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Added missing maxfilter scripts
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‎code/meg_preprocessing/maxfilter_get_bad_channels_from_fiff.m

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function badstr = bad_channels_from_mf(raw_file, raw_file_out, badfile, out_dir, finstr, Nbuf, OverWrite, ParType, do_eval)
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% get bad channels for one fiff-file from maxfilter using -autobad
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% raw_file: fiff-file for which bad channels needed
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% raw_file_out: name of output fiff-file from maxfilter
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% badfile: file that records bad channel information
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% out_dir: output directory
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% finstr: text string with maxfilter parameters
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% Nbuf: number of buffers from fiff-file
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% OverWrite: 0/1, whether output files to be overwritten
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% ParType: Parallelisation option
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% do_eval: 0/1, whether commands to be executed, or only to be displayed at command line
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% Olaf Hauk, Sep 14 (adapated from RH script)
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outfile = fullfile(out_dir,sprintf('%s_bad',raw_file_out));
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if ~exist(badfile) | OverWrite
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% Write out movements too...
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posfile = fullfile(out_dir,sprintf('%s_headpos.txt',raw_file_out));
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finstr = [finstr ' -hp ' posfile];
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finstr = [finstr ' -v | tee ' outfile '.log'];
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fprintf(1, '\n\nMF command for bad channel detection: \n%s\n\n', finstr);
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if do_eval
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if ParType==1
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spmd; eval(finstr);
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end
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else
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eval(finstr);
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end
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end
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% Pull out bad channels from logfile:
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cat_bad_cmd = sprintf('!cat %s.log | sed -n -e ''/Detected/p'' -e ''/Static/p'' | cut -f 5- -d '' '' >> %s',outfile,badfile);
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fprintf(1, '\n\nNow attempting:\n%s\n\n', cat_bad_cmd);
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fp = fopen(badfile,'w'); fprintf(fp,' '); fclose(fp);
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if do_eval
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eval(cat_bad_cmd);
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end
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end
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fprintf(1, '\nDetermining bad channels\n');
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tmp=dlmread(badfile,' '); % Nbuf = size(tmp,1);
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tmp=reshape(tmp,1,prod(size(tmp)));
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tmp=tmp(tmp>0); % Omit zeros (padded by dlmread):
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% Get frequencies (number of buffers in which chan was bad):
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[frq,allbad] = hist(tmp,unique(tmp));
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% Mark bad based on threshold (currently ~5% of buffers (assuming 500 buffers)):
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badchans = allbad(frq>0.05*Nbuf);
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if isempty(badchans)
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badstr = '';
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else
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badstr = sprintf(' -bad %s',num2str(badchans))
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end
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end

‎code/meg_preprocessing/maxfilter_one_subject.m

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function maxfilter_one_subject(cstr, datinfo, s, ParType)
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% run Maxfilter on sessions within sub-directory for one subject
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% cstr: structure with maxfilter commands
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% datinfo: data information (files, directories etc.)
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% s: subject index to process here
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% ParType: Parallelisation option
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% Olaf Hauk, Sep 14 (adapted from RH script)
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% for ease of use, get info from datinfo structure
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data_in_dir = datinfo.data_in_dir;
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data_out_dir = datinfo.data_out_dir;
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sub_dirs = datinfo.sub_dirs;
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nr_subs = datinfo.nr_subs;
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bad_chans = datinfo.bad_chans;
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OverWrite = datinfo.OverWrite;
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movfile = datinfo.movfile;
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Nbuf = datinfo.Nbuf;
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raw_files_in = datinfo.raw_files_in;
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raw_files_out = datinfo.raw_files_out;
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nr_raw_files = length(raw_files_in);
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if ~isempty(datinfo.mvcomp_fail) % if individual movecomp failures specified
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mvcomp_fail = datinfo.mvcomp_fail{s};
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else % if no movecomp failures specified
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mvcomp_fail = zeros(1,length(raw_files_in));
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end;
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finstr = []; % initialise final Maxfilter command string
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% Output directory
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out_dir = fullfile(data_out_dir, sub_dirs{s}),
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if datinfo.do_eval % delete/create file for movement parameters
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if exist(movfile)
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delete(movfile)
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end
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eval(sprintf('!touch %s',movfile));
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end
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log_filename = [num2str(s) '_' datinfo.logfilestem];
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log_fid = fopen( log_filename, 'w' );
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fprintf(log_fid, '%s\n', sub_dirs{s});
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for r = 1:nr_raw_files
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raw_file = fullfile(data_in_dir,sub_dirs{s},sprintf('/%s.fif',raw_files_in{r})); % Get raw FIF file
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fprintf(log_fid, '\n%s\n', raw_file);
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raw_stem = raw_file(1:(end-4));
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badstr = cstr.badstr; % will be altered during loop
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% determine sphere origin
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% Fit sphere (since better than MaxFilter does)
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if isempty(cstr.headori)
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if r == 1 % fit sphere doesn't change with run!
