Hi

I want to analyze the fNIRs equipment ISS imagent Boxy generated log files that give oxy and deoxy hemoglobin measures. I recorded 24 channels of data: 12 from prefrontal cortex and 12 from motor cortex. I want to know the brain circuitry for the decision-making cognitive task related changes compared to the baseline. Could you please suggest an open source platform for analyzing this type of data. I tried using NIRS-SPM but the ISS Imagent log files cannot get converted to spm.mat files. The files are not loading. 

Is there any other technique that you are aware of? 

Please let me know.
Thanks
Amrita

Hi
If you want to use of spm, you should generate log file like structure of .mat.
In my idea find the structure of .mat.

I tried using NIRS_Data_Conversion utility but it gets stuck at load file.

Originally posted by Amrita Pal : Hi,
Your code is not correct. 

Here is the code that comes with the NIRS_SPM software.
function varargout = NIRS_Data_Conversion(varargin)
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @NIRS_Data_Conversion_OpeningFcn, ...
'gui_OutputFcn', @NIRS_Data_Conversion_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
function NIRS_Data_Conversion_OpeningFcn(hObject, eventdata, handles, varargin)
handles.output = hObject;
%%%% initilization (OXYMON MK III)
set(handles.Pop_SystemConfig,'value',1);
set(handles.checkbox_system, 'value',1);
set(handles.checkbox_manual, 'value',0);
set(handles.edit_nch, 'enable', 'off', 'string', '24');
set(handles.edit_fs, 'enable', 'on');
set(handles.edit_distance, 'enable', 'on', 'string', '3.5');
set(handles.edit_wavelength, 'enable', 'on', 'string', '856 781');
set(handles.edit_DPF, 'enable', 'on', 'string', '4');
set(handles.checkbox_DPF_correction, 'value', 1, 'enable', 'on');
set(handles.push_load_param, 'enable', 'off');
set(handles.edit_extinc, 'string', ' ', 'enable', 'off');
set(handles.text9, 'enable', 'off');
set(handles.text10, 'enable', 'off');
guidata(hObject, handles);
% --- Outputs from this function are returned to the command line.
function varargout = NIRS_Data_Conversion_OutputFcn(hObject, eventdata, handles)
varargout{1} = handles.output;
% --- Executes on button press in push_nirfile.
function push_nirfile_Callback(hObject, eventdata, handles)
h = get(handles.Pop_SystemConfig, 'value');
h2 = get(handles.checkbox_system, 'value');
if h2 == 1 %%% system configuration
if h == 1 %%% OXYMON MK III
[filen, pathn] = uigetfile('*.nir; *.csv; *.xls', 'Select a data file measured by Oxymon MKIII system');
path_file_n = [pathn filen];
if filen(1) == 0 || pathn(1) == 0
return;
end
[tmp1, tmp2, ext] = fileparts(path_file_n);
if strcmpi(ext, '.nir') == 1 % optical density changes
fs = str2num(get(handles.edit_fs, 'string'));
dist = str2num(get(handles.edit_distance, 'string'));
wavelength = str2num(get(handles.edit_wavelength, 'string'));
rwavelength = round(wavelength);
DPF = str2num(get(handles.edit_DPF, 'string'));
if isempty(fs) == 1 || isempty(dist) == 1 || isempty(wavelength) == 1 || isempty(DPF) == 1
errordlg('Please enter all required parameter values.');
return;
end
flag_DPF_correction = get(handles.checkbox_DPF_correction, 'value');
if flag_DPF_correction == 1
if (sum(rwavelength >= 704) + sum(rwavelength <= 972)) ~= 4
errordlg('NIRS-SPM allows the wavelength range of DPF correction between 704nm and 972nm');
flag_DPF_correction = 0;
set(handles.checkbox_DPF_correction, 'value', 0);
return;
end
end
nirs_data = nir_to_mat(path_file_n, fs, dist, rwavelength, DPF, flag_DPF_correction);
nirs_data.wavelength = wavelength;
nirs_data.distance = dist;
nirs_data.DPF = DPF;
if flag_DPF_correction == 1
nirs_data.DPF_correction = 'Charite correction';
elseif flag_DPF_correction == 0
nirs_data.DPF_correction = 'none';
end
elseif strcmpi(ext, '.csv') == 1 || strcmpi(ext, '.txt') == 1
fid = fopen(path_file_n);
while 1
tline = fgetl(fid);
nindex = find(tline == ',');
tline(nindex) = ' ';
[token, remain] = strtok(tline);
switch token
case 'Export'
if isempty(strfind(remain, 'sample rate')) == 0
idx1 = strfind(remain, 'rate');
idx2 = strfind(remain, 'Hz');
fs = str2num(remain(idx1+5:idx2-1));
end
case 'Column'
oxy_col = [];
deoxy_col = [];
while 1
tline = fgetl(fid);
nindex = find(tline == ',');
tline(nindex) = ' ';
[token, remain] = strtok(tline);
if isempty(strfind(remain, 'Event')) == 0, break, end,
if isempty(strfind(remain, 'O2Hb')) == 0
oxy_col = [oxy_col str2num(token)];
elseif isempty(strfind(remain, 'HHb')) == 0
deoxy_col = [deoxy_col str2num(token)];
end
end
tmp = fgetl(fid); % blank line;
tmp = fgetl(fid); % column number
count = 1;
while 1 % reading the data
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
tline(nindex) = ' ';
tmp = str2num(tline);
oxyData(count,:) = tmp(oxy_col);
dxyData(count,:) = tmp(deoxy_col);
count = count + 1;
end
break;
end
end
nirs_data.oxyData = oxyData;
nirs_data.dxyData = dxyData;
nirs_data.fs = fs;
elseif strcmpi(ext, '.xls') == 1
fs = str2num(get(handles.edit_fs, 'string'));
tmp_data = xlsread(path_file_n, -1);
nirs_data.oxyData = tmp_data(:,1:3:end);
nirs_data.dxyData = tmp_data(:,2:3:end);
nirs_data.fs = fs;
end
prompt = {'Please enter the channels which will be used for further analysis.'};
dlg_title = 'Input dialog';
num_lines = 1;
tmp = 1:size(nirs_data.oxyData,2);
def = {num2str(tmp)};
answer = inputdlg(prompt, dlg_title, num_lines, def);
nirs_data.oxyData = nirs_data.oxyData(:,str2num(answer{1}));
nirs_data.dxyData = nirs_data.dxyData(:,str2num(answer{1}));
nirs_data.nch = size(nirs_data.oxyData,2);
