Dear AFNI experts,
I have been convinced to use fMRIprep for the initial steps of the preprocessing.
First question: motion parameter file
fMRIprep returns a very large file with all the regressors that one might want to remove (e.g., the motion parameters, among others). However, I’m unsure how to correctly create the motion regressor file to possibly continue using AFNIproc.py.
1- I’ve opened a dfile_rall.1D from prior preprocessing with AFNI, and I see what I suppose are the six motion parameters (one per column). Is the order relevant? 2- Can I create this file with a simple text editor by copying and pasting?
3- If I call my file with the same name, will it be possible to use AFNIproc.py with the remaining blocs for motion correction, censoring, and first-level analyses?
4- Some suggest adding a few more noise regressors to the basic 6 motion parameters; should this be done at this level? Will it impact the motion censor step?
Another difference with fMRIprerp is the reference used in the slice timing correction. Apparently, for short TRs, the difference in slice timing correction is not relevant. I’m unsure what is a short TR. My study has a 1020ms TR. Is this TR short enough to make the difference irrelevant, or should I correct the Stimuli times by subtracting TR/2?
After fMRIprep, I hope to run the following blocks: blur, scale (I don’t think it’s being done in fMRIprep), and regress.
I believe that the equivalent of shift, align, tlrc, and volreg is performed with fMRIprep.
Thank you for your insight and guidance,