Software tools to load and analyze physiology monitoring log files from the Philips MRI scanner.
%
% [OUTPARAMS, WAVEFORMS] = LOADSCANPHYSLOG(SCANPHYSLOG_FILE_NAME)
%
% Loads data from the Philips MRI scanner SCANPHYSLOG file
% SCANPHYSLOG_FILE_NAME and returns the structures OUTPARAMS and WAVEFORMS
%
% outParams.scanphyslog_file_name % file name of loaded scanphyslog
% outParams.site_name % site name
% outParams.SRN % scanner registration number
% outParams.release % software release
% outParams.SWID % software identifier
% outParams.date % date (yyyy-mm-dd)
% outParams.time % time (HH:MM:SS)
% outParams.dockable_table % flag for dockable table
% outParams.nSamples % number of samples
% outParams.sample_time_seconds % sample time spacing
% outParams.time_duration_file_seconds % time duration of the file
% outParams.time_duration_scan_seconds % time duration of the scan
% outParams.scan_start_sample % sample index of the scan start (mark==0x10)
% outParams.scan_stop_sample % sample index of the scan stop (mark==0x20)
%
% waveforms.v1raw % VKG v1raw waveform
% waveforms.v2raw % VKG v2raw waveform
% waveforms.v1 % VKG v1 waveform
% waveforms.v2 % VKG v2 waveform
% waveforms.ppu % peripheral pulse unit (PPU) waveform
% waveforms.resp % respiratory bellows waverform
% waveforms.gx % x gradient waveform
% waveforms.gy % y gradient waveform
% waveforms.gz % z gradient waveform
% waveforms.mark_hex % acquisition mark labels hexadecimal number
% waveforms.mark_dec % acquisition mark labels as decimal number
% waveforms.time_seconds % time in seconds
%
% mark is stored in the file as a hexadecimal bitmask but returned as a
% decimal value. The meaning of the mark values are as follows:
%
% 0x01 = VKG trigger point
% 0x02 = ppu trigger point
% 0x04 = resp trigger point
% 0x08 = measurement marker
% 0x10 = start scan marker
% 0x20 = stop scan marker
%
% Since physiology data is collected from the start of the preparation
% phases, working backward from the stop scan marker by a known scan
% duration is one way to examine the physiology measurements occuring
% during the scan itself.
%
% Developed with MATLAB R2014b
%
% Supported by a grant from the National Institutes of Health (NIH), National
% Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) - R01DK105371
%
%
% OUTPARAMS = PROCESS_SCANPHYSLOG_PARENT_FOLDER(PARENT_FOLDER_NAME)
%
% Processes all SCANPHYSLOG files in the folder PARENT_FOLDER_NAME and
% returns the array of structures OUTPARAMS containing
%
% outParams(:).date % date (yyyy-mm-dd)
% outParams(:).time % time (HH:MM:SS)
% outParams(:).N_heart_rate % number of heart rate windows
% outParams(:).heart_rate_mean % heart rate mean
% outParams(:).heart_rate_sigma % heart rate standard deviation
% outParams(:).heart_rate_CI_HW % heart rate confidence interval half-width
% outParams(:).heart_rate_CI_LB % heart rate confidence interval lower bound
% outParams(:).heart_rate_CI_UB % heart rate confidence interval upper bound
% outParams(:).N_breath_rate % number of breath rate windows
% outParams(:).breath_rate_mean % breath rate mean
% outParams(:).breath_rate_sigma % breath rate standard deviation
% outParams(:).breath_rate_CI_HW % breath rate confidence interval half-width
% outParams(:).breath_rate_CI_LB % breath rate confidence interval lower bound
% outParams(:).breath_rate_CI_UB % breath rate confidence interval upper bound
%
% OUTPARAMS = PROCESS_SCANPHYSLOG_PARENT_FOLDER(PARENT_FOLDER_NAME, PROCESSPARAMS)
%
% A comma separated variable file names 'SCANPHYSLOG.csv' is also written
% to disk.