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incEEG = 0;
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% if exist(fullfile(out_dir,'fittmp.txt')); delete(fullfile(out_dir,'fittmp.txt')); end
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% if exist(fullfile(out_dir,sprintf('run_%02d_hpi.txt',raw_files_out{r}))); delete(fullfile(out_dir,sprintf('run_%02d_hpi.txt',raw_files_out{r}))); end
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% [orig,rad,fit] = meg_fit_sphere(raw_file,out_dir,sprintf('%s_hpi.txt',raw_files_out{r}),incEEG);
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% delete(fullfile(out_dir,'fittmp.txt'));
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if exist(fullfile(out_dir,sprintf('run_%02d_hpi.txt',raw_files_out{r}))); delete(fullfile(out_dir,sprintf('run_%02d_hpi.txt',raw_files_out{r}))); end
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cwd = pwd;
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[orig,rad,fit] = meg_fit_sphere(raw_file,out_dir,sprintf('%s_hpi.txt',raw_files_out{r}),incEEG);
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cd( cwd ); % back to original working directory
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end
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cstr.origstr = sprintf(' -origin %d %d %d -frame head',orig(1),orig(2),orig(3));
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else,
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% use pre-defined origin
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cstr.origstr = sprintf(' -origin %d %d %d -frame head',cstr.headori(1),cstr.headori(2),cstr.headori(3))
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end;
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fprintf(1, '\nHead origin: %s\n', cstr.origstr);
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%% 1. Bad channel detection (this email says important if doing tSSS later https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=NEUROMEG;d3f363f3.1205)
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outfile = fullfile(out_dir,sprintf('%s_bad',raw_files_out{r}));
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badfile = sprintf('%s.txt',outfile);
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bad_filename = [outfile '.fif'];
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Dout = dir( bad_filename );
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% if output file exists, get date
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if isempty( Dout )
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bad_datenum = 0;
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else
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bad_datenum = datenum( Dout.date )
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end
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cstr.filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
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finstr_bad = [cstr.maxfstr cstr.filestr cstr.origstr cstr.basestr cstr.badstr cstr.compstr_bad];
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% get bad channels from maxfilter
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bad_str_tmp = maxfilter_get_bad_channels_from_fiff(raw_file, raw_files_out{r}, badfile, out_dir, finstr_bad, Nbuf, OverWrite, ParType, datinfo.do_eval);
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% Take note whether output files were successfully created or not
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Dout = dir( bad_filename );
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if isempty( Dout )
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bad_datenum2 = 0;
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else
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bad_datenum2 = datenum( Dout.date )
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end
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if (bad_datenum2 > bad_datenum),
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fprintf(log_fid, 'Created: %s\n', bad_filename);
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fprintf(log_fid, '%d %s\n', Dout.bytes, Dout.date);
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else
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fprintf(log_fid, 'NOT created: %s\n', bad_filename);
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end
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% delete current fiff-file if desired
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if datinfo.del_bads && exist(bad_filename, 'file')
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delete( bad_filename );
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end
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% add manually specified bad channels
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if ~isempty(bad_chans)
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if isempty(bad_str_tmp) && ~isempty(bad_chans{s}), % if -bad wasn't added during bad channel detection
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bad_str_tmp = ' -bad ';
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end
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badstr = [badstr bad_str_tmp];
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for bb = 1:length(bad_chans{s}),
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badstr = [badstr ' ' bad_chans{s}{bb} ' '];
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end
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end
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fprintf(1, 'Bad channels: %s\n\n', badstr);
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%% 2. tSSS (incl. align within subject if multiple runs)
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outfile = fullfile(out_dir,sprintf('%s', raw_files_out{r}));
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% trans to first file in list
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if r == 1
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transfstfile = [outfile '.fif'];
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cstr.transtr = '';
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else
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cstr.transtr = sprintf(' -trans %s ', transfstfile);
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end
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% get date of existing file
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Dout = dir( [outfile '.fif'] );
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if isempty( Dout )
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out_datenum = 0;
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else
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out_datenum = datenum( Dout.date )
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end
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if ~exist(sprintf('%s.fif',outfile)) | OverWrite
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cstr.filestr = sprintf(' -f %s -o %s.fif', raw_file,outfile);
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% check if movement compensation shall be applied
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if mvcomp_fail, % if not
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finstr = [cstr.maxfstr cstr.filestr cstr.basestr badstr cstr.tSSSstr cstr.origstr cstr.transtr cstr.dsstr sprintf(' -v | tee %s.log',outfile)]
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fprintf(1, 'No movement compensation applied for %s\n', outfile);
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fprintf(log_fid, 'No movement compensation requested for %s\n', outfile);
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else, % if yes