elseif h == 2 %%% Hitachi ETG4000 (1set)
[filen, pathn] = uigetfile('*.csv','Select File to Convert');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
h_wait = waitbar(0, 'Please wait... ');
while 1
tline = fgetl(fid);
% update, May 6, 2012
if isempty(strfind(tline, 'Wave Length')) == 0 %reading wave lengths on each probe
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_wavelength = tline(nindex(1)+1:end);
error_index = strfind(txt_wavelength, '..');
txt_wavelength(error_index) = [];
remain = txt_wavelength;
ndata = 0;
wav_mat = [];
while 1
[token remain] = strtok(remain);
if isempty(token) == 1
break;
end
sind = find(token == '(')+1;
eind = find(token == ')')-1;
wav_mat = [wav_mat str2num(token(sind:eind))];
ndata = ndata + 1;
end
waitbar(1/3, h_wait, 'Data reading (1/3) has been completed.');
elseif isempty(strfind(tline, 'Sampling Period[s]')) == 0 % reading sampling period
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_fs = tline(nindex(1)+1:end);
try
fs = 1./mean(str2num(txt_fs));
catch
error_index = strfind(txt_fs, '..');
txt_fs(error_index) = [];
fs = 1./mean(str2num(txt_fs));
end
waitbar(2/3, h_wait, 'Data reading (2/3) has been completed.');
elseif isempty(strfind(tline, 'Probe1')) == 0
disp('Reading the data from Probe1 ...');
nindex = find(tline == ',');
txt_probe = tline(nindex(1)+1:end);
index_tmp = find(txt_probe == ',');
txt_probe(index_tmp) = ' ';
[token remain] = strtok(txt_probe);
count = 3;
while isempty(token) ~= 1
[token remain] = strtok(remain);
if strcmp(token, 'Mark') == 1
col_mark = count;
end
if strcmp(token, 'PreScan') == 1
col_prescan = count;
end
count = count + 1;
end
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
try
count = str2num(tline(1:nindex(1)-1));
tline(nindex) = ' ';
try
mes(count, :) = str2num(tline(nindex(1)+1:nindex(ndata+1)-1));
catch
str = tline(nindex(1)+1:nindex(ndata+1)-1);
error_index = strfind(str, '..');
str(error_index) = [];
mes(count, :) = str2num(str);
end
try
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:nindex(col_prescan)-1));
catch
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:end));
end
try
vector_onset(count) = str2num(tline(nindex(col_mark-1)+1:nindex(col_mark)-1));
end
end
end
waitbar(3/3, h_wait,'Data reading (3/3) has been completed.');
disp('Completed.');
break,
end
end
close(h_wait);
fclose(fid);
index_base = find(baseline == 1);
h_wait = waitbar(0, 'Data conversion processing... ');
nch = ndata./2;
for kk = 1:nch
waitbar(kk/(nch-1), h_wait);
[hb_tmp, hbo_tmp, hbt_tmp] = mes2hb(mes(:,2*kk-1:2*kk), [wav_mat(1,2*kk-1) wav_mat(1,2*kk)], [index_base(1) index_base(end)]);
nirs_data.oxyData(:,kk) = hbo_tmp;
nirs_data.dxyData(:,kk) = hb_tmp;
end
close(h_wait);
try
vector_onset(index_base(1):index_base(end)) = [];
nirs_data.vector_onset = vector_onset(:);
end
nirs_data.fs = fs;
nirs_data.nch = nch;
set(handles.edit_fs,'string', num2str(fs));
set(handles.edit_nch, 'string', num2str(nch));
elseif h == 3 %%% Hitachi ETG4000 (2set)
[filen, pathn] = uigetfile('*.csv','Select File (1st set of optodes) to Convert');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
h_wait = waitbar(0, 'Please wait... ');
% start reading data
while 1
tline = fgetl(fid);
% update, May 6, 2012
if isempty(strfind(tline, 'Wave Length')) == 0 %reading wave lengths on each probe
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_wavelength = tline(nindex(1)+1:end);
error_index = strfind(txt_wavelength, '..');
txt_wavelength(error_index) = [];
remain = txt_wavelength;
ndata = 0;
wav_mat = [];
while 1
[token remain] = strtok(remain);
if isempty(token) == 1
break;
end
sind = find(token == '(')+1;
eind = find(token == ')')-1;
wav_mat = [wav_mat str2num(token(sind:eind))];
ndata = ndata + 1;
end
waitbar(1/3, h_wait, 'Data reading (1/3) has been completed.');
elseif isempty(strfind(tline, 'Sampling Period[s]')) == 0 % reading sampling period
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_fs = tline(nindex(1)+1:end);
try
fs = 1./mean(str2num(txt_fs));
catch
error_index = strfind(txt_fs, '..');
txt_fs(error_index) = [];
fs = 1./mean(str2num(txt_fs));
end
waitbar(2/3, h_wait, 'Data reading (2/3) has been completed.');
elseif isempty(strfind(tline, 'Probe1')) == 0
disp('Reading the data from Probe1 ...');
nindex = find(tline == ',');
txt_probe = tline(nindex(1)+1:end);
index_tmp = find(txt_probe == ',');
txt_probe(index_tmp) = ' ';
[token remain] = strtok(txt_probe);
count = 3;
while isempty(token) ~= 1
[token remain] = strtok(remain);
if strcmp(token, 'Mark') == 1
col_mark = count;
end
if strcmp(token, 'PreScan') == 1
col_prescan = count;
end
count = count + 1;
end
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
try
count = str2num(tline(1:nindex(1)-1));
tline(nindex) = ' ';
try
mes(count, :) = str2num(tline(nindex(1)+1:nindex(ndata+1)-1));
catch
str = tline(nindex(1)+1:nindex(ndata+1)-1);
error_index = strfind(str, '..');
str(error_index) = [];
mes(count, :) = str2num(str);
end
try
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:nindex(col_prescan)-1));
catch
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:end));
end
try
vector_onset1(count) = str2num(tline(nindex(col_mark-1)+1:nindex(col_mark)-1));
end
end
end
waitbar(3/3, h_wait,'Data reading (3/3) has been completed.');
disp('Completed.');
break,
end
end
close(h_wait);
fclose(fid);
index_base = find(baseline == 1);
h_wait = waitbar(0, 'Data conversion processing... ');
nch = ndata./2;
for kk = 1:nch
waitbar(kk/(nch-1), h_wait);
