proc_physio

 phys = proc_physio(subid, expanme);

 ps - is a structure returned by init_phys_struct which contains all of the
      information necessary to perform the conversion.

 Adapted from modfmri/convert_physio.m

 Wrapper for script which converts ASCII file with physiological monitoring
 data into a mat file that can then be used for design matrix creation.

 The intent of this function is for it to ultimately handle multiple types of
 input data formats

0001 function phys = proc_physio(ps)
0002 % phys = proc_physio(subid, expanme);
0003 %
0004 % ps - is a structure returned by init_phys_struct which contains all of the
0005 %      information necessary to perform the conversion.
0006 %
0007 % Adapted from modfmri/convert_physio.m
0008 %
0009 % Wrapper for script which converts ASCII file with physiological monitoring
0010 % data into a mat file that can then be used for design matrix creation.
0011 %
0012 % The intent of this function is for it to ultimately handle multiple types of
0013 % input data formats
0014 %
0015 
0016 % 10/27/05 Petr Janata - adapted script
0017 insane = 0;  % Flag for something having gone quite wrong
0018 phys = [];
0019 
0020 % Extract some variables from the ps struct
0021 sinfo = ps.sinfo;
0022 sid = sinfo.id;
0023 pp = ps.pp;
0024 logfid = ps.logfid;
0025 
0026 phys_fname = fullfile(ps.datapath, sid, sprintf('%s%s%s', sid,ps.phys_data_stub,ps.phys_data_suffix));
0027 check_exist(phys_fname);
0028 
0029 % Call the parser
0030 ri = read_physmon(phys_fname, ps.pp);
0031 
0032 % Eliminate a run up front if desired
0033 if ~isempty(ps.elim_runs)
0034   fprintf(logfid, 'Eliminating run(s) %s\n', sprintf('%d ', ps.elim_runs));
0035   ri(ps.elim_runs) = [];
0036 end
0037 
0038 % Number of runs is determined by runs flagged for analysis in
0039 % get_<expname>_sinfo.m
0040 use_runs = sinfo.use_runs;
0041 nruns = length(use_runs);
0042 
0043 if nruns ~= length(ri)
0044   error_str = sprintf('ERROR:proc_physio:Expected %d runs, detected %d\n', nruns, length(ri));
0045   fprintf(logfid, error_str);
0046   error(error_str);
0047   return
0048 else
0049   for irun = 1:nruns
0050     ri(irun).id = use_runs(irun);
0051   end
0052 end
0053 
0054 %
0055 % NOTE, from here on out, we assume that the entries in ri reflect the runs
0056 % specified in sinfo.use_run
0057 %
0058 
0059 %
0060 % Perform some data integrity checks
0061 %
0062 fprintf(logfid, 'Performing data integrity checks ...\n');
0063 
0064 
0065 ps.expect.nslice = sum(sinfo.nvol(use_runs)*ps.nslice_per_vol);
0066 
0067 if nruns ~= ps.expect.nruns
0068   fprintf(logfid,'WARNING:proc_physio:Really wanted %d runs; found %d\n', ps.expect.nruns, nruns);
0069   insane = 0;
0070   
0071   % Change expectations for number of events given non-canonical number of
0072   % runs.
0073   ps.expect.pos_events = nruns*ps.expect.pos_events_per_run;
0074   ps.expect.neg_events = nruns*ps.expect.neg_events_per_run;
0075 end
0076 
0077 npos = length(cat(1,ri.pos_events));
0078 if npos ~= ps.expect.pos_events
0079   fprintf(logfid,'WARNING:proc_physio:Expected %d positive markers, detected %d\n', ps.expect.pos_events, npos);
0080   insane = 1;
0081 end
0082 
0083 nneg = length(cat(1,ri.neg_events));
0084 if ~any(ismember(nneg, ps.expect.neg_events))
0085   fprintf(logfid,'WARNING:proc_physio:Expected %d negative markers, detected %d\n', ps.expect.neg_events(1), nneg);
0086   insane = 1;
0087 end
0088 