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finstr = [cstr.maxfstr cstr.filestr cstr.basestr badstr cstr.tSSSstr cstr.compstr cstr.origstr cstr.transtr sprintf(' -v | tee %s.log',outfile)]
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end;
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fprintf(1, '\nFinal Maxfilter command:\n%s\n\n', finstr);
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if r == 1
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fprintf(log_fid, '%s\n\n', finstr);
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end;
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if datinfo.do_eval % only execute if desired
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if ParType==1
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spmd; eval(finstr); end
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else
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eval(finstr);
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end
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eval(sprintf('!echo ''Trans 1st...'' >> %s', movfile));
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eval(sprintf('!cat %s.log | sed -n ''/Position change/p'' | cut -f 7- -d '' '' >> %s', outfile,movfile));
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end
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end
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% Take note whether output files were successfully created or not
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% try again without movecomp first
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Dout = dir( [outfile '.fif'] );
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if isempty( Dout )
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out_datenum2 = 0;
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else
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out_datenum2 = datenum( Dout.date )
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end
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if datinfo.do_eval % only execute if desired
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if (out_datenum2 == out_datenum) && OverWrite, % if date of output file has not changed when it should have...
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finstr = [cstr.maxfstr cstr.filestr cstr.basestr badstr cstr.tSSSstr cstr.origstr cstr.transtr cstr.dsstr sprintf(' -v | tee %s.log',outfile)]
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fprintf(1, 'Trying again without movement compensation for %s\n', outfile);
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fprintf(log_fid, 'NOT created at first attempt: %s\n', [outfile '.fif']);
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if ParType==1
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spmd; eval(finstr); end;
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else
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eval(finstr);
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end
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Dout = dir( [outfile '.fif'] );
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if isempty( Dout )
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out_datenum2 = 0;
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else
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out_datenum2 = datenum( Dout.date )
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end
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if out_datenum2 > out_datenum,
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fprintf(log_fid, 'Created (2nd attempt): %s\n', [outfile '.fif']);
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fprintf(log_fid, '%d %s\n', Dout.bytes, Dout.date);
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else
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fprintf(log_fid, 'NOT created (2nd attempt): %s\n', [outfile '.fif']);
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end
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elseif (out_datenum2 > out_datenum) && (out_datenum>0)
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fprintf(log_fid, 'Created and overwritten: %s\n', [outfile '.fif']);
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elseif (out_datenum2 > out_datenum) && (out_datenum==0)
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fprintf(log_fid, 'Created new: %s\n', [outfile '.fif']);
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elseif (out_datenum > 0) && ~OverWrite,
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fprintf(log_fid, 'Existing not overwritten: %s\n', [outfile '.fif']);
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elseif (out_datenum == 0) && (out_datenum2==0),
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fprintf(log_fid, 'Nothing created for: %s\n', [outfile '.fif']);
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else
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fprintf(log_fid, 'Not sure what do to with: %s\n', [outfile '.fif']);
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end
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end % if datinfo...
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% if downsampling specified
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if ~isempty(cstr.dsstr)
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outfile_ds = [outfile '_ds'];
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cstr.filestr = sprintf(' -f %s.fif -o %s.fif', outfile, outfile_ds);
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Dout = dir( [outfile_ds '.fif'] );
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if isempty( Dout )
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out_datenum = 0;
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else
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out_datenum = datenum( Dout.date )
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end
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finstr = [cstr.maxfstr cstr.filestr cstr.dsstr sprintf(' -nosss -force -v | tee %s.log',outfile_ds)];
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if datinfo.do_eval
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fprintf(1, '\nDownsampling to: %s\n', outfile_ds);
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eval(finstr);
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else
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fprintf(1, '\nDownsampling command:\n %s\n', finstr);
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end
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Dout = dir( [outfile_ds '.fif'] );
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if isempty( Dout )
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out_datenum2 = 0;
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else
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out_datenum2 = datenum( Dout.date )
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end
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if out_datenum2 > out_datenum,
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fprintf(log_fid, 'Successfully downsampled: %s\n', [outfile_ds '.fif']);
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fprintf(log_fid, '%d %s\n', Dout.bytes, Dout.date);
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else
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fprintf(log_fid, 'NOT downsampled: %s\n', [outfile_ds '.fif']);
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end
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end
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end % for r...
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fprintf(log_fid, '\n\nI''ve done everything I could!');
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fclose( log_fid );

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