[hb_tmp, hbo_tmp, hbt_tmp] = mes2hb(mes(:,2*kk-1:2*kk), [wav_mat(1,2*kk-1) wav_mat(1,2*kk)], [index_base(1) index_base(end)]);
oxyData1(:,kk) = hbo_tmp;
dxyData1(:,kk) = hb_tmp;
end
close(h_wait);
try
vector_onset1(index_base(1):index_base(end)) = [];
end
clear mes
clear baseline
% reading the dataset from the 2nd probe
[filen, pathn] = uigetfile('*.csv','Select File (2nd set of optodes) to Convert');
path_file_n = [pathn filen];
if filen(1) == 0 || pathn(1) == 0
return;
end
fid = fopen(path_file_n);
h_wait = waitbar(0, 'Please wait... ');
while 1
tline = fgetl(fid);
% update, May 6, 2012
if isempty(strfind(tline, 'Wave Length')) == 0 %reading wave lengths on each probe
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_wavelength = tline(nindex(1)+1:end);
error_index = strfind(txt_wavelength, '..');
txt_wavelength(error_index) = [];
remain = txt_wavelength;
ndata = 0;
wav_mat = [];
while 1
[token remain] = strtok(remain);
if isempty(token) == 1
break;
end
sind = find(token == '(')+1;
eind = find(token == ')')-1;
wav_mat = [wav_mat str2num(token(sind:eind))];
ndata = ndata + 1;
end
waitbar(1/2, h_wait, 'Data reading (1/2) has been completed.');
elseif isempty(strfind(tline, 'Probe2')) == 0
disp('Reading the data from Probe2 ...');
nindex = find(tline == ',');
txt_probe = tline(nindex(1)+1:end);
index_tmp = find(txt_probe == ',');
txt_probe(index_tmp) = ' ';
[token remain] = strtok(txt_probe);
count = 3;
while isempty(token) ~= 1
[token remain] = strtok(remain);
if strcmp(token, 'Mark') == 1
col_mark = count;
end
if strcmp(token, 'PreScan') == 1
col_prescan = count;
end
count = count + 1;
end
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
try
count = str2num(tline(1:nindex(1)-1));
tline(nindex) = ' ';
try
mes(count, :) = str2num(tline(nindex(1)+1:nindex(ndata+1)-1));
catch
str = tline(nindex(1)+1:nindex(ndata+1)-1);
error_index = strfind(str, '..');
str(error_index) = [];
mes(count, :) = str2num(str);
end
try
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:nindex(col_prescan)-1));
catch
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:end));
end
try
vector_onset2(count) = str2num(tline(nindex(col_mark-1)+1:nindex(col_mark)-1));
end
end
end
waitbar(2/2, h_wait,'Data reading (2/2) has been completed.');
disp('Completed.');
break,
end
end
close(h_wait);
fclose(fid);
index_base = find(baseline == 1);
h_wait = waitbar(0, 'Data conversion processing... ');
for kk = 1:nch
waitbar(kk/(nch-1), h_wait);
[hb_tmp, hbo_tmp, hbt_tmp] = mes2hb(mes(:,2*kk-1:2*kk), [wav_mat(1,2*kk-1) wav_mat(1,2*kk)], [index_base(1) index_base(end)]);
oxyData2(:,kk) = hbo_tmp;
dxyData2(:,kk) = hb_tmp;
end
close(h_wait);
try
vector_onset2(index_base(1):index_base(end)) = [];
index_onset = find(vector_onset1 ~= vector_onset2);
if isempty(index_onset) == 1
nirs_data.vector_onset = vector_onset1(:);
end
end
nch = size(oxyData1, 2) + size(oxyData2, 2);
nirs_data.oxyData = zeros(size(oxyData1,1), nch);
nirs_data.dxyData = zeros(size(dxyData1,1), nch);
nirs_data.oxyData(:, 1:size(oxyData1,2)) = oxyData1(:,:);
nirs_data.oxyData(:, size(oxyData1,2)+1:end) = oxyData2(:,:);
nirs_data.dxyData(:, 1:size(dxyData1,2)) = dxyData1(:,:);
nirs_data.dxyData(:, size(dxyData1,2)+1:end) = dxyData2(:,:);
nirs_data.fs = fs;
nirs_data.nch = nch;
set(handles.edit_fs,'string', num2str(fs));
set(handles.edit_nch, 'string', num2str(nch));
elseif h == 4 %%% Hitachi ETG-4000 (HbO, HbR, HbT)
%%% read the oxy-hb data
[filen, pathn] = uigetfile('*.csv','Select the OxyHb (HbO) file');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
disp('Loading the OxyHb data starts...');
while 1
tline = fgetl(fid);
if isempty(strfind(tline, 'Sampling Period[s]')) == 0
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_fs = tline(nindex(1)+1:end);
fs = 1./mean(str2num(txt_fs));
end
if isempty(strfind(tline, 'Data')) == 0
tline = fgetl(fid);
nch = length(strfind(tline, 'CH'));
nindex = find(tline == ',');
if isempty(strfind(tline, 'Oxy')) == 1
errordlg('Please select the Oxy-Hb file.');
return;
end
try
col_mark = strfind(tline, 'Mark');
col_mark = col_mark(1);
col_mark = find(nindex == col_mark - 1) + 1;
end
try
col_prescan = strfind(tline, 'PreScan');
col_prescan = col_prescan(1);
col_prescan = find(nindex == col_prescan - 1)+1;
end
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
tline_data = tline(nindex(1)+1:nindex(nch+1)-1);
nindex_d = find(tline_data == ',');
tline_data(nindex_d) = ' ';
tline_data = str2num(tline_data);
count = str2num(tline(1:nindex(1)-1));
nirs_data.oxyData(count, :) = tline_data;
try
vector_onset(count) = str2num(tline(nindex(col_mark-1)+1:nindex(col_mark)-1));
end
try
baseline(count) = str2num(tline(nindex(col_prescan-1)+1:nindex(col_prescan)-1));
end
end
break;
end
end
disp('HbO data loading has been finished.');
%%% read the deoxy-hb data
[filen, pathn] = uigetfile('*.csv','Select the DeoxyHb (HbR) file');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
disp('Loading the DeoxyHb data starts...');
while 1
tline = fgetl(fid);
if isempty(strfind(tline, 'Sampling Period[s]')) == 0
if ismember('fs', who) == 0
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_fs = tline(nindex(1)+1:end);
fs = 1./mean(str2num(txt_fs));
end
end
if isempty(strfind(tline, 'Data')) == 0
tline = fgetl(fid);
nch = length(strfind(tline, 'CH'));
nindex = find(tline == ',');
if isempty(strfind(tline, 'Deoxy')) == 1
errordlg('Please select the Deoxy-Hb file.');
return;
end
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
tline_data = tline(nindex(1)+1:nindex(nch+1)-1);
nindex_d = find(tline_data == ',');
