Home > utils > physio > init_physmon_params.m

init_physmon_params

PURPOSE ^

params = init_physmon_params(config);

SYNOPSIS ^

function p = init_physmon_params(config)

DESCRIPTION ^

 params = init_physmon_params(config);

 Initializes parameter structure for reading physiological monitoring files.

 config - specifies a particular physiological monitoring system/configuration.

 See also README_physio.txt

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function p = init_physmon_params(config)
0002 % params = init_physmon_params(config);
0003 %
0004 % Initializes parameter structure for reading physiological monitoring files.
0005 %
0006 % config - specifies a particular physiological monitoring system/configuration.
0007 %
0008 % See also README_physio.txt
0009 
0010 % 1/10/02 PJ
0011 % 05/27/04 PJ  Added .is_event_trig_pos and .is_button_trig_pos fields
0012 % 10/25/04 PJ  Added .neg_trig_thresh_key
0013 % 07/20/06 PJ  Modified to handle multiple acquisition systems
0014 
0015 p.source = config;
0016 p.loaddata = 1;
0017 p.savedata = 0;
0018 p.outsuffix = '';
0019 p.savefixed = 0;            % save data after it has been adjusted
0020                                         % for dropped volumes, etc.
0021 
0022 switch config
0023   case 'keithley'
0024     p.Fs = 250;                % sampling rate (Hz)
0025     p.bipolar = 0;            % are event marker pulses bipolar?
0026     p.pos_trig_thresh = 2;
0027     p.neg_trig_thresh = -2;
0028     p.neg_trig_thresh_key = -4;        % threshold for key press events
0029     p.is_event_trig_pos = 1;
0030     p.is_button_trig_pos = 1;
0031     
0032     % if markers are bipolar, this is the window within which negative/positive transition should occur
0033     p.event_window_ms = 30;            
0034     
0035     % time from EPI start to first stimulus marker
0036     p.epi_start_to_first_stim = 17500;    
0037     
0038     % tolerance for marker locations
0039     p.event_slop = 2;        
0040     
0041     % for finding runs based on receiver unblank maximum duration of a run, in seconds)
0042     p.slice_diff_thresh = 100;        
0043 
0044     % Channel assignments
0045     p.cardiac_chan = 1;
0046     p.respir_chan = 2;
0047     p.slice_chan = 3;
0048     p.button_chan = 4;
0049     p.event_chan = 5;
0050 
0051     % Removal of mean from event channels prior to locating trigger evenets
0052     p.remove_dc = 1;        
0053 
0054     % Slice timing channel parameters
0055     p.TR = 3;
0056     p.nslice_per_vol = 27;            % number of slices per volume
0057 
0058     % number of dummy volumes at the beginning of each run
0059     p.ndummy_vol = 2;            
0060 
0061     % Physiological channel post-processing
0062 
0063     % cutoff frequency for filtering respiratory data. Leave empty if no filtering is desired
0064     p.low_pass_cutoff = 5;        
0065                     
0066   case 'mate'
0067     
0068     % Scanner trigger related variables
0069     p.trig_thresh = -2.5;
0070     p.trig_dir = 'neg';
0071     p.Fs_trig = 100;
0072     p.trig_slop_sec = 0.02; 
0073     p.trig_is_vol = 1;  % volume or slice triggers
0074     
0075     p.pulse_thresh = -2.5;
0076     p.pulse_dir = 'neg';
0077     p.Fs_pulse = 50;
0078     p.Fs_resp = 50;
0079 
0080   case 'biopac'
0081     p.thresh = 2.5;
0082     p.dir = 'pos';
0083 
0084     % cutoff frequency for filtering respiratory data. Leave empty if no filtering is desired
0085     p.low_pass_cutoff = 5;        
0086                     
0087   otherwise
0088     fprintf('Unknown configuration: %s\n', config)
0089 end

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