Plot cardiac and respiratory signals if available

[chrisgorgo]

Above the carpet plot.

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[oesteban]

I would add events files to this

/cc @celprov

Credits of the idea to @tsalo, who mentioned this eons ago.

[oesteban]

@smoia - look at the date this issue was posted.

[m-miedema]

I'm taking a look at this! I do wonder how much pre-processing might be appropriate for the physiological signals in this context.

[smoia]

To compare the signals to a carpet plot, you do need to process them a little. In the case of ventilation, a rough respiratory variance (here) could be a proper alternative to preprocessing. For pulse/heart rate, you do need peak detection unfortunately.

[m-miedema]

Yes! We've talked about the difference between adding useful physio info to MRIQC workflow, which will require the preprocessing you mentioned, and emulating the functionality of MRIQC in a separate PHYSIOQC report.

[celprov]

@m-miedema in the last physiopy codesprint I participated in, I started trying to plot the events and the physio atop the carpetplotin MRIQC visual report but did not go very far. I worked in this branch https://github.com/celprov/mriqc/tree/enh/plot-events and this branch https://github.com/celprov/mriqc/tree/enh/plot-physio. However, I had not considered pre-processing of the physiological signals, my idea was first to really just integrate events and physio into the workflow and naively plot them. I stopped at the step of loading the physio file into the workflow.

[smoia]

Perhaps useful here, if I remember correctly one of the issue for putting this signal was to find them first. @drombas worked a while back on a way to do so, perhaps he can help?

[celprov]

@oesteban had proposed finding the physio file by extracting the bids entities from the fMRI name and reconstructing the physio bids name by replacing the suffix. That is one of my commit in the enh/plot-physio branch https://github.com/nipreps/mriqc/commit/47786babe89a220c7b56579a14a347c67fd10935. But very open to suggestion on how to implement this better.

[oesteban]

Let's first address nipreps/nireports#120, which is not concerned with finding the data. Once we are able to generate reportlets with physio signals, we can come back to MRIQC and see how these are located (which, trust me, should not be a big deal with pybids).

[smoia]

Oh, sorry, let me explain better: I doubt the problem is finding the file they're in, but then finding which channel is which physio signal seemed problematic (if I remember correctly). That's why @drombas was looking at a way to distinguish them.

[oesteban]

Okay, yes, that may require some extra configuration of MRIQC.

[smoia]

At a certain point we were working on it for phys2bids, so if you don't want to have it in MRIQC, I'd be happy to see it implemented in phys2bids (and it's useful for us, since it's a way to check and automatically label the content of the channels)

[m-miedema]

I think it makes most sense to implement within phys2bids, since the inputs of MRIQC need to be in BIDS format anyways. Ideally what I'm looking to add on to MRIQC is a very preliminary version of a physioprep workflow that generates something similar to the confounds output in fmriprep that can then be quickly read in and plotted by nireports.