tline_data(nindex_d) = ' ';
tline_data = str2num(tline_data);
count = str2num(tline(1:nindex(1)-1));
nirs_data.dxyData(count, :) = tline_data;
end
break;
end
end
disp('HbR data loading has been finished.');
%%% read the total-hb data
[filen, pathn] = uigetfile('*.csv','Select the TotalHb (HbT) file');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
disp('Loading the TotalHb data starts...');
while 1
tline = fgetl(fid);
if isempty(strfind(tline, 'Sampling Period[s]')) == 0
if ismember('fs', who) == 0
nindex = find(tline == ',');
tline(nindex) = ' ';
txt_fs = tline(nindex(1)+1:end);
fs = 1./mean(str2num(txt_fs));
end
end
if isempty(strfind(tline, 'Data')) == 0
tline = fgetl(fid);
nch = length(strfind(tline, 'CH'));
nindex = find(tline == ',');
if isempty(strfind(tline, 'Total')) == 1
errordlg('Please select the Total-Hb file.');
return;
end
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
tline_data = tline(nindex(1)+1:nindex(nch+1)-1);
nindex_d = find(tline_data == ',');
tline_data(nindex_d) = ' ';
tline_data = str2num(tline_data);
count = str2num(tline(1:nindex(1)-1));
nirs_data.tHbData(count, :) = tline_data;
end
break;
end
end
disp('HbT data loading has been finished.');
try
nirs_data.vector_onset = vector_onset(:);
end
try
index_base = find(baseline == 1);
nirs_data.vector_onset(index_base(1):index_base(end)) = [];
nirs_data.oxyData(index_base(1):index_base(end)) = [];
nirs_data.dxyData(index_base(1):index_base(end)) = [];
nirs_data.tHbData(index_base(1):index_base(end)) = [];
end
nirs_data.fs = fs;
nirs_data.nch = nch;
set(handles.edit_fs,'string', num2str(fs));
set(handles.edit_nch, 'string', num2str(nch));
elseif h == 5 %%% ISS Imagent
[filen, pathn] = uigetfile('*.log; *.txt','Select File to Read the HbR/HbT Concentration Changes');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
tline = fgetl(fid);
index = 1;
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
tline = str2num(tline);
nirs_data.oxyData(index, :) = tline(1,6:2:end-2);
nirs_data.dxyData(index, :) = tline(1,7:2:end-1);
nirs_data.vector_onset(index,1) = tline(1,end);
time(index,1) = tline(1,1);
index = index + 1;
end
fclose(fid);
nirs_data.vector_onset = nirs_data.vector_onset(:);
fs = 1./(mean(diff(time)));
set(handles.edit_fs, 'string', num2str(fs));
nirs_data.nch = size(nirs_data.oxyData,2);
set(handles.edit_nch, 'string', num2str(nirs_data.nch));
set(handles.edit_fs, 'enable', 'on');
elseif h == 6 %%% Hamamatsu NIRO-200
[filen, pathn] = uigetfile('*.NI2','Select File to Read the HbO/HbR Concentration Changes');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
count = 1;
while 1
tline = fgetl(fid);
nindex= find(tline == ',');
if isempty(nindex) == 0 & isempty(str2num(tline(2:nindex(1)-2))) == 0
elpsec(count,1) = str2num(tline(nindex(1)+1:nindex(2)-1));
nirs_data.oxyData(count,1) = str2num(tline(nindex(2)+1:nindex(3)-1));
nirs_data.dxyData(count,1) = str2num(tline(nindex(3)+1:nindex(4)-1));
nirs_data.oxyData(count,2) = str2num(tline(nindex(6)+1:nindex(7)-1));
nirs_data.dxyData(count,2) = str2num(tline(nindex(7)+1:nindex(8)-1));
count = count + 1;
elseif ischar(tline) == 0, break, end,
end
fclose(fid);
fs = 1./mean(diff(elpsec));
set(handles.edit_fs, 'string', num2str(fs));
nirs_data.nch = size(nirs_data.oxyData,2);
set(handles.edit_nch, 'string', num2str(nirs_data.nch));
set(handles.edit_fs, 'enable', 'on');
elseif h == 7 %%% NIRX DYNOT-232
%%% read the parameters
disp('Reading the parameters for modified Beer-Lambert law starts...');
nch = str2num(get(handles.edit_nch,'string'));
fs = str2num(get(handles.edit_fs, 'string'))';
dist = str2num(get(handles.edit_distance, 'string'))';
wavelength = str2num(get(handles.edit_wavelength, 'string'));
DPF = str2num(get(handles.edit_DPF, 'string'));
ecoef = str2num(get(handles.edit_extinc, 'string'));
if isempty(fs) == 1 || isempty(dist) ==1 || isempty(wavelength) == 1 || isempty(DPF) == 1 || isempty(ecoef) == 1
errordlg('Please enter all required parameter values.');
return;
end
try
config = handles.config;
catch
errordlg('Please load the channel configuration');
return;
end
disp('Completed.');
[filen, pathn] = uigetfile('*.wl1','Select the First File to Read the Optical Density Changes'); % load the *.wl1 file
path_file_n = [pathn filen];
if filen(1) == 0 || pathn(1) == 0
return;
end
fid = fopen(path_file_n);
count = 1;
disp(['Reading optical density changes from ' filen ' starts...']);
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end
tline = str2num(tline);
mes1(count,:) = tline;
count = count + 1;
end
fclose(fid);
disp('Completed.');
[filen, pathn] = uigetfile('*.wl2', 'Select the Second File to Read the Optical Density Changes'); %% load the *.wl2 file
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
count = 1;
disp(['Reading optical density changes from ' filen ' starts...']);
while 1
tline = fgetl(fid);
if ~ischar(tline); break, end;
tline = str2num(tline);
mes2(count,:) = tline;
count = count + 1;
end
fclose(fid);
disp('Completed.');
disp('Converting optical density changes to hemoglobin changes starts...');
nTx = max(config(:,1));
nRx = max(config(:,2));
if size(mes1, 2) ~= nTx*nRx || size(mes2, 2) ~= nTx*nRx
nTx = inputdlg('Please enter the number of sources');
nTx = str2num(cell2mat(nTx));
nRx = inputdlg('Please enter the number of detectors');
nRx = str2num(cell2mat(nRx));
end
%eingef?t analog nilab2 nur der Fall "mean of whole timecourse"
s1 = count-1;
mes2_log = real(-log10( (mes2 )./ ...
( repmat(mean(mes2,1), [s1,1])) )) ;
mes1_log = real(-log10( (mes1 )./ ...
