Is smoothing meant to be listed in report.html?

[aritche]

Hi,

I want to apply FWHM smoothing to my data as one of my preprocessing steps. I have modified one of the example .ini files, and have successfully preprocessed my data. However, the report.html for each subject lists every preprocessing step, except for smoothing. Is smoothing supposed to show up in this report file if it has been applied?

I have attached my .ini file, as well as example report.html and report_log.html files.
I've renamed these to .txt files so I could upload them here.

my_config.txt
report_log.txt
report.txt

Thank you for your time

[bthirion]

Hi,
In the lab we prefer not to store smoothed data, as we consider than smoothing can be applied during a posteriori analysis (e.g. with NiftiMaskers).
Nervertheless, I understand that you might want to do otherwise. Would you like to submit a PR ?

[aritche]

No worries. I am a beginner when it comes to preprocessing, so I was just wanting to make sure I wasn't doing anything wrong. So am I understanding correctly that the smoothing is not applied to files that are output from pypreprocess, so I should apply the smoothing separately afterwards?

[bthirion]

You can apply smoothing during preprocessing and store smoothed files.
My opinion is that this is not a very good thing to do, because it is irreversible, hence if you want to be able to work on unsmoothed data, you need to store both the smoothed and unsmoothed data. So my advice is to only store unsmoothed data and perform smoothing later, when you load the data for a given analytic task. Smoothing becomes a processing parameter.

[aritche]

Thank you, your argument is convincing. I will do that.

But, since I have already run pypreprocessing on my data using this attached my_config.txt as my .ini file, it brings me back to my original question. How can I tell if smoothing was applied to my data? The .ini file contains "smooth_software = spm" and "fwhm = [5, 5, 5]", but the report.html does not mention that the smoothing occurred. Is there a way for me to verify if the data was smoothed or not?

[bthirion]

I think that applying smoothing would prepend an s to the filename.
With a bit of experience, you can also see that by eye ;-)