Hello,

I am running a resting state analysis. I preprocessed my fMRI and anatomical data using fMRIprep and now I am denoising the data in AFNI. For each model, I am including 24 head motion parameters, volumes identified as non-steady state by fMRIprep, cosine regressors generated by fMRIprep for high-pass filtering, and polort 2 to remove linear trends.

For each subject, I compiled a confound text file containing time series regressors (see attached). The first 24 columns are the 6 head motion parameters, their first temporal derivatives, and square terms. Columns 25-29 are the cosine regressions, and column 30 is a regressor indicating the volume identified as non-steady state. Is there any issue with the organization of the confound file?

Subsequently, I used 3dTproject to regress the nuisance confounds, as indicated below:

3dTproject -polort 2 -input ${sid}_${filename} -mask ${sid}_${maskname} -ort ${outdir}/RegMatrices/${pipe}/${sid}_${pipe}_confounds.txt -blur 6 -prefix errt_${sid}_${pipe}.nii.gz

Is this specification correct to perform nuisance regression?

Thank you!
Jenna