( repmat(mean(mes1,1), [s1,1])) )) ;
coefMat = dist.*(diag(DPF) * [ecoef(1,1:2); ecoef(1,3:4)]);
coefMat = pinv(coefMat);
for kk = 1:nch
index = (config(kk, 1)-1)* nRx + config(kk,2);
oxydxy = coefMat * [mes1_log(:, index)'; mes2_log(:, index)'];
oxyData(:, kk) = oxydxy(1,:)';
dxyData(:, kk) = oxydxy(2,:)';
end
disp('Completed.');
nirs_data.oxyData = oxyData;
nirs_data.dxyData = dxyData;
nirs_data.nch = nch;
nirs_data.fs = fs;
nirs_data.wavelength = wavelength;
nirs_data.distance = dist;
nirs_data.DPF = DPF;
elseif h == 8 %%%% Spectratech OEG-16
[filen, pathn] = uigetfile('*.csv', 'Select File to Convert');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
while 1
tline = fgetl(fid);
nindex = find(tline == ',');
tline(nindex) = ' ';
[token, remain] = strtok(tline);
if strcmp(token, 'evt') == 1
count = 1;
while isempty(remain) ~= 1
[token remain] = strtok(remain);
index1 = find(token == '(');
index2 = find(token == ')');
switch token(index1+1:index2-1)
case 'O'
try
col_oxy(end+1) = count + 1;
catch
col_oxy(1) = count + 1;
end
case 'D'
try
col_dxy(end+1) = count + 1;
catch
col_dxy(1) = count + 1;
end
case 'O+D'
try
col_tHb(end+1) = count + 1;
catch
col_tHb(1) = count + 1;
end
end
count = count + 1;
end
count = 1;
while 1
tline = fgetl(fid);
if ischar(tline) == 0, break, end,
nindex = find(tline == ',');
tline(nindex) = ' ';
mes(count,:) = str2num(tline);
count = count + 1;
end
break,
end
end
nirs_data.oxyData = mes(:, col_oxy);
nirs_data.dxyData = mes(:, col_dxy);
nirs_data.tHbData = mes(:, col_tHb);
nirs_data.fs = str2num(get(handles.edit_fs, 'string'));
nirs_data.nch = size(nirs_data.oxyData, 2);
elseif h == 9 %%% Shimadzu OMM,FOIRE-3000
[filen, pathn] = uigetfile('*.txt','Select File to Read OMM TXT file');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
h_wait = waitbar(0, 'Data loading... ');
while 1
tline = fgetl(fid);
nindex = find(tline == ',');
tline(nindex) = ' ';
[token, remain] = strtok(tline);
if strncmp(tline, 'Time Range',10) == 1
[token remain] = strtok(remain);
[token remain] = strtok(remain);
stt = str2num(token);
[token remain] = strtok(remain);
stp = str2num(token);
end
%%%%'Time(sec)'
if strcmp(token, 'Time(sec)') == 1
index = 1;
while 1
tline2 = fgetl(fid);
if ischar(tline2) == 0, break, end,
newlabel = strrep(tline2, 'Z', '');
nindex = find(newlabel == ',');
newlabel = str2num(newlabel);
nirs_data.oxyData(index, :) = newlabel(1,5:3:end-2);
nirs_data.dxyData(index, :) = newlabel(1,6:3:end-1);
nirs_data.tHbData(index, :) = newlabel(1,7:3:end);
waitbar((newlabel(1,1)-stt)/(stp-stt), h_wait);
time(index,1) = newlabel(1,1);
index = index + 1;
end
break
end
end
close(h_wait);
fclose(fid);
fs = 1./(mean(diff(time)));
nirs_data.fs = fs;
set(handles.edit_fs, 'string', num2str(fs));
nirs_data.nch = size(nirs_data.oxyData,2);
set(handles.edit_nch, 'string', num2str(nirs_data.nch));
set(handles.edit_fs, 'enable', 'on');
elseif h == 10 % BIOPAC fNIR
[filen, pathn] = uigetfile('*.oxy','Select File to Read HbO/HbR Chanes');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
if filen(1) == 0 | pathn(1) == 0
return;
end
index = 1;
disp('Reading the data of BIOPAC system starts...');
while 1
tline = fgetl(fid);
tline = str2num(tline);
if isempty(tline) == 0
time(index) = tline(1);
nirs_data.dxyData(index, :) = tline(1,2:2:end);
nirs_data.oxyData(index, :) = tline(1,3:2:end);
index = index + 1;
while 1
tline = fgetl(fid);
if isempty(strfind(tline, 'Device Stopped')) == 0
break;
end
tline = str2num(tline);
time(index) = tline(1);
nirs_data.dxyData(index, :) = tline(1,2:2:end);
nirs_data.oxyData(index, :) = tline(1,3:2:end);
index = index + 1;
end
break;
end
end
fclose(fid);
fs = 1./(mean(diff(time)));
nirs_data.fs = fs;
set(handles.edit_fs, 'string', num2str(fs));
nirs_data.nch = size(nirs_data.oxyData,2);
set(handles.edit_nch, 'string', num2str(nirs_data.nch));
set(handles.edit_fs, 'enable', 'on');
disp('Finished.');
elseif h == 11 % HomER Software
% first, load the raw data '*.nir' to read the model parameter and channel
% configuration.
[filen, pathn] = uigetfile('*.nirs', 'Select ''*.nirs'' File to Read the Model Parameters');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
disp('Reading the HomER data starts...');
load(path_file_n, '-mat');
%second, load the *.mat file to read the Hb concentration changes
[filen, pathn] = uigetfile('*.mat', 'Select ''*.mat'' File to Read HbO/HbR/HbT Changes');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
load(path_file_n);
fs = 1./mean(diff(t));% sampling frequency
set(handles.edit_fs, 'string', num2str(fs));
set(handles.edit_wavelength, 'string', num2str(SD.Lambda));
set(handles.edit_nch, 'string', num2str(size(dataSave.HbO, 2)));
nirs_data.oxyData = dataSave.HbO;
nirs_data.dxyData = dataSave.HbR;
try
nirs_data.tHbData = dataSave.HbT;
catch
nirs_data.tHbData = nirs_data.oxyData + nirs_data.dxyData;
end
nirs_data.fs = fs;
nirs_data.wavelength = SD.Lambda;
nirs_data.nch = size(dataSave.HbO,2);
nirs_data.ch_config = SD.MeasList;
disp('Finished.');
end
elseif h2 == 0 %% manual input
if h == 1 %%% optical density changes
nch = str2num(get(handles.edit_nch, 'string'));
fs = str2num(get(handles.edit_fs, 'string'))';
dist = str2num(get(handles.edit_distance, 'string'))';
wavelength = str2num(get(handles.edit_wavelength, 'string'));
rwavelength = round(wavelength);
rwavelength = reshape(rwavelength, [2 size(rwavelength,2)/2])';
DPF = str2num(get(handles.edit_DPF,'string'))';
flag_DPF_correction = get(handles.checkbox_DPF_correction,'value');
try
ext_coef = str2num(get(handles.edit_extinc, 'string'))';
catch
ext_coef = [];
end
if isempty(fs) == 1 || isempty(dist) == 1 || isempty(wavelength) == 1 || isempty(DPF) == 1 || isempty(nch) == 1
errordlg('Please enter all required parameter values.');
return;
end
%% check if source-detector distance, wavelength, and DPF depend on
%% specific channels or not.
