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Error running PhysIO: Item matlabbatch: No repeat named physio #264

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LLouedKhen opened this issue May 2, 2024 · 4 comments
Open

Error running PhysIO: Item matlabbatch: No repeat named physio #264

LLouedKhen opened this issue May 2, 2024 · 4 comments
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@mrikasper
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physio Issues related to PhysIO Toolbox
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PhysIO

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@LLouedKhen
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Hi,
I would like to create physiological regressors using a script but it keep crashing with the following message:
error: Item matlabbatch: No repeat named physio

The same batch works fine in the GUI, although I have to manually add the TAPAS toolbox to the gui Batch. TAPAS doesn't otherwise appear in the options under tools in the GUI.
I have used TAPAS PhysIO before in preprocessing pipeline but I don't recall running into this problem.

I am running scripts on SPM12 (updated), Matlab 2023a.

Here is my code:

for i = 1:length(subjects)
    thisPhysPath = physPaths{i};
    cd(thisPhysPath)
    physFiles = dir('Sess*');
    physFile1 = physFiles(1).name;
    physFile2 = physFiles(2).name;
    thisMRPath1 = imgPaths1{i};
    thisMRPath2 = imgPaths2{i};
    thisNScan1 = imgNum1(i);
    thisNScan2 = imgNum2(i);
    for r = 1:2
        if r == 1
            physFile = physFile1;
            epifolder = thisMRPath1;
            nscans = thisNScan1;

        elseif r == 2
            physFile = physFile2;
            epifolder = thisMRPath2;
            nscans = thisNScan2;
        end
        spm('Defaults','fMRI');
        spm_jobman('initcfg');
        matlabbatch{1}.physio.log_files.vendor = 'Biopac_Mat';
        matlabbatch{1}.physio.log_files.cardiac = physFile;
        matlabbatch{1}.physio.log_files.respiration = physFile;
        matlabbatch{1}.physio.log_files.scan_timing = {''};
        matlabbatch{1}.physio.log_files.sampling_interval = [];
        matlabbatch{1}.physio.log_files.relative_start_acquisition = 0;
        matlabbatch{1}.physio.log_files.align_scan = 'last';
        matlabbatch{1}.physio.scan_timing.sqpar.Nslices = 40;
        matlabbatch{1}.physio.scan_timing.sqpar.NslicesPerBeat = [];
        matlabbatch{1}.physio.scan_timing.sqpar.TR = 2.48;
        matlabbatch{1}.physio.scan_timing.sqpar.Ndummies = 0;
        matlabbatch{1}.physio.scan_timing.sqpar.Nscans = nscans;
        matlabbatch{1}.physio.scan_timing.sqpar.onset_slice = 20;
        matlabbatch{1}.physio.scan_timing.sqpar.time_slice_to_slice = [];
        matlabbatch{1}.physio.scan_timing.sqpar.Nprep = [];
        matlabbatch{1}.physio.scan_timing.sync.nominal = struct([]);
        matlabbatch{1}.physio.preproc.cardiac.modality = 'ECG';
        matlabbatch{1}.physio.preproc.cardiac.filter.no = struct([]);
        matlabbatch{1}.physio.preproc.cardiac.initial_cpulse_select.auto_matched.min = 0.4;
        matlabbatch{1}.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';
        matlabbatch{1}.physio.preproc.cardiac.initial_cpulse_select.auto_matched.max_heart_rate_bpm = 90;
        matlabbatch{1}.physio.preproc.cardiac.posthoc_cpulse_select.off = struct([]);
        matlabbatch{1}.physio.preproc.respiratory.filter.passband = [0.01 2];
        matlabbatch{1}.physio.preproc.respiratory.despike = false;
        matlabbatch{1}.physio.model.output_multiple_regressors = 'multiple_regressors.txt';
        matlabbatch{1}.physio.model.output_physio = ['physio', num2str(r), '.mat'];
        matlabbatch{1}.physio.model.orthogonalise = 'none';
        matlabbatch{1}.physio.model.censor_unreliable_recording_intervals = false;
        matlabbatch{1}.physio.model.retroicor.yes.order.c = 3;
        matlabbatch{1}.physio.model.retroicor.yes.order.r = 4;
        matlabbatch{1}.physio.model.retroicor.yes.order.cr = 1;
        matlabbatch{1}.physio.model.rvt.no = struct([]);
        matlabbatch{1}.physio.model.hrv.no = struct([]);
        matlabbatch{1}.physio.model.noise_rois.no = struct([]);
        matlabbatch{1}.physio.model.movement.no = struct([]);
        matlabbatch{1}.physio.model.other.no = struct([]);
        matlabbatch{1}.physio.verbose.level = 2;
        matlabbatch{1}.physio.verbose.fig_output_file = '';
        matlabbatch{1}.physio.verbose.use_tabs = false;
        save('matlabbatch');
       
        spm_jobman('run',matlabbatch);
       

        copyfile('multiple_regressors.txt', 'epiFolder')
        copyfile('physio.mat', 'epiFolder')

        clear;clc

    end
end

Thank you so much for your help.
Best,
Leyla
@mrikasper
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Dear Leyla,

Could you please try to replace matlabbatch{1}.physio by matlabbatch{1}.spm.tools.physio in all lines of your script?

All the best,
Lars

@mrikasper mrikasper self-assigned this May 2, 2024
@mrikasper mrikasper added the physio Issues related to PhysIO Toolbox label May 2, 2024
@mrikasper mrikasper added this to To do in PhysIO via automation May 2, 2024
@LLouedKhen
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LLouedKhen commented May 3, 2024 via email

@LLouedKhen
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LLouedKhen commented May 3, 2024 via email

@mrikasper
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mrikasper commented May 4, 2024 via email

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