0089 nslice = length(cat(1,ri.slice_onsets));
0090 nslice_per_vol = ps.nslice_per_vol;
0091 if nslice ~= ps.expect.nslice
0092   for irun = 1:nruns
0093     run_idx = ri(irun).id;  % use this to index into original sinfo structures
0094     expect_nslice = sinfo.nvol(run_idx)*nslice_per_vol;
0095     actual_nslice = length(ri(irun).slice_onsets);
0096     if actual_nslice ~= expect_nslice
0097       fprintf(logfid,'WARNING:proc_physio:Run %d: Expected %d slices, detected %d\n', irun, expect_nslice, actual_nslice);
0098 
0099       if expect_nslice == actual_nslice-nslice_per_vol
0100     ndiff = actual_nslice-expect_nslice;
0101     fprintf(logfid,'Eliminating %d excess slices from beginning of run %d\n', ndiff, irun);
0102     
0103     % When volumes are dropped, they are dropped at the beginning of the
0104     % run.  Therefore, all timing info has to be changed to accommodate this.
0105     ri(irun).slice_onsets(1:ndiff) = [];
0106     
0107     new_start_time = ri(irun).slice_onsets(1);
0108     
0109     ri(irun).slice_onsets = ri(irun).slice_onsets - new_start_time;
0110     
0111     ri(irun).pos_events(2:end) = ...
0112         ri(irun).pos_events(2:end)-new_start_time;
0113     ri(irun).neg_events = ri(irun).neg_events - new_start_time;
0114     ri(irun).key_events = ri(irun).key_events - new_start_time;
0115     
0116     ri(irun).cardiac = ri(irun).cardiac - new_start_time;
0117     elim_idx = find(ri(irun).cardiac < 0);
0118     ri(irun).cardiac(elim_idx) = [];
0119     
0120     elim_idx = find(((0:length(ri(irun).respir)-1)/pp.Fs ...
0121         -new_start_time) < 0);
0122     ri(irun).respir(elim_idx) = [];
0123       elseif expect_nslice < actual_nslice
0124     % Scanner crash scenario
0125     ndiff = actual_nslice-expect_nslice;
0126     fprintf(logfid,'Eliminating %d excess slices from end of run %d\n', ndiff, irun);
0127     ri(irun).slice_onsets(actual_nslice ...
0128         -(actual_nslice-expect_nslice)+1:end) = []; 
0129     
0130     % Eliminate all responses and event markers that occurred after
0131     % scanner quit saving the data
0132     stop_time = ri(irun).slice_onsets(end);
0133     bad_idx = find(ri(irun).pos_events > stop_time);
0134     ri(irun).pos_events(bad_idx) = [];
0135 
0136     bad_idx = find(ri(irun).neg_events > stop_time);
0137     ri(irun).neg_events(bad_idx) = [];
0138 
0139     bad_idx = find(ri(irun).key_events > stop_time);
0140     ri(irun).key_events(bad_idx) = [];
0141 
0142     % Let us capture next heartbeat so that we can compute phase in
0143     % cardiac cycle during design matrix construction
0144     bad_idx = find(ri(irun).cardiac > stop_time + ps.cardiac_slop_s);
0145     ri(irun).cardiac(bad_idx) = [];
0146 
0147     bad_idx = find((0:length(ri(irun).respir)-1)/pp.Fs > stop_time);
0148     ri(irun).respir(bad_idx) = [];
0149     
0150       else
0151     insane = 1;
0152       end
0153     end
0154   end % for irun = 1:nruns
0155 end % if nslice ~= expect.nslice
0156 
0157 ps.insane = insane;
0158 if insane
0159   fprintf(logfid,'\tErrors detected!\n');
0160 else
0161   fprintf(logfid,'\tNo errors found\n');
0162 end
0163 
0164 % Pack the return structure
0165 phys.ps = ps;
0166 phys.ri = ri;
0167 
0168 if pp.savedata
0169   phys_matname = fullfile(ps.datapath, sid, sprintf('%s_phys.mat', sid));
0170   fprintf(logfid,'Saving physio information to: %s\n', phys_matname);
0171   save(phys_matname, 'phys')
0172 end
0173 
0174 return