flag_param = 0;
if length(dist) == 1
dist = dist * ones(nch,1);
flag_param = flag_param + 1;
end
if length(rwavelength) == 2
rwavelength = ones(nch,1) * rwavelength;
flag_param = flag_param + 1;
end
if length(DPF) == 1
DPF = DPF * ones(nch,1);
flag_param = flag_param + 1;
end
if length(ext_coef) == 4 || isempty(ext_coef) == 1
try
ext_coef = ext_coef * ones(1, nch);
ext_coef = ext_coef(:);
flag_param = flag_param + 1;
end
end
disp('Generating a coefficient matrix from input variables...');
if flag_param == 4 % same parameters will be applied to all channels
if isempty(ext_coef) == 1
load COPE_e_coef; % load the extinction coefficient file
index_wav1 = find(e_coef(:,1) == rwavelength(1,1));
index_wav2 = find(e_coef(:,1) == rwavelength(1,2));
wav1_ecoef = e_coef(index_wav1,2:3);
wav2_ecoef = e_coef(index_wav2,2:3);
elseif isempty(ext_coef) == 0
wav1_ecoef = ext_coef(1:2,1)';
wav2_ecoef = ext_coef(3:4,1)';
end
if flag_DPF_correction == 1
if (sum(rwavelength(1,:) >= 704) + sum(rwavelength(1,:) <= 972)) == 4
load Charite_DPF_correction
index_DPF1 = find(DPF_correction(:,1) == rwavelength(1,1));
index_DPF2 = find(DPF_correction(:,1) == rwavelength(1,2));
wav1_ecoef = wav1_ecoef .* DPF_correction(index_DPF1, 2);
wav2_ecoef = wav2_ecoef .* DPF_correction(index_DPF2, 2);
else
errordlg('NIRS-SPM allows the wavelength range of DPF correction between 704nm and 972nm');
flag_DPF_correction = 0;
set(handles.checkbox_DPF_correction, 'value', 0);
return;
end
end
tot_ecoef = [wav1_ecoef; wav2_ecoef];
tot_ecoef = tot_ecoef .* DPF(1,1) .* dist(1,1);
coefMat = pinv(tot_ecoef);
coefMat = reshape(coefMat(:) * ones(1, nch), [2 2 nch]);
else %% channel-wise parameters (DPF, extinction coefficient, distance)
coefMat = zeros(2, 2, nch);
for kk = 1:nch
if isempty(ext_coef) == 1
load COPE_e_coef; % load the extinction coefficient file
index_wav1 = find(e_coef(:,1) == rwavelength(kk,1));
index_wav2 = find(e_coef(:,1) == rwavelength(kk,2));
wav1_ecoef = e_coef(index_wav1,2:3);
wav2_ecoef = e_coef(index_wav2,2:3);
elseif isempty(ext_coef) == 0
wav1_ecoef = ext_coef(4*kk-3:4*kk-2,1)';
wav2_ecoef = ext_coef(4*kk-1:4*kk,1)';
end
if flag_DPF_correction == 1
if (sum(rwavelength(kk,:) >= 704) + sum(rwavelength(kk,:) <= 972)) == 4
load Charite_DPF_correction
index_DPF1 = find(DPF_correction(:,1) == rwavelength(kk,1));
index_DPF2 = find(DPF_correction(:,1) == rwavelength(kk,2));
wav1_ecoef = wav1_ecoef .* DPF_correction(index_DPF1, 2);
wav2_ecoef = wav2_ecoef .* DPF_correction(index_DPF2, 2);
else
disp(['DPF correction was not applied to ' num2str(kk) 'th channel, wavelength range of ' num2str(kk) 'th channel is not between 704nm and 972nm.']);
end
end
tot_ecoef = [wav1_ecoef; wav2_ecoef];
tot_ecoef = tot_ecoef .* DPF(kk,1) .* dist(kk,1);
coefMat(:,:, kk) = pinv(tot_ecoef);
end
end % reading the coefficient matrix
disp('Reading optical density changes from an input file...');
%% read the optical density changes
[filen, pathn] = uigetfile('*.csv; *.txt','Select File to Read the Optical Density Changes');
path_file_n = [pathn filen];
if filen(1) == 0 || pathn(1) == 0
return;
end
fid = fopen(path_file_n);
index = 1;
switch filen(end-2:end)
case 'csv'
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
index_comma = find(tline == ',');
tline(index_comma) = ' ';
tline = str2num(tline);
mes(index,:) = tline;
index = index + 1;
end
case 'txt'
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
tline = str2num(tline);
mes(index,:) = tline;
index = index + 1;
end
end
fclose(fid);
disp('Calculating oxy- and deoxy-hemoglobin changes using modified Beer-Lambert law...');
%% calculate the oxy- and deoxy-hemoglobin changes using modified
%% Beer-Lambert law
for kk = 1:nch
oxydxy = (coefMat(:,:,kk) * [mes(:,2*(kk-1)+1)'; mes(:, 2*kk)'])';
oxyData(:,kk) = oxydxy(:,1);
dxyData(:,kk) = oxydxy(:,2);
end
nirs_data.oxyData = oxyData;
nirs_data.dxyData = dxyData;
nirs_data.nch = nch;
nirs_data.fs = fs;
nirs_data.wavelength = wavelength;
nirs_data.distance = dist;
nirs_data.DPF = DPF;
if flag_DPF_correction == 0
nirs_data.DPF_correction = 'none';
elseif flag_DPF_correction == 1
nirs_data.DPF_correction = 'Charite correction';
end
elseif h == 2 %%%% converted HbO and HbR
fs = str2num(get(handles.edit_fs, 'string'));
if isempty(fs) == 1
errordlg('Sampling frequency is not specified.');
return;
end
[filen, pathn] = uigetfile('*.csv; *.txt','Select File to Read the HbR/HbT Concentration Changes');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
fid = fopen(path_file_n);
index = 1;
switch filen(end-2:end)
case 'csv'
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
index_comma = find(tline == ',');
tline(index_comma) = ' ';
tline = str2num(tline);
nirs_data.oxyData(index, :) = tline(1,1:2:end-1);
nirs_data.dxyData(index, :) = tline(1,2:2:end);
index = index + 1;
end
case 'txt'
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
tline = str2num(tline);
nirs_data.oxyData(index, :) = tline(1,1:2:end-1);
nirs_data.dxyData(index, :) = tline(1,2:2:end);
index = index + 1;
end
end
fclose(fid);
nch = size(nirs_data.oxyData,2);
set(handles.edit_nch, 'string', num2str(nch));
nirs_data.nch = nch;
nirs_data.fs = fs;
end
end
handles.nirs_data = nirs_data;
guidata(hObject, handles);
% --- Executes on button press in push_save.
function push_save_Callback(hObject, eventdata, handles)
nirs_data = handles.nirs_data;
if get(handles.checkbox_system, 'value') == 1 && (get(handles.Pop_SystemConfig, 'value') == 5 || get(handles.Pop_SystemConfig, 'value') == 6 || get(handles.Pop_SystemConfig, 'value') == 9 || get(handles.Pop_SystemConfig, 'value') == 10)%% 5: ISS imagent, 6: Hamamatsu NIRO-200, 9 : Shimadzu FOIRE-3000, 10: BIOPAC fNIR
nirs_data.fs = str2num(get(handles.edit_fs, 'string'));
end
% for HomER software
if get(handles.checkbox_system, 'value') == 1 && get(handles.Pop_SystemConfig, 'value') == 11
try
[filen, pathn] = uiputfile('*.txt', 'Select File to Save the Channel Configuration');
path_filen = [pathn filen];
if path_filen == 0
return;
end
fid = fopen(path_filen, 'w');
fprintf(fid, '%s\r\n', 'Channel Configuration adapted from the HomER software');
fprintf(fid, '%s\r\n', [num2str(nirs_data.nch) 'ch']);
fprintf(fid, '%s\r\n', ' set');
fprintf(fid, '%s\r\n', '');
[r c] = find(nirs_data.ch_config(:,3) == 1 & nirs_data.ch_config(:,4) == 1);
for kk = 1:length(r)
fprintf(fid, '%s\r\n', num2str(nirs_data.ch_config(r(kk),1:2)));
end
fclose(fid);
nirs_data = rmfield(nirs_data, 'ch_config');
catch
errordlg('Failed to save the channel configuration automatically!! Please manually write the channel configuration and save it as txt format.');
end
end
if isempty(nirs_data) == 0
[filen, pathn] = uiputfile('*.mat');
path_filen = [pathn filen];
if path_filen == 0
return;
end
save(path_filen, 'nirs_data');
else
errordlg('Optical density data is not converted. Please execute the converting routing again','Error');
return;
end
function edit_fs_Callback(hObject, eventdata, handles)
function edit_fs_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_nch_Callback(hObject, eventdata, handles)
function edit_nch_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in Pop_SystemConfig.
