Dear AFNI experts，
I preprocessed my data using fmriprep and I set --dummy scans 5 so that early unstable volumes are not included in the analysis. However, the length of the nifti file output by fmriprep is the same as the length of the original input file. In the confound file, the first 5 timepoints of compcor are populated with 0s.
My previous experience was to delete the first 5 volumes with 3dTcat, then delete the first 5 time points of confound, and finally move the stimulation time forward by 5 TRs. These steps are very inefficient. I noticed that 3dDeconvolve has the -nfirst parameter. Can it exclude the first few volumes from the analysis (e.g. -nfirst 5). In afni, is the index starting at 0 or 1? The first 5 volumes are not included in the preprocessing analysis. In 3dDeconvolve, -nfirst should it be set to 5 or 6?
When -nfirst is used, will the first few data of the confound timing file passed in via -stim_file are corresponding excluded in the analysis? And the stimulation time does not need to be moved forward, right?
Thanks,
Yang