fieldtrip · neurofractal · May 3, 2023 · May 3, 2023
diff --git a/fileio/ft_chantype.m b/fileio/ft_chantype.m
@@ -236,7 +236,7 @@
   for sel=find([input.orig.chs.kind]==602)' % Resp
     chantype(sel) = {'respiration'};
   end
-  
+
 elseif ft_senstype(input, 'babysquid74')
   % the name can be something like "MEG 001" or "MEG001" or "MEG 0113" or "MEG0113"
   % i.e. with two or three digits and with or without a space
@@ -308,7 +308,17 @@
   chantype(sel) = {'refmag'};             % reference magnetometers
   sel = myregexp('^[GPQR][0-9][0-9]$', label);
   chantype(sel) = {'refgrad'};            % reference gradiometers
-
+
+elseif isheader && ft_senstype(input,'QZFM_UCL')
+    chantype = input.orig.channels.type;
+
+    sel = myregexp('^MEGMAG$', chantype);
+    chantype(sel) = {'megmag'};            % magnetometers
+    sel = myregexp('^MEGREFMAG$', chantype);
+    chantype(sel) = {'refmag'};            % reference magnetemeters
+    sel = myregexp('TRIG', chantype);
+    chantype(sel) = {'trigger'};           % trigger channels
+
 elseif ft_senstype(input, 'bti')
   if isfield(input, 'orig') && isfield(input.orig, 'config')
     configname = {input.orig.config.channel_data.name};

diff --git a/fileio/ft_filetype.m b/fileio/ft_filetype.m
@@ -1271,7 +1271,10 @@
   type = 'neuroelectrics_nedf';
   manufacturer = 'Neurolectrics';
   content = 'EEG binary data (Enobio & Starstim)';
-
+elseif filetype_check_extension(filename, '.bin') && exist([filename(1:(end-4)) '.json'], 'file')
+  type = 'QZFM_UCL';
+  manufacturer = 'QuSpin';
+  content = 'OPM-MEG data';
   % some other known file types
 elseif filetype_check_extension(filename, '.hdf5')
   type = 'gtec_hdf5';

diff --git a/fileio/ft_read_data.m b/fileio/ft_read_data.m
@@ -1568,7 +1568,10 @@
         dat(spikesel(i),j) = dat(spikesel(i),j) + 1;
       end
     end
-
+
+  case {'QZFM_UCL'}
+    dat = opm_fil(filename, hdr, begsample, endsample, chanindx);
+
   case 'read_nex_data' % this is an alternative reader for nex files
     dat = read_nex_data(filename, hdr, begsample, endsample, chanindx);
 

diff --git a/fileio/ft_read_header.m b/fileio/ft_read_header.m
@@ -2589,7 +2589,16 @@
     end
     hdr.label = hdr.label(:);
     hdr.nChans = length(hdr.label);
-
+
+  case {'QZFM_UCL'}
+      % Use the opm_fil function
+      hdr = opm_fil(filename);
+      % Fix the hdr.chantype using ft_chantype
+      hdr.chantype = ft_chantype(hdr);
+      % This is needed so ft_read_header doesn't over-ride with raw BIDS
+      % info
+      readbids = 'no';
+
   case {'ricoh_ave', 'ricoh_con', 'ricoh_mrk'}
     % header can be read with Ricoh MEG Reader
     hdr = read_ricoh_header(filename);

diff --git a/fileio/private/opm_fil.m b/fileio/private/opm_fil.m
@@ -75,10 +75,20 @@
     case 'double'
       samplesize = 8;
   end
+
+  % Try to get the type of sensor array (helmet) used
+  if isfield(header, 'HelmetManufacturer')
+      type = ['QZFM' '_' header.HelmetManufacturer];  
+  else
+      type = ['QZFM' '_' header.HelmetManufacturer];
+      ft_warning(['No HelmetManufacturer specified in the accompanying' ...
+          ' meg.json file. Assuming the sensor type is ''QZFM_UCL''']);
+  end
 
+  % Read the channels
   channels  = readtable(channelsfile, 'Delimiter', 'tab', 'FileType', 'text');
 
-  % this one is optional
+  % Get the coordsysfile - this one is optional
   if exist(coordsysfile, 'file')
     fid = fopen(coordsysfile, 'rt');
     coordsys = jsondecode(fread(fid, [1 inf], 'char=>char'));
@@ -87,24 +97,24 @@
     coordsys = [];
   end
 
-  % this one is optional
+  % Get the positions file - this one is optional
   if exist(positionsfile, 'file')
     positions = readtable(positionsfile, 'Delimiter', 'tab', 'FileType', 'text');
   else
     positions = [];
   end
 
   d = dir(datafile);
-
+
+  % Construct the hdr
   hdr.label       = channels.name;
   hdr.nChans      = size(channels, 1);
   hdr.nSamples    = (d.bytes/(size(channels, 1) * samplesize))-1;
   hdr.nSamplesPre = 0; % continuous data
   hdr.nTrials     = 1; % continuous data
   hdr.Fs          = header.SamplingFrequency;
-  hdr.chantype    = channels.type;
   try
-    hdr.chanunit    = channels.unit;
+    hdr.chanunit    = channels.units;
   catch
     hdr.chanunit    = repmat({'unknown'}, size(hdr.label));
   end
@@ -120,8 +130,15 @@
     hdr.grad.label = positions.name;
     hdr.grad.coilpos = [positions.Px positions.Py positions.Pz];
     hdr.grad.coilori = [positions.Ox positions.Oy positions.Oz];
-    hdr.grad.type = 'meg';
+    hdr.grad.type = type;
+    hdr.grad.chantype = repmat({'megmag'},size(positions.name));
+    hdr.grad.chanunit = repmat({'fT'},size(positions.name));
     hdr.grad.tra  = diag(ones(1,length(positions.name)));
+
+    if isfield(header, 'HelmetManufacturer')
+        hdr.grad.HelmetManufacturersModelName = header.HelmetManufacturersModelName;
+    end
+
     if ~isempty(coordsys)
       hdr.grad.unit = coordsys.MEGCoordinateUnits;
       hdr.grad.coordsys = coordsys.MEGCoordinateSystem;

diff --git a/test/test_issue1395.m b/test/test_issue1395.m
@@ -47,6 +47,14 @@
 cfg.dataset = datafile;
 data = ft_preprocessing(cfg);
 
+%%
+% Test without specifying cfg.headerformat and cfg.dataformat and
+% cfg.eventformat
+cfg         = [];
+cfg.dataset = datafile;
+data_auto   = ft_preprocessing(cfg);
+clear data_auto
+
 %%
 
 cfg = [];

diff --git a/utilities/ft_channelselection.m b/utilities/ft_channelselection.m
@@ -364,10 +364,10 @@
     % all itab MEG channels start with MAG
     labelmeg = datachannel(strncmp('MAG', datachannel, length('MAG')));
 
-  case{'qzfm_gen2'}
-    % This is for use with QZFM_Gen2 Optically Pumped Magnetometers manufactured by QuSpin Inc.
+  case{'QZFM_UCL'}
+    % This is for use with UCL-OPM Lab which uses QZFM Optically Pumped 
+    % % Magnetometers manufactured by QuSpin Inc. 
     % SPECS: https://quspin.com/qzfm-gen-2-update/
-
     labelmeg    = datachannel(strncmp('meg', datachantype, 3));
     labelmegref = datachannel(strncmp('refmag', datachantype, 3));