mrikasper
commented
4 years ago Dear Alego,
thank you for considering our toolbox!
- For my project I need to extract the number of peaks occurred during a task for every subject, so is there a way to have as output a mat. file with the number of peak detected and to save it for further analysis?
If you specify an output .mat file in parameter physio.model.output_physio, a lot of extra data is saved in a structured variable physio, computed during the run of the main function.
For example, physio.ons_secs.cpulse will contain all indices of cardiac pulse events. Therefore, numel(cpulse) should give you the number of heartbeats during the task.
More information can be found in the comments in tapas_physio_new or in the FAQ.
- It's important that I can check if peaks are detected correcly, so is there an automatic peak rejection option BUT ALSO an option to change manually if a peak is rejected or not?
We spent a lot of care designing the peak detection algorithm, see the section in our paper, Fig. 4 and 5. So in general, you can be quite confident about the quality of the detection, especially with the pulse oximeter, which is more robust than the ECG.
If you want to check, there is a diagnostics figure showing you peak-to-peak interval time courses. The green line there should not have to many spikes and averages around 1s (60bpm)
If you want to manually change outliers in that time course, we provide the option, as explained in Fig. 3 of the paper. Just set physio.preproc.cardiac.posthoc_cpulse_select = 'manual'.
Note that all mentioned parameters are from the matlab input structure. They have slightly different names in the SPM Batch Editor GUI.
I hope that helps.
All the best, Lars
neuralego
Dear experts, I am working on a project with fMRI Siemens and recording physio data with the pulse oximeter of the scanner. I would like to use your nice toolbox for the analysis of physio data but I have some questions:
For my project I need to extract the number of peaks occurred during a task for every subject, so is there a way to have as output a mat. file with the number of peak detected and to save it for further analysis?
It's important that I can check if peaks are detected correcly, so is there an automatic peak rejection option BUT ALSO an option to change manually if a peak is rejected or not?
Thank you in advance for your availability