NITRC PhysIO Toolbox Forum: physio-support

How to apply BrainProducts data to PhysIO Toolbox

kazuaki sajima — Tue, 12 Jul 2022 7:04:01 GMT

Hi, everyone.
Thank you for the great work.

I got cardiac data and respiration data using BrainProducts, and I removed MRI noise from these data using EEGLAB(referring this site: https://fsl.fmrib.ox.ac.uk/eeglab/fmribplugin/).
So, I got the original cardiac and respiration data("data.eeg") and MRI-noise-removed data("data.CLEAN.set").
I'm in trouble because I don't understand which data I should use on SPM PhysIO Toolbox batch editer.
For "log_cardiac" and "log_respiration" items, I should put "data.eeg", "data.CLEAN.set", or anything else?
I'd appreciate it if you could answer my question.

RE: PhysIO toolbox for to use both .ecg and .resp logs

Lars Kasper — Mon, 20 Jun 2022 12:35:27 GMT

Dear Shahin,

It should be possible to combine ECG and respiratory data in a single run of PhysIO. Your error message looks more like an issue with the function filtfilt. Could you paste the full error message, please?

Also, could you type "which filtfilt" in the Matlab command window to make sure you have the Matlab signal processing toolbox installed and that it's not using the one in SPM?

As this forum is not regularly monitored, would you be able to post on github in the future, please?

https://github.com/translationalneuromodeling/tapas/issues

PhysIO toolbox for to use both .ecg and .resp logs

shahin — Fri, 17 Jun 2022 15:24:42 GMT

Hello,

When I use both .ecg and .resp files, PhysIO returns an error for the .resp file:

[i]Error using tapas_physio_filter_respiratory (line 137)[/i]
[i]Usage: y=filtfilt(b,a,x)[/i]

In the exmaple files of PhysIO, I see that .resp file is used with .puls file, and .ecg file is used separately. So, is it not possible to use .resp and .ecg file (without .puls) to generate one regressor file?

Thanks in davance for your help.

No effect of denoising

Bram Beckers — Fri, 19 Mar 2021 14:00:05 GMT

Dear Lars,

I am currently using the PhysIO toolbox for denoising of 7T multi-echo data.
My goal is to compare denoising efficiency of RETROICOR to multi-echo ICA.
I therefore have a preprocessed (but uncleaned) optimally combined dataset that I want to clean using RETROICOR regressor files.
I have Siemens (VB) .puls and .resp files. I used a batch script which didn't run into any trouble. I have used the multiple regressor files in two ways:

1) as regressor file input in the SPM first level GLM. When doing this, my first level results still look very noisy (lots of clusters, most of which not in grey matter)
2) as regressor to create a confound corrected time-series in the CONN toolbox. This toolbox also creates QC figures, eg. plots of connectivity value distribution. After denoising these plots should approximate a normal distribution, but nothing really seems to change (i.e. I still see a skewed distribution in most cases).

It would seem that I am not running the PhysIO toolbox correctly, or at least in a way that it doesn't provide valid multiple regressor files.
Could you please have a look at the input&output to see what might have gone wrong?

Note that for synchronization I have also tried the nominal option and setting the relative start of acquisition at 25.7 (which I know is pretty much the same for all puls and resp files), but this didn't change the outcome of the denoising.

Many thanks in advance.
Best regards,
Bram

Recordings from Different Sources

Krzysztof Bielski — Wed, 15 Jul 2020 16:05:45 GMT

Dear TAPAS experts,

I would like to apply RETROICOR to physiological data recording heart-rate and respiration. Unfortunately, I have HR recorded with Siemens Tools installed in the MRI scanner (.puls file), while respiration was recorded with Brain Products. As far as I understood, the toolbox takes only data from one manufacturer. What can I do with that? Does conversion to BIDS is the only one solution? How can I perform this?

Best regards,
Krzysztof Bielski

RE: GE Physio Data processing

Lars Kasper — Sat, 22 Sep 2018 22:58:26 GMT

Dear Anant,

my apologies for the late reply, I don't check this forum regularly, since we try to bundle all user requests on GitHub:

[url=https://github.com/translationalneuromodeling/tapas/issues]https://github.com/translationalneuromodeling/tapas/issues[/url]

Q1: With respect to your question, it is very hard to tell from the error message. It occurs, because the time vector and the respiratory trace do not seem to have the same length. It would probably be easiest, if you sent me your logfile and the changed batch file example so that I can reproduce the error.

NslicesPerBeat can be left empty, unless you use cardiac triggering/gating for your sequence.

Q2: You probably will not need the trigger files, I suspect they are onset times of cardiac R-peak and breathing amplitude max events. But PhysIO calculates these peak onsets on its own.

I hope that (still) helps.

