new github workflow for clone count

.github/workflows/clone.yml

@@ -0,0 +1,63 @@
+name: Clone Count Update
+
+on:
+  schedule:
+    - cron: "10 0 * * SUN"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: clone_count
+
+      - name: gh login
+        run: echo "${{ secrets.SECRET_TOKEN }}" | gh auth login --with-token
+
+      - name: parse latest clone count
+        run: |
+          curl --user "${{ github.actor }}:${{ secrets.SECRET_TOKEN }}" \
+            -H "Accept: application/vnd.github.v3+json" \
+            https://api.github.com/repos/${{ github.repository }}/traffic/clones \
+            > clone.json
+
+      - name: create gist and download previous count
+        id: set_id
+        run: |
+          if gh secret list | grep -q "GIST_ID"
+          then
+              echo "GIST_ID found"
+              echo "GIST=${{ secrets.GIST_ID }}" >> $GITHUB_OUTPUT
+              curl https://gist.githubusercontent.com/${{ github.actor }}/${{ secrets.GIST_ID }}/raw/clone.json > clone_before.json
+              if cat clone_before.json | grep '404: Not Found'; then
+                echo "GIST_ID not valid anymore. Creating another gist..."
+                gist_id=$(gh gist create clone.json | awk -F / '{print $NF}')
+                echo $gist_id | gh secret set GIST_ID
+                echo "GIST=$gist_id" >> $GITHUB_OUTPUT
+                cp clone.json clone_before.json
+                git rm --ignore-unmatch  CLONE.md
+              fi
+          else
+              echo "GIST_ID not found. Creating a gist..."
+              gist_id=$(gh gist create clone.json | awk -F / '{print $NF}')
+              echo $gist_id | gh secret set GIST_ID
+              echo "GIST=$gist_id" >> $GITHUB_OUTPUT
+              cp clone.json clone_before.json
+          fi
+
+      - name: update clone.json
+        run: |
+          curl https://raw.githubusercontent.com/MShawon/github-clone-count-badge/master/main.py > main.py
+          python3 main.py
+
+      - name: Update gist with latest count
+        run: |
+          content=$(sed -e 's/\\/\\\\/g' -e 's/\t/\\t/g' -e 's/\"/\\"/g' -e 's/\r//g' "clone.json" | sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g')
+          echo '{"description": "${{ github.repository }} clone statistics", "files": {"clone.json": {"content": "'"$content"'"}}}' > post_clone.json
+          curl -s -X PATCH \
+            --user "${{ github.actor }}:${{ secrets.SECRET_TOKEN }}" \
+            -H "Content-Type: application/json" \
+            -d @post_clone.json https://api.github.com/gists/${{ steps.set_id.outputs.GIST }} > /dev/null 2>&1

PhysIO/examples/tapas_physio_example_bids_cpulse3t_spm_job.m

@@ -0,0 +1,39 @@
+matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
+matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BIDS';
+matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'sub-s998_task-random_run-99_physio.tsv'};
+matlabbatch{1}.spm.tools.physio.log_files.respiration = {''};
+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 = [];
+matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'first';
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 16;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 1.45;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 474;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 9;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = 0.090625;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = 0;
+matlabbatch{1}.spm.tools.physio.scan_timing.sync.scan_timing_log = 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 = [0.05 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.yes.method = 'hilbert';
+matlabbatch{1}.spm.tools.physio.model.rvt.yes.delays = 0;
+matlabbatch{1}.spm.tools.physio.model.hrv.yes.delays = 0;
+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 = 'physio.jpeg';
+matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;

PhysIO/examples/tapas_physio_example_bids_ppu3t_spm_job.m

@@ -0,0 +1,40 @@
+matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
+matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BIDS';
+matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'sub-s999_task-random_run-99_physio.tsv.gz'};
+matlabbatch{1}.spm.tools.physio.log_files.respiration = {''};
+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 = 'first';
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 16;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 1.45;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 408;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 9;
+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.scan_timing_log = 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.auto_matched.min = 0.4;
+matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';
+matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.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;

PhysIO/examples/tapas_physio_example_biopac_txt_ppu3t_spm_job.m

@@ -0,0 +1,40 @@
+matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
+matlabbatch{1}.spm.tools.physio.log_files.vendor = 'Biopac_Txt';
+matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'Biopac_Physio_Data_Export.txt'};
+matlabbatch{1}.spm.tools.physio.log_files.respiration = {'Biopac_Physio_Data_Export.txt'};
+matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {'Biopac_Physio_Data_Export.txt'};
+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 = 36;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 3;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 100;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 18;
+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.scan_timing_log = 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_matched.min = 0.4;
+matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';
+matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.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;

