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iCAPs_v2/packages/spm12/external/mne/mne_ex_read_evoked.m
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mne_ex_read_evoked.m
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function [res] = mne_ex_read_evoked(fname,setno,apply_proj,dest_comp,use_ctf_head)
%
% Load one evoked-response data set and do various kinds
% of preprocessing
%
% [res] = mne_ex_read_evoked(fname,setno,apply_proj,dest_comp,use_ctf_head)
%
% fname - Name of the data file
% setno - Data set number (default = 1)
% apply_proj - Apply SSP to the data (default = true)
% dest_comp - Desired (CTF/4D) compensation in the output data (default = keep the one in the file)
% use_ctf_head - Use the CTF/4D head coordinate system instead of the
% Neuromag one if available
%
%
% Author : Matti Hamalainen, MGH Martinos Center
% License : BSD 3-clause
%
% Revision 1.3 2008/11/18 02:38:51 msh
% Modified mne_ex_read_evoked to apply projection and compensation
% Modified mne_ex_read_raw to call mne_set_current_comp
%
% Revision 1.2 2006/04/23 15:29:40 msh
% Added MGH to the copyright
%
% Revision 1.1 2006/04/21 17:31:07 msh
% Added the examples.
% Modified the formatting of some informative output.
%
%
me='MNE:mne_ex_read_evoked';
%
% Different cases for the input arguments
%
if nargin == 1
setno = 1;
apply_proj = true;
use_ctf_head = false;
keep_comp = true;
elseif nargin == 2
apply_proj = true;
use_ctf_head = false;
keep_comp = true;
elseif nargin == 3
use_ctf_head = false;
keep_comp = true;
elseif nargin == 4
use_ctf_head = false;
keep_comp = false;
elseif nargin == 5
keep_comp = false;
else
error(me,'Incorrect number of arguments');
end
%
% Load the desired data
%
fprintf(1,'\nLoading set %d from %s...\n\n',setno,fname);
%
try
res = fiff_read_evoked(fname,setno);
catch
error(me,'%s',mne_omit_first_line(lasterr));
end
%
% Go ahead and do all kinds of interesting stuff
%
fprintf(1,'\nPreprocessing...\n');
%
% Omit bad channels and pick MEG
% (Change this according to your needs)
%
want_meg = true;
want_eeg = false;
want_stim = false;
%
%include{1} = 'STI 014';
include = [];
%
res = fiff_pick_types_evoked(res,want_meg,want_eeg,want_stim,include,res.info.bads);
fprintf(1,'\t%d channels remain after picking\n',res.info.nchan);
%
% Handle the software gradient compensation
%
comp=[];
current_comp = mne_get_current_comp(res.info);
if current_comp > 0
fprintf(1,'\tCurrent compensation grade : %d\n',current_comp);
end
if keep_comp
dest_comp = current_comp;
end
if current_comp ~= dest_comp
try
comp = mne_make_compensator(res.info,current_comp,dest_comp);
res.info.chs = mne_set_current_comp(res.info.chs,dest_comp);
fprintf(1,'\tAppropriate compensator created to change to grade %d.\n',dest_comp);
catch
error(me,'%s',mne_omit_first_line(lasterr));
end
end
if ~isempty(comp)
for k = 1:length(res.evoked)
res.evoked(k).epochs = comp*res.evoked(k).epochs;
end
fprintf(1,'\tThe data are now compensated to grade %d.\n',dest_comp);
end
%
% Set up projection
%
if apply_proj
if isempty(res.info.projs)
fprintf(1,'\tNo projector specified in these data\n');
else
%
% Activate the projection items
%
for k = 1:length(res.info.projs)
res.info.projs(k).active = true;
end
fprintf(1,'\t%d projection items activated\n',length(res.info.projs));
%
% Create the projector
%
[res.info.proj,nproj] = mne_make_projector_info(res.info);
if nproj == 0
fprintf(1,'\tThe projection vectors do not apply to these channels\n');
else
fprintf(1,'\tCreated an SSP operator (subspace dimension = %d)\n',nproj);
for k = 1:length(res.evoked)
res.evoked(k).epochs = res.info.proj*res.evoked(k).epochs;
end
fprintf(1,'\tSSP operator applied to the evoked data\n');
end
end
end
%
% Select the head coordinate system
%
if use_ctf_head
if isempty(res.info.dev_ctf_t)
error(me,'No CTF head transformation available');
end
meg_trans = res.info.dev_ctf_t;
eeg_trans = fiff_invert_transform(res.info.ctf_head_t);
fprintf(1,'\tEmploying the CTF/4D head coordinate system\n');
else
meg_trans = res.info.dev_head_t;
eeg_trans = [];
fprintf(1,'\tEmploying the Neuromag head coordinate system\n');
end
%
% Transform coil and electrode locations to the desired coordinate frame
%
res.info.chs = fiff_transform_meg_chs(res.info.chs,meg_trans);
res.info.chs = fiff_transform_eeg_chs(res.info.chs,eeg_trans);
%
% Create the coil definitions
%
try
accuracy = 1; % Use accuracy = 2 for accurate coil definitions
res.info.chs = mne_add_coil_defs(res.info.chs,accuracy);
catch
fprintf(1,'\tCoil definitions not added\n');
end
%
% N.B. If a nonstandard (in MNE sense) coil def file is used, do
%
if false
coil_def_file = 'whatever';
templates = mne_load_coil_def(coil_def_file);
res.info.chs = mne_add_coil_defs(res.info.chs,accuracy,templates);
end
fprintf(1,'\nReady.\n\n');
return;
end
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