%
% Uses the structure PROCESSPARAMS to control the processing of the
% SCANPHYSLOG files. Options and default values are:
%
% processParams.heart_rate_time_window_seconds = 30; % heart rate time window duration in seconds
% processParams.heart_rate_time_window_overlap_fraction = 0.5; % heart rate window overlap fraction
% processParams.breath_rate_time_window_seconds = 60; % breath rate time window duration in seconds
% processParams.breath_rate_time_window_overlap_fraction = 0.5; % breath rate window overlap fraction
% processParams.confidence_level_interval_probability = 0.95; % level for reported confidence intervals
% processParams.heart_rate_max = 200; % maxmimum detectable heart rate (beats per minute)
% processParams.heart_rate_min = 30; % minimum detectable heart rate (beats per minute)
% processParams.breath_rate_max = 30; % maxmimum detectable breath rate (breaths per minute)
% processParams.breath_rate_min = 8; % minimum detectable breath rate (breaths per minute)
% processParams.match_pattern = '*SCANPHYSLOG*'; % pattern to detect SCANPHYSLOG files to process
% processParams.output_csv_filename = 'SCANPHYSLOG.csv'; % name for output CSV file
% processParams.output_folder = PARENT_FOLDER_NAME; % name of parent folder containing SCANPHYSLOG files
% processParams.verbose = true; % print progress messages
%
% Developed with MATLAB R2014b
%
% Supported by a grant from the National Institutes of Health (NIH), National
% Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) - R01DK105371
%
%% Run example SCANPHYSLOG processing
| idx | date | time | N_heart_rate | heart_rate_mean | heart_rate_sigma | heart_rate_CI_HW | heart_rate_CI_LB | heart_rate_CI_UB | N_breath_rate | breath_rate_mean | breath_rate_sigma | breath_rate_CI_HW | breath_rate_CI_LB | breath_rate_CI_UB |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2016-02-01 | 09:50:15 | 9.00 | 57.11 | 1.76 | 1.09 | 56.02 | 58.20 | 4.00 | 9.25 | 0.50 | 0.59 | 8.66 | 9.84 |
| 2 | 2016-02-01 | 09:54:16 | 9.00 | 52.44 | 1.94 | 1.20 | 51.24 | 53.65 | 4.00 | 9.50 | 0.58 | 0.68 | 8.82 | 10.18 |
| 3 | 2016-02-01 | 09:58:53 | 8.00 | 52.75 | 4.13 | 2.77 | 49.98 | 55.52 | 4.00 | 11.50 | 3.11 | 3.66 | 7.84 | 15.16 |
| 4 | 2016-02-01 | 10:02:26 | 9.00 | 60.00 | 5.10 | 3.16 | 56.84 | 63.16 | 4.00 | 9.50 | 0.58 | 0.68 | 8.82 | 10.18 |
| 5 | 2016-02-01 | 10:06:07 | 8.00 | 60.00 | 2.14 | 1.43 | 58.57 | 61.43 | 4.00 | 10.25 | 0.50 | 0.59 | 9.66 | 10.84 |
| 6 | 2016-02-01 | 10:09:39 | 9.00 | 58.22 | 3.07 | 1.90 | 56.32 | 60.13 | 4.00 | 10.75 | 1.26 | 1.48 | 9.27 | 12.23 |
| 7 | 2016-02-01 | 10:13:21 | 9.00 | 58.22 | 1.86 | 1.15 | 57.07 | 59.37 | 4.00 | 11.00 | 2.16 | 2.54 | 8.46 | 13.54 |
| 8 | 2016-02-01 | 10:16:59 | 8.00 | 57.00 | 1.85 | 1.24 | 55.76 | 58.24 | 4.00 | 11.50 | 0.58 | 0.68 | 10.82 | 12.18 |
| 9 | 2016-02-01 | 10:21:58 | 8.00 | 56.00 | 3.38 | 2.26 | 53.74 | 58.26 | 4.00 | 10.25 | 1.50 | 1.77 | 8.48 | 12.02 |
| 10 | 2016-02-01 | 10:25:32 | 9.00 | 48.44 | 7.99 | 4.95 | 43.49 | 53.39 | 4.00 | 8.75 | 0.96 | 1.13 | 7.62 | 9.88 |
| 11 | 2016-02-01 | 10:29:08 | 8.00 | 54.25 | 7.05 | 4.72 | 49.53 | 58.97 | 4.00 | 8.25 | 0.50 | 0.59 | 7.66 | 8.84 |
| 12 | 2016-02-01 | 10:32:40 | 9.00 | 53.78 | 4.52 | 2.80 | 50.98 | 56.58 | 4.00 | 8.25 | 0.50 | 0.59 | 7.66 | 8.84 |
| 13 | 2016-02-01 | 10:36:15 | 8.00 | 53.75 | 4.06 | 2.72 | 51.03 | 56.47 | 4.00 | 9.50 | 1.73 | 2.04 | 7.46 | 11.54 |
| 14 | 2016-02-01 | 10:39:47 | 8.00 | 55.75 | 3.11 | 2.08 | 53.67 | 57.83 | 4.00 | 11.50 | 1.29 | 1.52 | 9.98 | 13.02 |
| 15 | 2016-02-01 | 10:43:19 | 9.00 | 50.00 | 7.81 | 4.84 | 45.16 | 54.84 | 4.00 | 13.75 | 2.63 | 3.09 | 10.66 | 16.84 |
| 16 | 2016-02-01 | 10:46:59 | 9.00 | 51.11 | 5.49 | 3.40 | 47.71 | 54.51 | 4.00 | 15.75 | 2.63 | 3.09 | 12.66 | 18.84 |
Supported by a grant from the National Institutes of Health (NIH), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) - R01DK105371