Hi Alfonso,

I’m working with fMRIPrep-preprocessed data and using the CONN GUI to import the data for denoising. After importing using the import fMRIPrep dataset and labeling the structural and functional scans as secondary datasets under the "Preprocessing" step, I proceed to the "Denoising" step and attempt to include the confound regressors from the desc-confounds_timeseries.tsv files generated by fMRIPrep.

However, I encounter an error when CONN tries to process the confounds. From what I’ve read, this may be due to some regressors containing NaN values in the first row. Is there a known solution for this? If not, would replacing the initial NaNs with zeros be an acceptable workaround?

Additionally, I noticed that when importing fMRIPrep data, CONN seems to recompute white matter (WM), CSF, realignment, and scrubbing confounds. Could you clarify whether CONN's WM and CSF confounds correspond to signal averages from those compartments, or if they correspong to the compcor of WM and CSF?

Thanks in advance for your help, and for all the work you’ve put into maintaining CONN!

Best,
Clara