[FieldTrip] trial error
Evelyne Fraats
e.fraats at kpnmail.nl
Fri Jun 9 15:03:49 CEST 2023
Dear all,
My name is Evelyne and I am just started to explore fieldtrip.
I use fieldtrip to define trials in physiological recordings to estimate
physiological regressors for MRI preprocessing.
However, when using the physio toolbox, no trials are detected within my
data.
When I run the separate ft_definetrial function, I get trials, but I seem to
fail to include this in my matlabbatch.
This is my output with error message:
evaluating trial function 'ft_trialfun_general'
reading the header from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
reading the events from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
found 169 events
created 20 trials
the call to "ft_definetrial" took 0 seconds and required the additional
allocation of an estimated 0 MB
Item model: No field(s) named
event
------------------------------------------------------------------------
09-Jun-2023 15:02:40 - Running job #41
------------------------------------------------------------------------
09-Jun-2023 15:02:40 - Running 'TAPAS PhysIO Toolbox'
Warning: cfg.trialdef.eventtype='?' is deprecated, please specify
cfg.trialfun='ft_trialfun_show'
evaluating trial function 'ft_trialfun_show'
reading the events from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
the following events were found in the data
event type: 'New Segment'
with event values:
event type: 'Response'
with event values: 'R 1'
event type: 'Stimulus'
with event values: 'S 1' 'S 97'
no trials have been defined yet, see FT_DEFINETRIAL for further help
found 169 events
the call to "ft_definetrial" took 0 seconds and required the additional
allocation of an estimated 0 MB
evaluating trial function 'ft_trialfun_general'
reading the header from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
reading the events from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
09-Jun-2023 15:02:41 - Failed 'TAPAS PhysIO Toolbox'
Error using ft_definetrial
no trials were defined, see FT_DEFINETRIAL for help
The following modules did not run:
Failed: TAPAS PhysIO Toolbox
Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB
command window, starting with the lines (look for the line showing the
exact #job as displayed in this error message)
------------------
Running job #41
------------------
This is my code:
if physio_regressor == 1
%cd /home/affneu/evefra/Spinalcord/data/Physio/
%define log input
data_path_physio = fullfile(data_path, 'Physio');
data_path_physio_sub = dir(fullfile(data_path_physio,
sprintf('subx%d*threat*.eeg', sub))) ; %CHANE FORMAT
filenames = {data_path_physio_sub.name};
filenames = filenames';
filefolder = {data_path_physio_sub.folder};
filefolder = filefolder';
filename_folder = cellfun(@(folder, name) fullfile(folder, name),
filefolder, filenames, 'UniformOutput', false);
%define vhdr
data_path_physio_sub = dir(fullfile(data_path_physio,
sprintf('subx%d*threat*.vhdr', sub))) ; %CHANE FORMAT
filenames = {data_path_physio_sub.name};
filenames = filenames';
filefolder = {data_path_physio_sub.folder};
filefolder = filefolder';
filename_folder_vhdr = cellfun(@(folder, name) fullfile(folder,
name), filefolder, filenames, 'UniformOutput', false);
%define vmkr
data_path_physio_sub = dir(fullfile(data_path_physio,
sprintf('subx%d*threat*.vmrk', sub))) ; %CHANE FORMAT
filenames = {data_path_physio_sub.name};
filenames = filenames';
filefolder = {data_path_physio_sub.folder};
filefolder = filefolder';
filename_folder_vmrk = cellfun(@(folder, name) fullfile(folder,
name), filefolder, filenames, 'UniformOutput', false);
%define trials
cfg = [];
cfg.headerfile = char(filename_folder_vhdr);
cfg.eventfile = char(filename_folder_vmrk);
cfg.trialdef.eventtype = 'Stimulus';
cfg.trialdef.eventvalue = 'S 1';
cfg.trialdef.prestim = 0;
cfg.trialdef.poststim = 0;
%cfg.trialfun = 'ft_trialfun_show';
trials = ft_definetrial(cfg);
%run regressor estimation
clear matlabbatch
matlabbatch{1}.spm.tools.physio.save_dir =
{fullfile(data_path_tos_brain,'physio_regressors')};
matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BrainProducts';
matlabbatch{1}.spm.tools.physio.log_files.cardiac = filename_folder;
matlabbatch{1}.spm.tools.physio.log_files.respiration =
filename_folder;
matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};
matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = [];
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 = 44;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat =
[];
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 3.39;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 147;
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 = 'ECG';
matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no =
struct([]);
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_m
atched.min = 0.4;
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_m
atched.file = 'initial_cpulse_kRpeakfile.mat';
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_m
atched.max_heart_rate_bpm = 90;
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 = '';
matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;
matlabbatch{1}.spm.tools.physio.model.event.trials =
trials.trl(:,1);
spm_jobman('run', matlabbatch)
end
If anybody has some tips, it would be greatly appreciated.
Best,
Evelyne
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