function Pop_SystemConfig_Callback(hObject, eventdata, handles)
h = get(handles.Pop_SystemConfig, 'value');
h2 = get(handles.checkbox_system, 'value');
set(handles.edit_extinc, 'enable', 'off', 'string', ' ');
set(handles.text9, 'enable','off');
set(handles.text10, 'enable', 'off');
if h2 == 1 %%% System Configuration
if h == 1 %%%OXYMON MK3
set(handles.edit_nch,'enable', 'off', 'string', '24');
set(handles.edit_fs, 'enable', 'on');
set(handles.edit_distance, 'enable', 'on', 'string', '3.5');
set(handles.edit_wavelength, 'enable', 'on', 'string', '856 781');
set(handles.checkbox_DPF_correction, 'value', 1, 'enable', 'on');
set(handles.edit_DPF, 'enable', 'on', 'string', '4');
set(handles.push_load_param, 'enable', 'off');
elseif h == 2 || h == 3 || h == 4 || h == 5 || h == 6 || h == 9 || h == 10 || h == 11%%%% Hitachi ETG 4000 (1set) || Hitachi ETG4000 (2set) || Hitachi ETG4000 (HbO, HbR, HbT) || ISS Imagent || Hamamatsu NIRO-200 || Shimadzu OMM,FOIRE-3000 || BIOPAC fNIR || HomER software
set(handles.edit_nch,'enable', 'off', 'string', '');
set(handles.edit_fs, 'enable', 'off', 'string', '');
set(handles.edit_distance, 'enable', 'off', 'string', '');
set(handles.edit_wavelength, 'enable', 'off', 'string', '');
set(handles.checkbox_DPF_correction, 'value', 0, 'enable', 'off');
set(handles.edit_DPF, 'enable', 'off', 'string', '');
set(handles.push_load_param, 'enable', 'off');
elseif h == 7 %%%% DYNOT 232 System (NIRX)
%% under construction
set(handles.edit_extinc, 'enable', 'on', 'string', '1.4866 3.8437 2.2314 1.7917');
set(handles.text9, 'enable','on');
set(handles.text10, 'enable', 'on');
set(handles.edit_nch,'enable', 'on','string','80');
set(handles.edit_fs, 'enable', 'on');
set(handles.edit_distance, 'enable', 'on', 'string', '2.5');
set(handles.edit_wavelength, 'enable', 'on','string', '760 830');
set(handles.edit_DPF, 'enable', 'on','string', '7.15 5.98');
set(handles.push_load_param, 'enable', 'on', 'string', 'Load Ch. configuration');
set(handles.checkbox_DPF_correction, 'value', 0, 'enable', 'off');
elseif h == 8 %%%%% Spectratech OEG-16
set(handles.edit_nch,'enable', 'off', 'string', '');
set(handles.edit_fs, 'enable', 'on', 'string', '');
set(handles.edit_distance, 'enable', 'off', 'string', '');
set(handles.edit_wavelength, 'enable', 'off', 'string', '');
set(handles.checkbox_DPF_correction, 'value', 0, 'enable', 'off');
set(handles.edit_DPF, 'enable', 'off', 'string', '');
set(handles.push_load_param, 'enable', 'off');
end
elseif h2 == 0 %%% Manual configuration
if h == 1 %%% optical density changes
set(handles.edit_nch, 'enable', 'on', 'string', '');
set(handles.edit_fs, 'enable', 'on');
set(handles.edit_distance, 'enable', 'on');
set(handles.edit_wavelength, 'enable', 'on');
set(handles.checkbox_DPF_correction, 'value', 1, 'enable', 'on');
set(handles.edit_DPF, 'enable', 'on');
set(handles.push_load_param, 'enable', 'on', 'string', 'Load parameters');
set(handles.text9, 'enable', 'on');
set(handles.text10, 'enable', 'on');
set(handles.edit_extinc,'enable','on');
elseif h == 2 %%% converted HbO and HbR concentration changes
set(handles.edit_nch, 'enable', 'off', 'string', '');
set(handles.edit_fs, 'enable', 'on');
set(handles.edit_distance, 'enable', 'off', 'string', '');
set(handles.edit_wavelength, 'enable', 'off', 'string', '');
set(handles.checkbox_DPF_correction, 'value', 0, 'enable', 'off');
set(handles.edit_DPF, 'enable', 'off','string', '');
set(handles.push_load_param, 'enable', 'off');
end
end
% --- Executes during object creation, after setting all properties.
function Pop_SystemConfig_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in checkbox_manual.
function checkbox_manual_Callback(hObject, eventdata, handles)
h = get(handles.checkbox_manual, 'value');
set(handles.checkbox_system, 'value', 1-h);
if h == 1
str{1} = 'Optical density changes';
str{2} = 'Converted HbO and HbR changes';
set(handles.edit_nch, 'enable', 'on', 'string', '');
set(handles.edit_distance, 'enable', 'on', 'string', '');
set(handles.edit_wavelength, 'enable', 'on', 'string', '');
set(handles.edit_DPF, 'enable', 'on', 'string', '');
set(handles.push_load_param, 'enable', 'on', 'string', 'Load parameters');
set(handles.edit_extinc, 'enable', 'on', 'string', ' ');
set(handles.text9, 'enable', 'on');
set(handles.text10, 'enable', 'on');
else
str{1} = 'OXYMON MK III';
str{2} = 'Hitachi ETG-4000 (1 set, Optical density)';
str{3} = 'Hitachi ETG-4000 (2 set, Optical density)';
str{4} = 'Hitachi ETG-4000 (HbO, HbR, HbT)';
str{5} = 'ISS Imagent';
str{6} = 'Hamamatsu NIRO-200';
str{7} = 'NIRX DYNOT-232';
str{8} = 'Spectratech OEG-16';
str{9} = 'Shimadzu OMM,FOIRE-3000';
str{10} = 'BIOPAC fNIR';
str{11} = 'HomER Software';
set(handles.edit_nch, 'enable', 'off', 'string', '24');
set(handles.edit_distance, 'enable', 'on', 'string', '3.5');
set(handles.edit_wavelength, 'enable', 'on', 'string', '856 781');
set(handles.edit_DPF, 'enable', 'on', 'string', '4');
set(handles.push_load_param, 'enable', 'off');
set(handles.edit_extinc, 'enable', 'off', 'string', ' ');
set(handles.text9, 'enable','off');
set(handles.text10, 'enable', 'off');
end
set(handles.edit_fs, 'enable', 'on');
set(handles.checkbox_DPF_correction, 'value', 1, 'enable', 'on');
set(handles.Pop_SystemConfig, 'string',str);
set(handles.Pop_SystemConfig, 'value',1);
% --- Executes on button press in checkbox_system.
