Error in Pre-processing of respiratory data (tapas_physio_filter_respiratory.m)

[murban198]

Hello there,

I am trying to set-up PhysIO to extract regressors from custom vendor log_files with respiratory and cardiac (PPU, also including respiratory peaks in second column) data. As the data is already pre-processed (missing segments in the time courses interpolated, smoothed and band-pass filtered, truncated to match length of my MRI scans), I would actually prefer to just omit every further pre-processing and just extract RETROICOR regressors. This seems to be possible for the cardiac data, not for the respiratory data though which apparently is bandpass filtered by default. I would assume that this is not a major problem, i.e. using the default boundaries of 0.01-2Hz should leave my signal intact and allow me to proceed with regressor generation. However, when running my batch script, I get the following error:

Failed 'TAPAS PhysIO Toolbox'
In an assignment A(:) = B, the number of elements in A and B must be the same.
In file "/usr/local/spm12/toolbox/PhysIO/preproc/tapas_physio_filter_respiratory.m" (???), function "tapas_physio_filter_respiratory" at line 138.
In file "/usr/local/spm12/toolbox/PhysIO/tapas_physio_main_create_regressors.m" (???), function "tapas_physio_main_create_regressors" at line 225.
In file "/usr/local/spm12/toolbox/PhysIO/tapas_physio_cfg_matlabbatch.m" (???), function "run_physio" at line 1664.

In line 138:

rpulset_padded(1:n_pad) = padding_window(1:n_pad) .* rpulset_padded(1:n_pad);

the left side of the assignment expects a vector while the right side of the assignment is a matrix.
This seems to be more or less unrelated to the structure of my input files, but for the sake of completeness, the respiratory input are 60.000x1 .log files with pre-processed amplitude values.

A similar issue has been brought up in this thread:
#272
but the solution (removing PhysIO toolbox from MATLAB search path) provided in there does not work for me.

I would be very glad to get some insight on this, if anybody encountered and solved this problem as well or has a potential solution for me...

Best regards,
murban

This is the batch script if relevant:
matlabbatch{1}.spm.tools.physio.save_dir = {'../physio_out'};
matlabbatch{1}.spm.tools.physio.log_files.vendor = 'Custom';
matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'../PeakVec.log'};
matlabbatch{1}.spm.tools.physio.log_files.respiration = {'../RespVec.log'};
%matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};
matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = 0.01;
%matlabbatch{1}.spm.tools.physio.log_files.relative_start_acquisition = 0;
matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'last';
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 30;
%matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 1.5;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 400;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 1;
%matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = [];
%matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = [];
matlabbatch{1}.spm.tools.physio.scan_timing.sync.nominal = struct([]);
matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'PPU';
matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no = struct([]);
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.load_from_logfile = struct([]);
matlabbatch{1}.spm.tools.physio.preproc.cardiac.posthoc_cpulse_select.off = struct([]);
matlabbatch{1}.spm.tools.physio.preproc.respiratory.filter.passband = [0.01 2];
matlabbatch{1}.spm.tools.physio.preproc.respiratory.despike = false;
matlabbatch{1}.spm.tools.physio.model.output_multiple_regressors = 'multiple_regressors.txt';
matlabbatch{1}.spm.tools.physio.model.output_physio = 'physio.mat';
matlabbatch{1}.spm.tools.physio.model.orthogonalise = 'none';
matlabbatch{1}.spm.tools.physio.model.censor_unreliable_recording_intervals = false;
matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.c = 3;
matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.r = 4;
matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.cr = 1;
matlabbatch{1}.spm.tools.physio.model.rvt.no = struct([]);
matlabbatch{1}.spm.tools.physio.model.hrv.no = struct([]);
matlabbatch{1}.spm.tools.physio.model.noise_rois.no = struct([]);
matlabbatch{1}.spm.tools.physio.model.movement.no = struct([]);
matlabbatch{1}.spm.tools.physio.model.other.no = struct([]);
matlabbatch{1}.spm.tools.physio.verbose.level = 2;
matlabbatch{1}.spm.tools.physio.verbose.fig_output_file = 'test_run_PhysIO_output.fig';
matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;

[murban198]

transposing the first vector, solves the problem:
rpulset_padded(1:n_pad) = padding_window(1:n_pad)' .* rpulset_padded(1:n_pad);

however, i am wondering how it can be that this problem was not encountered before...