PhysIO/examples/tapas_physio_example_ge_ppu3t_spm_job.m

@@ -0,0 +1,40 @@
+matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
+matlabbatch{1}.spm.tools.physio.log_files.vendor = 'GE';
+matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'ECGData_epiRT_phys_0921201215_38_08'};
+matlabbatch{1}.spm.tools.physio.log_files.respiration = {'RespData_epiRT_phys_0921201215_38_08'};
+matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};
+matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = 0.025;
+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 = 35;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = 35;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 1.925;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 434;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 17;
+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.auto_matched.min = 0.4;
+matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';
+matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.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;

PhysIO/examples/tapas_physio_example_multi_subjects.m

@@ -0,0 +1,82 @@
+% Script tapas_physio_example_multi_subjects(input)
+% Shows how to generalize single-subject batch for all subjects 
+%
+%
+%   See also tapas_physio_new
+
+% Author: Lars Kasper
+% Created: 2015-07-31
+% Copyright (C) 2015 TNU, Institute for Biomedical Engineering,
+%                    University of Zurich and ETH Zurich.
+%
+% This file is part of the TAPAS PhysIO Toolbox, which is released under the terms of the GNU General Public
+% License (GPL), version 3. You can redistribute it and/or modify it under the terms of the GPL
+% (either version 3 or, at your option, any later version). For further details, see the file
+% COPYING or <http://www.gnu.org/licenses/>.
+
+
+%% # MOD - Change parameters to your needs in this section %%%%%%%%%%%%%%%%
+
+% set 1 to look at batch, to 0 for running it for all subjects
+doReviewBatch       = false; 
+
+pathStudy           = '/Users/kasperla/studies/physiotest';
+
+dirSubjectArray     = {
+    'subject10'
+    'subject11'
+    };
+
+pathStudy = '/Users/kasperla/Documents/code/matlab/smoothing_trunk/PhysIOToolbox/examples/Philips';
+dirSubjectArray = {
+    'ECG3T'
+    'ECG3T'
+    };
+
+% folder, where multiple_regressors, physio.mat and output figures are saved,
+% typically analysis folder of the subject
+dirOutput           = 'glm'; 
+
+filePhysCardiac     = 'SCANPHYSLOG.log';
+filePhysRespiratory = 'SCANPHYSLOG.log';
+fileRealignmentPar  = 'rp_fmri.txt';
+jobfile             = 'tapas_physio_example_spm_job_ECG3T.m';
+
+
+
+%% # END MOD Loop over subjects, filling in subject-specific data
+
+nSubjects = numel(dirSubjectArray);
+spm('defaults', 'FMRI');
+
+for iSubject = 1:nSubjects
+
+    % load template matlabbatch
+    clear matlabbatch
+    run(jobfile);
+    physio = matlabbatch{1}.spm.tools.physio;
+
+    % construct subject-specific data
+    pathSubject = fullfile(pathStudy, dirSubjectArray{nSubjects});
+    fullpathFilePhysCardiac = fullfile(pathSubject, filePhysCardiac);
+    fullpathFilePhysRespiratory = fullfile(pathSubject, filePhysRespiratory);
+    fullpathFileRealignment = fullfile(pathSubject, fileRealignmentPar);
+
+    % overwrite matlabbatch structure parameters
+    physio.save_dir = {pathSubject};
+    physio.log_files.cardiac = {fullpathFilePhysCardiac};
+    physio.log_files.respiration = {fullpathFilePhysRespiratory};
+    physio.log_files.scan_timing = {};
+
+    physio.model.movement.yes.file_realignment_parameters = ...
+        {fullpathFileRealignment};
+
+    % run/examine job for this subject
+    matlabbatch{1}.spm.tools.physio = physio;
+
+    if doReviewBatch
+        spm_jobman('interactive', matlabbatch);
+    else
+        spm_jobman('run', matlabbatch);
+    end
+end

PhysIO/examples/tapas_physio_example_philips_ecg3t_spm_job.m

@@ -0,0 +1,45 @@
+matlabbatch{1}.spm.tools.physio.save_dir = {'physio_out'};
+matlabbatch{1}.spm.tools.physio.log_files.vendor = 'Philips';
+matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'SCANPHYSLOG.log'};
+matlabbatch{1}.spm.tools.physio.log_files.respiration = {'SCANPHYSLOG.log'};
+matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {'SCANPHYSLOG.log'};
+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 = 37;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 2.5;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 3;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 495;
+matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 19;
+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.gradient_log.grad_direction = 'y';
+matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.zero = 0.4;
+matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.slice = 0.45;
+matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.vol = [];
+matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.vol_spacing = [];
+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.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.yes.file_realignment_parameters = {'rp_fMRI.txt'};
+matlabbatch{1}.spm.tools.physio.model.movement.yes.order = 6;
+matlabbatch{1}.spm.tools.physio.model.movement.yes.censoring_method = 'MAXVAL';
+matlabbatch{1}.spm.tools.physio.model.movement.yes.censoring_threshold = [3 Inf];
+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 = 'PhysIO_output.fig';
+matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;