function checkbox_system_Callback(hObject, eventdata, handles)
h = get(handles.checkbox_system, 'value');
set(handles.checkbox_manual, 'value', 1-h);
if h == 1
str{1} = 'OXYMON MK III';
str{2} = 'Hitachi ETG-4000 (1 set, Optical density)';
str{3} = 'Hitachi ETG-4000 (2 set, Optical density)';
str{4} = 'Hitachi ETG-4000 (HbO, HbR, HbT)';
str{5} = 'ISS Imagent';
str{6} = 'Hamamatsu NIRO-200';
str{7} = 'NIRX DYNOT-232';
str{8} = 'Spectratech OEG-16';
str{9} = 'Shimadzu OMM,FOIRE-3000';
str{10} = 'BIOPAC fNIR';
str{11} = 'HomER Software';
set(handles.edit_nch, 'enable', 'off', 'string', '24');
set(handles.edit_distance, 'enable', 'on', 'string', '3.5');
set(handles.edit_wavelength, 'enable', 'on', 'string', '856 781');
set(handles.edit_DPF, 'enable', 'on', 'string', '4');
set(handles.push_load_param, 'enable', 'off');
set(handles.edit_extinc, 'enable', 'off', 'string', ' ');
set(handles.text9, 'enable','off');
set(handles.text10, 'enable', 'off');
else
str{1} = 'Optical density changes';
str{2} = 'Converted HbO and HbR changes';
set(handles.edit_nch, 'enable', 'on', 'string', '');
set(handles.edit_distance, 'enable', 'on', 'string', '');
set(handles.edit_wavelength, 'enable', 'on', 'string', '');
set(handles.edit_DPF, 'enable', 'on', 'string', '');
set(handles.push_load_param, 'enable', 'on', 'string', 'Load parameters');
set(handles.edit_extinc, 'enable', 'on', 'string', ' ');
set(handles.text9, 'enable','on');
set(handles.text10, 'enable', 'on');
end
set(handles.text9, 'enable','off');
set(handles.text10, 'enable', 'off');
set(handles.edit_fs, 'enable', 'on');
set(handles.checkbox_DPF_correction, 'value', 1, 'enable', 'on');
set(handles.Pop_SystemConfig, 'string',str);
set(handles.Pop_SystemConfig, 'value',1);
% --- Executes on button press in checkbox_DPF_correction.
function checkbox_DPF_correction_Callback(hObject, eventdata, handles)
function edit_wavelength_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function edit_wavelength_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_DPF_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function edit_DPF_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_distance_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function edit_distance_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in push_load_param.
function push_load_param_Callback(hObject, eventdata, handles)
h2 = get(handles.checkbox_system, 'value');
nch = str2num(get(handles.edit_nch, 'string'));
if h2 == 1
[filen, pathn] = uigetfile('*.txt; *.mat','Select the file to contain the channel configuration.');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
switch filen(end-2:end)
case 'mat'
load(path_file_n);
IMGlabel = ni.IMGlabel;
for kk = 1:nch
tmp = IMGlabel{kk};
index = find(tmp == '-');
config(kk,1) = str2num(tmp(1:index-1));
config(kk,2) = str2num(tmp(index+1:end));
end
case 'txt'
fid = fopen(path_file_n);
for kk = 1:4
tline = fgetl(fid);
end
count = 1;
while 1
tline = fgetl(fid);
if ~ischar(tline); break, end;
tline = str2num(tline);
config(count,:) = tline;
count = count + 1;
end
fclose(fid);
end
handles.config = config;
guidata(hObject, handles);
elseif h2 == 0
[filen, pathn] = uigetfile('*.txt; *.csv','Select the parameter file used in modified Beer-lambert law.');
path_file_n = [pathn filen];
if filen(1) == 0 | pathn(1) == 0
return;
end
switch filen(end-2:end)
case 'txt' % text file format
fid = fopen(path_file_n);
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
index = find(tline == ' ');
% reading the parameter values from text file
if strcmpi(tline(1:index(1)-1), 'Total_number_of_Ch.') == 1
set(handles.edit_nch, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Sampling_freq.[Hz]') == 1
set(handles.edit_fs, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Distance[cm]') == 1
set(handles.edit_distance, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Wave_length[nm]') == 1
set(handles.edit_wavelength, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'DPF') == 1
set(handles.edit_DPF, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Correction') == 1
if strcmpi(tline(index(1)+1:end), 'yes') == 1
set(handles.checkbox_DPF_correction,'value',1);
elseif strcmpi(tline(index(1)+1:end), 'no') == 1
set(handles.checkbox_DPF_correction,'value',0);
end
elseif strcmpi(tline(1:index(1)-1),'Extinction_coefficient') == 1
set(handles.edit_extinc, 'string', tline(index(1)+1:end));
end
end
fclose(fid);
case 'csv' % .csv file format
disp('Reading the parameter values from *.csv file...');
fid = fopen(path_file_n);
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end;
index = find(tline == ',');
tline(index) = ' ';
% reading the parameter values from text file
if strcmpi(tline(1:index(1)-1), 'Total_number_of_Ch.') == 1
set(handles.edit_nch, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Sampling_freq.[Hz]') == 1
set(handles.edit_fs, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Distance[cm]') == 1
set(handles.edit_distance, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Wave_length[nm]') == 1
set(handles.edit_wavelength, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'DPF') == 1
set(handles.edit_DPF, 'string', tline(index(1)+1:end));
elseif strcmpi(tline(1:index(1)-1), 'Correction') == 1
if strcmpi(tline(index(1)+1:end), 'yes') == 1
set(handles.checkbox_DPF_correction,'value',1);
elseif strcmpi(tline(index(1)+1:end), 'no') == 1
set(handles.checkbox_DPF_correction,'value',0);
end
elseif strcmpi(tline(1:index(1)-1),'Extinction_coefficient') == 1
set(handles.edit_extinc, 'string', tline(index(1)+1:end));
end
end
fclose(fid);
% case 'mat' % .mat file format
% load(path_file_n);
% try
% set(handles.edit_nch, 'string', num2str(nch));
% end
% try
% set(handles.edit_fs, 'string', num2str(fs));
% end
% try
% set(handles.edit_distance, 'string', num2str(distance));
% end
% try
% set(handles.edit_wavelength, 'string', num2str(wavelength));
% end
% try
% set(handles.edit_DPF, 'string', num2str(DPF));
% end
% try
% switch DPF_correction
% case 'yes'
% set(handles.checkbox_DPF_correction, 'value',1);
% case 'no'
% set(handles.checkbox_DPF_correction, 'value',0);
% end
% end
% try
% set(handles.edit_extinc, 'string', num2str(ext_coef));
% end
end
end
function edit_extinc_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function edit_extinc_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end

What is your expected output? Please don't cut/paste whole code. We all have access to SPM. You don't need to flood the message with obvious code.
Originally posted by Amrita Pal :

Sorry for flooding the message box. The expected output is concentrations of the following channels, the distance between detector and sources are as under: 
A7=A8=3.836 cm=C7=C8
A1=A2=3.836 cm=C1=C2
A5=A6=3.836 cm= C5=C6 
A3=A4=2.605 cm=C3=C4 
B7=B8=4.53 cm=D7=D8 
B1=B2=3.015 cm=D1=D2
B3=B4= 4.530 cm= D3=D4 
B5=B6=3.6 cm= D5=D6 
 
I have attached a sample .txt file generated by Boxy. I want to create homer or spm files of boxy so I can analyze the data.