a specified directory
%
%
% Synopsis:
%
% Description:
%
% Examples:
%
% See also:
%

% This function is a part of Aedes 2.0 - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.


ind=[];

%% Check input arguments
if nargin<2
error('Too few input arguments!');
elseif nargin>2
error('Too many input erguments!')
end

if ~iscell(fnames)
fnames={fnames};
end

%% Get files in the specified directory
if ~isdir(fpath)
error('Directory "%s" does not exist!',fpath)
end
d=dir(fpath);
dir_files={d(~[d(:).isdir]).name};

if isempty(dir_files)
ind=false(size(fnames));
return
end

%% Check if any of the files exist
if ~isunix % Check file names, in windows ignore case
ind=ismember(lower(fnames),lower(dir_files));
else
ind=ismember(fnames,dir_files);
end

return
% - EOF -
@@ -0,0 +1,112 @@
function [isUpdateAvailable,HeadRev,WorkingCopyRev,error_msg]=aedes_check_updates()
% AEDES_CHECK_UPDATES - Check if Aedes updates are available
%
% Synopsis:
% [isUpdateAvailable,HeadRev,WorkingCopyRev] = aedes_check_updates()
%
% Description:
% Checks if there are updates available for Aedes. The
% "isUpdateAvailable" output argument is true if the head revision number
% in SVN repository is larger than working copy revision. If the
% "HeadRev" output argument is -1, there is a problem with the network.
% If "HeadRev" is empty, there is a problem running SVN commands.
%
% Examples:
%
%
% See also:
% AEDES, AEDES_UPDATE

% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.



isUpdateAvailable = false;
HeadRev = [];
error_msg = '';

% Get current revision and repository URL
[rev,repo,workingcopy] = aedes_revision;
if isempty(repo)
WorkingCopyRev = rev;
return
end
WorkingCopyRev = rev;

% Get head repository revision
[HeadRev,msg]=l_GetHeadRevision(repo);
if isempty(HeadRev)
% Something wrong with running SVN commands. Perhaps SVN is not
% installed? Network problems?
error_msg = msg;
else
if rev<HeadRev
isUpdateAvailable = true;
end
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Get Head Repository Revision
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [HeadRev,msg]=l_GetHeadRevision(repo_url)

HeadRev = [];
msg = '';

% Try to determine the head revision in svn
if isunix
% Unix/Linux
[s,w] = unix(['svn info ',repo_url]);
if s~=0
msg=w;
return
end
elseif ispc
% Windows
[s,w] = dos(['svn info ',repo_url]);
if s~=0
msg=w;
return
end
else
% Mac OS X
[s,w] = unix(['svn info ',repo_url]);
if s~=0
msg=w;
return
end
end

% Scan the lines from the output
C=textscan(w,'%s','delimiter','\n');
if ~isempty(C)
C=C{:};
else
return
end

% Get revision line
rev_ind = find(strncmpi(C,'Revision:',4));
if ~isempty(rev_ind)
rev_str = C{rev_ind};
else
return
end
HeadRev=str2num(rev_str(11:end));


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