All the best,
Lars

GE Physio Data processing

Anant Shinde — Mon, 16 Jul 2018 19:18:17 GMT

Hi
I have recorded Cardiac and Respiratory dataon GE 3T scanner.
Files I get from scanner are:
Filename                                                                                             No_Datapoints
PPGData_epiRT_0703201816_24_42_498                               148419
PPGTrig_epiRT_0703201816_24_42_498                                 1411
RESPData_epiRT_0703201816_24_42_498                             37105
RESPTrig_epiRT_0703201816_24_42_498                               385

Q1:
I tried to run the GE batch file example with the Data files. I changed TR, Number of slices, total volumes. I was not sure what 'Nslicesperbeat' meant , i left field empty.
Here is the output error.
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'TAPAS PhysIO Toolbox'
No scan trigger events provided
No cardiac R-peak (heartbeat) events provided
Failed 'TAPAS PhysIO Toolbox'
Error using plot
Vectors must be the same length.
In file "/usr/local/spm12/toolbox/PhysIO/tapas_physio_plot_raw_physdata.m" (???), function "tapas_physio_plot_raw_physdata" at line 75.
In file "/usr/local/spm12/toolbox/PhysIO/tapas_physio_main_create_regressors.m" (???), function "tapas_physio_main_create_regressors" at line 127.
In file "/usr/local/spm12/toolbox/PhysIO/tapas_physio_cfg_matlabbatch.m" (???), function "run_physio" at line 1467.

The following modules did not run:
Failed: TAPAS PhysIO Toolbox

Q2. How to use these Trigger info files?

RE: No consistent volume Amplitude

Brunno M. de Campos — Fri, 11 Aug 2017 10:58:53 GMT

Dear Lars,

Thank you very much for your response. Your suggestion solves the problem. I did not realise that I can leave a confounding (in my case) field as empty.
About the wrong "volume counting": this was happening because I set the thresholds wrongly. No more problems for now!

Thanks again and have a nice weekend!

RE: No consistent volume Amplitude

Lars Kasper — Thu, 10 Aug 2017 22:02:55 GMT

Dear Brunno,

my apologies for the late reply.

You are right, there is no consistent volume threshold in you log file - at least no positive one. It is an interesting idea to implement negative thresholds (or invert the gradient time course, for that purpose) that I can integrate into the toolbox in an upcoming version.

However, in your case, the solution is much simpler: If you run the toolbox with

thresh.zero = 1000
thresh.sli = 1300
thresh.vol = [] % i.e., without volume threshold

you will see in the lowest subplot of the Gradient Thresholding figure (see attached) that the volume start is indicated by a slightly smaller gap between the slice events: some 65 instead of 50 ms. So, if you set

thresh.vol_spacing = 0.06; % 60 ms = 0.06s

the toolbox finds the right events. I have pasted the corresponding SPM job-file below as well.

I hope that works for you as well.

Another thing you mentioned is that the toolbox did not count volume events correctly from the end of the time series. Could you show me such a case? In case there is no clear volume peak, this feature only works properly, if you set thresh.vol = [];

All the best,
Lars

%-----------------------------------------------------------------------
% Job saved on 10-Aug-2017 23:59:14 by cfg_util (rev $Rev: 6460 $)
% spm SPM - SPM12 (6906)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.tools.physio.save_dir = {''};
matlabbatch{1}.spm.tools.physio.log_files.vendor = 'Philips';
matlabbatch{1}.spm.tools.physio.log_files.cardiac = {'/Users/kasperla/Documents/Cooperations/physIO/BrunnoCampos/SCANPHYSLOG20170721130757.log'};
matlabbatch{1}.spm.tools.physio.log_files.respiration = {'/Users/kasperla/Documents/Cooperations/physIO/BrunnoCampos/SCANPHYSLOG20170721130757.log'};
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 = 40;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 2;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 5;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 400;
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 20;
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 = 1000;
matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.slice = 1300;
matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.vol = [];
matlabbatch{1}.spm.tools.physio.scan_timing.sync.gradient_log.vol_spacing = 0.06;
matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'PPU';
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.posthoc_cpulse_select.off = struct([]);
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.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 = {''};
matlabbatch{1}.spm.tools.physio.model.movement.yes.order = 6;
matlabbatch{1}.spm.tools.physio.model.movement.yes.outlier_translation_mm = Inf;
matlabbatch{1}.spm.tools.physio.model.movement.yes.outlier_rotation_deg = 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 = '';
matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;

RE: No consistent volume Amplitude

Brunno M. de Campos — Fri, 21 Jul 2017 19:58:53 GMT

Dear PhysIO Experts,

Attaching a figure with some thresholds applied to Y Grad. The Volume Peak is negative, and using a threshold like YGrad(YGrad>-1000 & YGrad<500) = 0; I got a figure like that, great (attached). Notice that even if I apply the abs, the volume marker has lower amplitude. And it is impossible to set the PhysIO Batch defining the volume peak with negative value.

Any idea?

Thanks again!